# hmmscan :: search sequence(s) against a profile database # HMMER 3.0 (March 2010); http://hmmer.org/ # Copyright (C) 2010 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: mTERF-Arabidopsis.fasta # target HMM database: /N/dc2/projects/marinovg/genomes/PFam/PFam27.0/Pfam-A.hmm # output directed to file: mTERF-Arabidopsis.PFam-27-A # number of worker threads: 16 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: gi|332003686|gb|AED91069.1| [L=1141] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-51 174.1 17.3 1.2e-15 56.9 0.5 6.1 6 mTERF mTERF 0.0024 18.0 0.3 0.61 10.2 0.0 4.3 6 RuvA_C RuvA, C-terminal domain ------ inclusion threshold ------ 0.011 15.6 0.2 26 4.7 0.0 3.2 3 T6SS_Vgr Putative type VI secretion system Rhs element Vgr Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.7 0.0 1.7e-06 0.0083 108 193 .. 173 259 .. 154 265 .. 0.88 2 ! 26.3 0.0 4.8e-10 2.4e-06 2 106 .. 277 380 .. 276 397 .. 0.81 3 ! 54.5 1.4 1.3e-18 6.5e-15 205 343 .. 422 560 .. 417 562 .. 0.90 4 ! 22.7 0.0 6.1e-09 3e-05 111 272 .. 695 855 .. 669 860 .. 0.92 5 ! 9.6 0.0 6.2e-05 0.3 18 93 .. 847 922 .. 844 942 .. 0.84 6 ! 56.9 0.5 2.5e-19 1.2e-15 207 344 .. 981 1118 .. 975 1119 .. 0.91 Alignments for each domain: == domain 1 score: 14.7 bits; conditional E-value: 1.7e-06 HHHHHHHTT--HHHHHHHHHH-CHHHHS-..HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT CS mTERF 108 nvsvlrelgvtrkllislliselqpvlgk..evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGf 187 n vl +gv +k i+ + e + v++ v+ ++k ++lg+++ l ++i pr+l+ + ++ ++v+ l+slGf gi|332003686|gb|AED91069.1| 173 NHHVLCYSGVDPK-RIGKIFKEAREVFSYetGVLASKIKAYEDLGFSRLFLSKLIVCSPRVLMGHTNIELVQVVKTLQSLGF 253 6678888999999.888899999999988677999*********************************************** PP --HHHH CS mTERF 188 skedvw 193 ++e v gi|332003686|gb|AED91069.1| 254 EFEWVM 259 998775 PP == domain 2 score: 26.3 bits; conditional E-value: 4.8e-10 HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-H CS mTERF 2 sllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiivad 83 sllr f + ir+ p+ll++++ k + + f + gas+sel + +++ P i +k v+++++ flk+i ++d gi|332003686|gb|AED91069.1| 277 SLLREICFDEEKLYGLIRNCPSLLFENSGKWTGILVGFETKLGASRSELCSLFQKFPLIQVEKCVSNLRQCFLFLKEIEMED 358 56777777777777779***************************************************************85 PP HHHHHHHHH-SHHHHS---HHHH CS mTERF 84 kDksskleklpeslpqsleenke 106 +++ +++ ++ l+ + +k gi|332003686|gb|AED91069.1| 359 DEIHKVFRSHSWWLGS-CKLKKT 380 5555555555555544.333333 PP == domain 3 score: 54.5 bits; conditional E-value: 1.3e-18 GGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 205 lsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 ++++ k + + ll ++ +e+ ++ a + + + +++ + + l +lGf+++++ mvk +P +l+ + + + k+ +l+ gi|332003686|gb|AED91069.1| 422 VDIESKSMKTQFLLDLGYKENSEEMETAMKNFRGKGSELRERFNVLVSLGFTKKDVKDMVKACPTMLSQTCDILESKVNYLI 503 5666666667888888888888777777888888999999****************************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHH CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeef 343 ke pl+ lv+fP l++ L r+k R ++ l+ +gk ++ +s +l csd+ f gi|332003686|gb|AED91069.1| 504 KELGYPLSTLVDFPSCLKFTLQ-RMKLRFAMFSWLQARGKvDRKIKVSTMLACSDKIF 560 *********************6.777788**********9999************988 PP == domain 4 score: 22.7 bits; conditional E-value: 6.1e-09 HHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH CS mTERF 111 vlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked 191 +l +lg++++ ++s li + +++l+ + e + + g+ +++++++ + r + + + +++ +++lGfsk gi|332003686|gb|AED91069.1| 695 FLESLGLKPS-EFSHLIPCDKMFLNEdAFLLENYHVFWNYGIGREKMGKIFKEA-REVFGYETGVLASKIKSYEDLGFSKLF 774 899*******.******999999999556678889999**********988777.5677777899***************** PP HHHHHHHTTTGGGGGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGG CS mTERF 192 vwailkkcPellglsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllg 272 + +++ + P++l+ + + l + +l+ + + v + + vs++ +++ + fl +l ++e ++++++P l++ gi|332003686|gb|AED91069.1| 775 LSKLIVCSPSILIGDMNVGLAKVMEMLKAIGFGVDWVTENLSEEVSYDWSSMHRCLSFLRDLYVDENELCELIRKMPRLIF 855 ******************99999999999999999*******************************************996 PP == domain 5 score: 9.6 bits; conditional E-value: 6.2e-05 HH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGG.S-.HHHHHHHHHHHTTTSS-HHHHHHHHHH- CS mTERF 18 irsyplllvadaekslqpklqfLesrgaskseltkilstvPkilg.kkkvksissvydflkkiivadkDkssklekl 93 ir++p+l+++d+ + f + g+s+sel + +++ P+ + +k v +++ flk+i + d+D++ k ++l gi|332003686|gb|AED91069.1| 847 IRKMPRLIFEDSGEWTLILAGFEAKLGSSRSELSSLFQKFPQCQSlGKFVLNLRHCFLFLKDIEM-DDDEIGKIFRL 922 68899*******999999***********************9854256699************99.56666666655 PP == domain 6 score: 56.9 bits; conditional E-value: 2.5e-19 S-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 207 ekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 k k+ + + ll ++ +e+ +++a + + + +++ + + l ++G +++++ mvk +P +l+ + + + k+ +lv gi|332003686|gb|AED91069.1| 981 TKSKTMKTQFLLDLGYKENSEEMERALKNFRGKGSELRERFNVLVSFGLTEKDVKDMVKACPSILTQACDILESKVNYLV 1060 444555558899999999998889999999999*********************************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 ke pl+ lv fP+ l+y L r+k R ++ l+ +gk +l +s +l csd+ f+ gi|332003686|gb|AED91069.1| 1061 KELGYPLSTLVTFPTCLKYTLQ-RMKLRFSMFSWLQDRGKaDPKLQVSTILVCSDKFFA 1118 *********************6.777788**********8899************9886 PP >> RuvA_C RuvA, C-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.4 0.0 0.07 3.5e+02 5 15 .. 243 253 .. 241 254 .. 0.91 2 ? -2.1 0.1 0.91 4.5e+03 10 17 .. 434 441 .. 434 442 .. 0.85 3 ! 10.2 0.0 0.00012 0.61 10 27 .. 467 484 .. 465 495 .. 0.90 4 ? -3.5 0.1 2.3 1.2e+04 10 19 .. 696 705 .. 696 705 .. 0.90 5 ? -1.4 0.0 0.53 2.6e+03 10 18 .. 991 999 .. 991 1012 .. 0.82 6 ? -2.1 0.0 0.89 4.4e+03 11 27 .. 1025 1041 .. 1024 1047 .. 0.81 Alignments for each domain: == domain 1 score: 1.4 bits; conditional E-value: 0.07 HCCHHHHHCT- CS RuvA_C 5 daveALlaLGY 15 ++v +L +LG+ gi|332003686|gb|AED91069.1| 243 QVVKTLQSLGF 253 79********9 PP == domain 2 score: -2.1 bits; conditional E-value: 0.91 HHHCT--C CS RuvA_C 10 LlaLGYke 17 Ll LGYke gi|332003686|gb|AED91069.1| 434 LLDLGYKE 441 788****8 PP == domain 3 score: 10.2 bits; conditional E-value: 0.00012 HHHCT--CCCCHHHHHHC CS RuvA_C 10 LlaLGYkekeAekAvakv 27 L++LG+++k+++ +v++ gi|332003686|gb|AED91069.1| 467 LVSLGFTKKDVKDMVKAC 484 9**************986 PP == domain 4 score: -3.5 bits; conditional E-value: 2.3 HHHCT--CCC CS RuvA_C 10 LlaLGYkeke 19 L++LG k++e gi|332003686|gb|AED91069.1| 696 LESLGLKPSE 705 89****9987 PP == domain 5 score: -1.4 bits; conditional E-value: 0.53 HHHCT--CC CS RuvA_C 10 LlaLGYkek 18 Ll LGYke+ gi|332003686|gb|AED91069.1| 991 LLDLGYKEN 999 788***985 PP == domain 6 score: -2.1 bits; conditional E-value: 0.89 HHCT--CCCCHHHHHHC CS RuvA_C 11 laLGYkekeAekAvakv 27 ++ G +ek+++ +v++ gi|332003686|gb|AED91069.1| 1025 VSFGLTEKDVKDMVKAC 1041 56689999**9999986 PP >> T6SS_Vgr Putative type VI secretion system Rhs element Vgr # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.3 0.0 0.03 1.5e+02 25 88 .. 22 85 .. 17 101 .. 0.84 2 ? 4.5 0.0 0.0061 30 25 58 .. 424 461 .. 419 466 .. 0.75 3 ? 4.7 0.0 0.0052 26 26 58 .. 984 1018 .. 975 1023 .. 0.74 Alignments for each domain: == domain 1 score: 2.3 bits; conditional E-value: 0.03 T6SS_Vgr 25 LasehaksqLnlGylvdqkdngrgekrGeGfeLrTdawgavRAgkGlllstearakasgeqldm 88 L+++ + s G+l + +++ r+ + +G e+ +++ + R +G ++ + r+ a++ +ld gi|332003686|gb|AED91069.1| 22 LETQLKPSISGTGFLLRCAQTPRSFATVTGNEVCSEKSKVKRTRNGFKITPNVRKLAEEAMLDY 85 5566666666689999999999999999***************************999999986 PP == domain 2 score: 4.5 bits; conditional E-value: 0.0061 T6SS_Vgr 25 Lasehaksq..LnlGylvdq..kdngrgekrGeGfeLr 58 ++s++ k+q L lGy ++ +++ +++rG+G eLr gi|332003686|gb|AED91069.1| 424 IESKSMKTQflLDLGYKENSeeMETAMKNFRGKGSELR 461 55555555543899**8887546677899********8 PP == domain 3 score: 4.7 bits; conditional E-value: 0.0052 T6SS_Vgr 26 asehaksqLnlGylvdq..kdngrgekrGeGfeLr 58 ++ +++ L lGy ++ +++ +++rG+G eLr gi|332003686|gb|AED91069.1| 984 KTMKTQFLLDLGYKENSeeMERALKNFRGKGSELR 1018 4445555699***9888435566689********8 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (1141 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 307 (0.0206999); expected 296.6 (0.02) Passed Vit filter: 26 (0.00175308); expected 14.8 (0.001) Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.38 # Mc/sec: 7837.87 // Query: gi|332658810|gb|AEE84210.1| [L=575] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-17 63.7 3.0 2.5e-08 32.8 0.2 4.1 3 mTERF mTERF Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.7 0.0 2e-09 3e-05 75 271 .. 103 292 .. 99 302 .. 0.79 2 ! 5.9 0.4 0.00026 3.8 43 136 .. 310 400 .. 303 414 .. 0.76 3 ! 32.8 0.2 1.7e-12 2.5e-08 206 344 .. 415 553 .. 374 554 .. 0.72 Alignments for each domain: == domain 1 score: 22.7 bits; conditional E-value: 2e-09 HHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHH CS mTERF 75 flkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpkt 155 +l+ki+ +kD+s+ l k ++ e++ + +lg+++ +++ + +++l+ +++e l + g+++ + gi|332658810|gb|AEE84210.1| 103 LLSKIDDNQKDVSKGLTKFLRY----NPI-NEFE-PFFESLGLCPY-EFETFLPRKLMFLSDdGIMFENFHALCNYGIPRGK 177 5666666666666665543333....332.1222.36679999999.9999999988888887899**************** PP HHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T............................ CS mTERF 156 lkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede..svikkapqi 235 ++r+ + r + + + +++ +++lG+sk v +++ +cP ll+ + ++ + ++ ++++++ + + gi|332658810|gb|AEE84210.1| 178 IGRMYKEA-REIFRYESGMLAMKLRGYENLGLSKATVIKLVTSCPLLLVGGIDAEFSS--VVDKLKGLQVGcdWLGRYLSDR 256 ****9988.6788888899******************************999984444..4444444443354555555577 PP .THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGG CS mTERF 236 vslseekilnkiefllglGfsreeiakmvkrfPqll 271 +s + il++iefl ++G+ +e + k +P+l gi|332658810|gb|AEE84210.1| 257 KTYSWRRILETIEFLDKVGCKEEKLSSLLKTYPALV 292 89*******************************985 PP == domain 2 score: 5.9 bits; conditional E-value: 0.00026 TT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHH CS mTERF 43 rgaskseltkilstvPkilgkkkvksissvydflkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrkllis 124 g++ e+ + +P+ l+ k vk+i++ +dfl i ++ + + ++l+ e+ + + + l +l v+++ l++ gi|332658810|gb|AEE84210.1| 310 AGLQVNEIYRLFIDNPEMLSDKCVKNIQKTLDFLIAIRMETQFITKILLSHMELIGSCSLP--APRTACL-SLNVKQDELCK 388 5666667777788899999999999999999999999999888888888888776654443..4455556.78999999999 PP HHHH-CHHHHS- CS mTERF 125 lliselqpvlgk 136 +l e++ ++++ gi|332658810|gb|AEE84210.1| 389 ILKKEPLRLFCF 400 998888877776 PP == domain 3 score: 32.8 bits; conditional E-value: 1.7e-12 GS-T............................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 206 sekkklqtkeilltrvlvede.svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 + k l++ e ll+++ ve+ ++k a + + + +++ + + l + G + + +++++ P +l ls + + kk+ l gi|332658810|gb|AEE84210.1| 415 DSRKYLEKTEFLLRLGYVENSdEMVK-ALKQFRGRGDQLQERFDCLVKAGLNYNVVTEIIRHAPMILNLSKDVIEKKIHSLT 495 22333444444444444444465555.455556778888899999999********************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 + p+++lv+fP++l y + +ri R ++ l ++ ls s +l+c d +f gi|332658810|gb|AEE84210.1| 496 ELLGYPIESLVRFPAYLCYDM-QRIHHRFSMYLWLRERDAaKPMLSPSTILTCGDARFV 553 *********************.5899998999999999955777788999999999996 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (575 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 310 (0.0209022); expected 296.6 (0.02) Passed Vit filter: 24 (0.00161823); expected 14.8 (0.001) Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.23 # Mc/sec: 6525.83 // Query: gi|332009269|gb|AED96652.1| [L=496] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-39 135.2 3.0 1.4e-21 76.4 0.1 2.2 2 mTERF mTERF ------ inclusion threshold ------ 0.049 13.7 16.3 0.085 13.0 11.3 1.3 1 SPT6_acidic Acidic N-terminal SPT6 0.48 8.5 3.0 0.68 8.0 2.1 1.1 1 DUF2151 Cell cycle and development regulator 0.48 8.8 6.2 0.65 8.4 4.3 1.1 1 Daxx Daxx Family 0.77 8.7 11.5 1.1 8.2 8.0 1.1 1 BUD22 BUD22 1.4 8.7 7.4 0.38 10.5 2.4 1.9 2 RXT2_N RXT2-like, N-terminal 2.3 7.7 9.2 3.9 7.0 6.3 1.3 1 YL1 YL1 nuclear protein Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 76.4 0.1 6.6e-25 1.4e-21 111 276 .. 190 362 .. 163 366 .. 0.89 2 ! 59.5 0.3 9.1e-20 1.9e-16 244 344 .. 366 465 .. 362 466 .. 0.89 Alignments for each domain: == domain 1 score: 76.4 bits; conditional E-value: 6.6e-25 HHHHTT--HHHHHHHHHH-CHHHHS-HHH..HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--H CS mTERF 111 vlrelgvtrkllislliselqpvlgkevf..eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfske 190 +l+ g++++ + + ++ p l+ vf +e++++l ++gv+ ++kr++ ++p++l + +++++k+ + +l +lG+ ++ gi|332009269|gb|AED96652.1| 190 YLSTFGLKES-HFVQMYERHMPSLQINVFsaQERLDYLLSVGVKHRDIKRMLLRQPQILQYTVENNLKAHISFLMGLGIPNS 270 6677777777.66677777777777755522689************************************************ PP HHHHHHHHTTTGGGGGS-T...............................THHHHHHHHHHHHHHT..TT--HHHHHHHHHT CS mTERF 191 dvwailkkcPellglsekkklq.tkeilltrvlvede...svikkapqivslseekilnkiefllg..lGfsreeiakmvkr 266 + +i++ +P+l+ +s+++ l t ++l v+ +++ +v++ pqi++ + + + n+ ++l+ lG r+ ++kmvk+ gi|332009269|gb|AED96652.1| 271 KIGQIVAATPSLFSYSVENSLRpTIRYLIEEVGIKETdvgKVVQLSPQILVQRLDITWNTRYMFLSkeLGAPRDSVVKMVKK 352 *******************9865888888887777777***********************9999999************** PP SGGGGGS-HH CS mTERF 267 fPqllglsve 276 Pqll +s++ gi|332009269|gb|AED96652.1| 353 HPQLLHYSID 362 ********98 PP == domain 2 score: 59.5 bits; conditional E-value: 9.1e-20 HHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--T CS mTERF 244 lnkiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallsk 324 l+ i+fl ++G+ +i k + q+l+ls+e +k+k+ +lv+e + ++ l ++P +l++SL++ri PR ++ l++ gi|332009269|gb|AED96652.1| 366 LPRINFLRSIGMCNSDILKVLTSLTQVLSLSLEDnLKPKYMYLVNELNNEVHILTKYPMYLSLSLDQRIRPR---HRFLVEL 444 789******************************99*************************************...9999998 PP TT..GGGGGS-HHHHHHHHHHT CS mTERF 325 gk..sillslsevlkcsdeefl 344 k +ls+ l +de+f+ gi|332009269|gb|AED96652.1| 445 KKvrKGPFPLSS-LVPNDESFC 465 865455566665.556777776 PP >> SPT6_acidic Acidic N-terminal SPT6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.0 11.3 4e-05 0.085 2 79 .. 74 152 .. 73 165 .. 0.64 Alignments for each domain: == domain 1 score: 13.0 bits; conditional E-value: 4e-05 SPT6_acidic 2 DsseEeddddDeeeark.vreGFIvddedeeeeeeeeskrrrkkkkrkrrereeeeealdedDleL.ieentgvkekree 79 Ds+e++ddddD+++++ ++F + e+++ +++k+ +kk k+ + ee + dedDl+L i n+ ++k+e+ gi|332009269|gb|AED96652.1| 74 DSDEDDDDDDDDDDDDWlLNDDFAEV-TEYEKKKPKSHKQTIAKKSVKKGIVKPEESETDEDDLDLgISPNATSEKKKES 152 67666655555555543356666654.3334555556667777788888888889999********66666666555543 PP >> DUF2151 Cell cycle and development regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.0 2.1 0.00032 0.68 601 692 .. 78 177 .. 48 179 .. 0.53 Alignments for each domain: == domain 1 score: 8.0 bits; conditional E-value: 0.00032 DUF2151 601 eraksvsdeeeeeleese.............aitdspdspeilekkkkvkiee..skkkeakkgevsllsllssriekaesk 667 + +++ d+++ + + +p+s +++ +kk+vk + +e+++ +++l ek+++ gi|332009269|gb|AED96652.1| 78 DDDDD-DDDDD------DdwllnddfaevteYEKKKPKSHKQTIAKKSVKKGIvkPEESETDEDDLDLGISPNATSEKKKES 152 11111.12222......13433334554433222233333333233333322222333333333334322222335999999 PP DUF2151 668 krreFvGRlesvgniAkLYpqlaek 692 r + G+++s + kLYp lae+ gi|332009269|gb|AED96652.1| 153 WRLDGRGKMSSRKYVEKLYPRLAEE 177 9**********************97 PP >> Daxx Daxx Family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.4 4.3 0.00031 0.65 428 524 .. 56 151 .. 31 169 .. 0.67 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 0.00031 Daxx 428 stesPllasqeseeeekaekeedeeddekeeedkseeeeeeeeeeeeeeeadneeeedleassegegddeeeeedeekndev 509 + +P ++s+ +++ + +++ed++dd+++++d+ +++ e e e+++ + +++ + ++s ++g ++ee e+++d+ gi|332009269|gb|AED96652.1| 56 KIINPKKKSRYGQTLSPYDSDEDDDDDDDDDDDDWLLNDDFAEVTEYEKKKPKSHKQTIAKKSVKKGIVKPEES-ETDEDDL 136 55688889999999999999999999888888876666666666666666666666666666666665555444.3446777 PP Daxx 510 akgirvseeqqkres 524 gi + k+++ gi|332009269|gb|AED96652.1| 137 DLGISPNATSEKKKE 151 788854444444433 PP >> BUD22 BUD22 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.2 8.0 0.00051 1.1 238 335 .. 75 174 .. 56 179 .. 0.69 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 0.00051 BUD22 238 esesesdeeeeedsds.rsvsdseeseppskkaKkkkaktsstfLPsLmggyfsgsedeeeede...dvapddvvkekt.kk 314 ++e ++d+++++d+d +++ +e +e ++kk+K++k +++ + s ++g ++++e+e +ed+ + p+ ++++k+ gi|332009269|gb|AED96652.1| 75 SDEDDDDDDDDDDDDWlLNDDFAEVTEYEKKKPKSHK---QTIAKKSVKKGIVKPEESETDEDDldlGISPNATSEKKKeSW 153 2222222222222222023444455667777777777...99999999***********99998988778888777777688 PP BUD22 315 rKNRrGQraRqkiwekKYGsk 335 r rG+ +k ek Y + gi|332009269|gb|AED96652.1| 154 RLDGRGKMSSRKYVEKLYPRL 174 999999999999999988665 PP >> RXT2_N RXT2-like, N-terminal # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.5 2.4 0.00018 0.38 25 70 .. 41 88 .. 35 106 .. 0.59 2 ? -1.1 0.2 0.65 1.4e+03 41 61 .. 113 135 .. 91 152 .. 0.46 Alignments for each domain: == domain 1 score: 10.5 bits; conditional E-value: 0.00018 RXT2_N 25 kslkekvveYnGserkvlsrkrkkk..kkepridedenelddededde 70 ++++ vv Y+ s+ k+++ k+k ++ +d+de+++dd+d+dd+ gi|332009269|gb|AED96652.1| 41 RKTRGFVVTYAHSNPKIINPKKKSRygQTLSPYDSDEDDDDDDDDDDD 88 5667779************33332234333333433333332222222 PP == domain 2 score: -1.1 bits; conditional E-value: 0.65 RXT2_N 41 vlsrkrkkk..kkepridedene 61 + +k++kk k+++++ de++ gi|332009269|gb|AED96652.1| 113 TIAKKSVKKgiVKPEESETDEDD 135 22223333322222222222222 PP >> YL1 YL1 nuclear protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.0 6.3 0.0018 3.9 57 149 .. 74 168 .. 56 181 .. 0.43 Alignments for each domain: == domain 1 score: 7.0 bits; conditional E-value: 0.0018 YL1 57 Dsdfddseddeeesddeeegekele.keekekkkkrkkkkaykeplkkkkkkkkkaakkkeaaaeekk.......kkkeeks 130 Dsd dd++dd+ ++dd ++ e e ++kk k + +++++kk kk +k +e++++e+ + ++ek+ gi|332009269|gb|AED96652.1| 74 DSDEDDDDDDDDDDDDWLLNDDFAEvTEYEKKKPK------SHKQTIAKKSVKKGIVKPEESETDEDDldlgispNATSEKK 149 23333333322222222222222222222222222......22222222222222233223322222222233332333333 PP YL1 131 eaetlldkkrRkSsRsstv 149 ++ +ld+ + SsR+ + gi|332009269|gb|AED96652.1| 150 KESWRLDGRGKMSSRKYVE 168 3444455567888887765 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (496 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 676 (0.0455802); expected 296.6 (0.02) Passed bias filter: 439 (0.0296002); expected 296.6 (0.02) Passed Vit filter: 59 (0.00397815); expected 14.8 (0.001) Passed Fwd filter: 8 (0.000539411); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.27 # Mc/sec: 4795.28 // Query: gi|332661488|gb|AEE86888.1| [L=378] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-45 153.0 0.9 7.4e-37 126.7 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.11 11.8 0.0 0.17 11.2 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.11 12.1 0.0 15 5.4 0.0 3.4 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.9 0.0 3.3e-10 1.6e-06 181 285 .. 12 121 .. 9 123 .. 0.72 2 ! 126.7 0.3 1.5e-40 7.4e-37 140 344 .. 115 321 .. 112 322 .. 0.93 Alignments for each domain: == domain 1 score: 26.9 bits; conditional E-value: 3.3e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661488|gb|AEE86888.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665577888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661488|gb|AEE86888.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888877676666666 PP == domain 2 score: 126.7 bits; conditional E-value: 1.5e-40 HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T........... CS mTERF 140 eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeillt 219 ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l++ gi|332661488|gb|AEE86888.1| 115 CPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLKS 196 56788899****************************************9986268**************9998747777888 PP ....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHH CS mTERF 220 rvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkel 296 +v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e+ gi|332661488|gb|AEE86888.1| 197 SVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDEV 278 88888889******************9862689************************************************* PP HCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 297 vefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661488|gb|AEE86888.1| 279 ASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 ******************...*9999999..***************96 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.2 0.0 3.4e-05 0.17 34 134 .. 219 328 .. 180 336 .. 0.78 Alignments for each domain: == domain 1 score: 11.2 bits; conditional E-value: 3.4e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661488|gb|AEE86888.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666556667788887777888888888888888888888777788887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPe 134 +++ Csl+e ++++++F e+fG e gi|332661488|gb|AEE86888.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSE 328 8899*********************765 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.5 0.0 0.047 2.3e+02 31 60 .. 93 122 .. 84 124 .. 0.75 2 ? -0.2 0.0 0.16 7.8e+02 16 52 .. 188 224 .. 181 241 .. 0.69 3 ? 5.4 0.0 0.0029 15 20 52 .. 265 297 .. 263 307 .. 0.92 Alignments for each domain: == domain 1 score: 1.5 bits; conditional E-value: 0.047 Fe_dep_repr_C 31 eevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661488|gb|AEE86888.1| 93 REVASAITKFPPILSHSVEEKLCPLLAFFQ 122 55555556666799***********99875 PP == domain 2 score: -0.2 bits; conditional E-value: 0.16 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrl 52 r +FL + +g++++ ++ + ++ +l ++ + l gi|332661488|gb|AEE86888.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKIL 224 55689********999988777766665555555555 PP == domain 3 score: 5.4 bits; conditional E-value: 0.0029 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661488|gb|AEE86888.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (378 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 382 (0.0257569); expected 296.6 (0.02) Passed bias filter: 348 (0.0234644); expected 296.6 (0.02) Passed Vit filter: 31 (0.00209022); expected 14.8 (0.001) Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.25 # Mc/sec: 3946.82 // Query: gi|332661487|gb|AEE86887.1| [L=363] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-45 153.2 1.0 5.6e-37 127.1 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.089 12.1 0.0 0.13 11.5 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.094 12.4 0.0 14 5.4 0.0 3.5 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di 0.16 11.7 0.0 1.7 8.4 0.0 2.5 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, ol Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.0 0.0 4e-10 1.5e-06 181 285 .. 12 121 .. 8 123 .. 0.73 2 ! 127.1 0.3 1.5e-40 5.6e-37 139 344 .. 114 321 .. 111 322 .. 0.93 Alignments for each domain: == domain 1 score: 27.0 bits; conditional E-value: 4e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661487|gb|AEE86887.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665577888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661487|gb|AEE86887.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888877676666666 PP == domain 2 score: 127.1 bits; conditional E-value: 1.5e-40 HHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T.......... CS mTERF 139 feesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeill 218 + ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l+ gi|332661487|gb|AEE86887.1| 114 LCPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLK 195 56788999*****************************************9986268**************999874777788 PP .....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHH CS mTERF 219 trvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplke 295 ++v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e gi|332661487|gb|AEE86887.1| 196 SSVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDE 277 888888889******************9862689************************************************ PP HHCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 296 lvefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 + ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661487|gb|AEE86887.1| 278 VASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 *******************...*9999999..***************96 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.5 0.0 3.6e-05 0.13 34 135 .. 219 329 .. 180 347 .. 0.79 Alignments for each domain: == domain 1 score: 11.5 bits; conditional E-value: 3.6e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661487|gb|AEE86887.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666556667788887777888888888888888888888777788887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPel 135 +++ Csl+e ++++++F e+fG e+ gi|332661487|gb|AEE86887.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSEV 329 8899*********************7665 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.6 0.0 0.06 2.2e+02 31 60 .. 93 122 .. 84 124 .. 0.75 2 ? -0.1 0.0 0.19 7.1e+02 16 52 .. 188 224 .. 180 241 .. 0.70 3 ? 5.4 0.0 0.0037 14 20 52 .. 265 297 .. 263 307 .. 0.92 Alignments for each domain: == domain 1 score: 1.6 bits; conditional E-value: 0.06 Fe_dep_repr_C 31 eevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661487|gb|AEE86887.1| 93 REVASAITKFPPILSHSVEEKLCPLLAFFQ 122 55555556666799***********99875 PP == domain 2 score: -0.1 bits; conditional E-value: 0.19 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrl 52 r +FL + +g++++ ++ + ++ +l ++ + l gi|332661487|gb|AEE86887.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKIL 224 56789********999988777766666555555555 PP == domain 3 score: 5.4 bits; conditional E-value: 0.0037 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661487|gb|AEE86887.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.48 1.8e+03 67 84 .. 12 29 .. 3 45 .. 0.68 2 ? 8.4 0.0 0.00045 1.7 55 90 .. 218 254 .. 205 267 .. 0.71 3 ? -0.2 0.0 0.21 7.9e+02 4 55 .. 255 301 .. 252 328 .. 0.66 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.48 CPSase_L_D3 67 eaKklGfsDaqiakllgv 84 ++ +Gf D i k+l++ gi|332661487|gb|AEE86887.1| 12 FFRDKGFDDPSIDKMLRK 29 567788888888888643 PP == domain 2 score: 8.4 bits; conditional E-value: 0.00045 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakll.gvteeevr 90 + ++ l+ + ++K+ Gf D+qia ++ g + ++ gi|332661487|gb|AEE86887.1| 218 RDVNKILKPNYDYLKECGFGDSQIATMVtGYPQILIK 254 4456677778899************886255554444 PP == domain 3 score: -0.2 bits; conditional E-value: 0.21 CPSase_L_D3 4 klkkptderlfaiaealrrgvsveeiheltkidpwFleklkeiveleeelkk 55 ++k+ + r+ +++ + rg++ e+ ++ ++F + lk+ ve +l k gi|332661487|gb|AEE86887.1| 255 SVKNSLQPRIRFLVQVMGRGMD-----EVASYPEFFHHGLKKKVESRFKLVK 301 5666677777778888877775.....5666778888888887777766665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (363 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 390 (0.0262963); expected 296.6 (0.02) Passed bias filter: 328 (0.0221158); expected 296.6 (0.02) Passed Vit filter: 30 (0.00202279); expected 14.8 (0.001) Passed Fwd filter: 4 (0.000269705); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.24 # Mc/sec: 3948.13 // Query: gi|332661486|gb|AEE86886.1| [L=333] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-45 153.8 0.9 5.1e-37 127.2 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.066 12.9 0.0 12 5.6 0.0 3.5 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di 0.077 12.3 0.0 0.12 11.7 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.12 12.1 0.0 1.4 8.6 0.0 2.6 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, ol Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.3 0.0 3.4e-10 1.2e-06 181 285 .. 12 121 .. 8 123 .. 0.73 2 ! 127.2 0.3 1.4e-40 5.1e-37 140 344 .. 115 321 .. 112 322 .. 0.93 Alignments for each domain: == domain 1 score: 27.3 bits; conditional E-value: 3.4e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661486|gb|AEE86886.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665677888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661486|gb|AEE86886.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888887676666666 PP == domain 2 score: 127.2 bits; conditional E-value: 1.4e-40 HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T........... CS mTERF 140 eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeillt 219 ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l++ gi|332661486|gb|AEE86886.1| 115 CPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLKS 196 56788899****************************************9986268**************9998747777888 PP ....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHH CS mTERF 220 rvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkel 296 +v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e+ gi|332661486|gb|AEE86886.1| 197 SVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDEV 278 88888889******************9862689************************************************* PP HCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 297 vefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661486|gb|AEE86886.1| 279 ASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 ******************...*9999999..***************96 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.8 0.0 0.052 1.9e+02 30 60 .. 92 122 .. 83 124 .. 0.76 2 ? 0.1 0.0 0.17 6.3e+02 16 53 .. 188 225 .. 180 241 .. 0.70 3 ? 5.6 0.0 0.0032 12 20 52 .. 265 297 .. 263 308 .. 0.92 Alignments for each domain: == domain 1 score: 1.8 bits; conditional E-value: 0.052 Fe_dep_repr_C 30 weevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661486|gb|AEE86886.1| 92 PREVASAITKFPPILSHSVEEKLCPLLAFFQ 122 555555556666799***********99875 PP == domain 2 score: 0.1 bits; conditional E-value: 0.17 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrld 53 r +FL + +g++++ ++ + ++ +l ++ + l+ gi|332661486|gb|AEE86886.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKILK 225 56789********9999887777666665555555555 PP == domain 3 score: 5.6 bits; conditional E-value: 0.0032 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661486|gb|AEE86886.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 3.1e-05 0.12 34 135 .. 219 329 .. 180 332 .. 0.78 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 3.1e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661486|gb|AEE86886.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666566667888887777888888888888888888888777888887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPel 135 +++ Csl+e ++++++F e+fG e+ gi|332661486|gb|AEE86886.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSEV 329 8899*********************8665 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.2 0.0 0.42 1.6e+03 67 84 .. 12 29 .. 3 46 .. 0.68 2 ? 8.6 0.0 0.00038 1.4 55 91 .. 218 255 .. 205 269 .. 0.71 3 ? -0.0 0.0 0.19 6.9e+02 4 55 .. 255 301 .. 252 328 .. 0.67 Alignments for each domain: == domain 1 score: -1.2 bits; conditional E-value: 0.42 CPSase_L_D3 67 eaKklGfsDaqiakllgv 84 ++ +Gf D i k+l++ gi|332661486|gb|AEE86886.1| 12 FFRDKGFDDPSIDKMLRK 29 567788888888888643 PP == domain 2 score: 8.6 bits; conditional E-value: 0.00038 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakll.gvteeevrk 91 + ++ l+ + ++K+ Gf D+qia ++ g + +++ gi|332661486|gb|AEE86886.1| 218 RDVNKILKPNYDYLKECGFGDSQIATMVtGYPQILIKS 255 4456677778899************8863555554544 PP == domain 3 score: -0.0 bits; conditional E-value: 0.19 CPSase_L_D3 4 klkkptderlfaiaealrrgvsveeiheltkidpwFleklkeiveleeelkk 55 ++k+ + r+ +++ + rg++ e+ ++ ++F + lk+ ve +l k gi|332661486|gb|AEE86886.1| 255 SVKNSLQPRIRFLVQVMGRGMD-----EVASYPEFFHHGLKKKVESRFKLVK 301 5666677777788888877775.....5666778888888887777766665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (333 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 463 (0.0312184); expected 296.6 (0.02) Passed bias filter: 443 (0.0298699); expected 296.6 (0.02) Passed Vit filter: 37 (0.00249477); expected 14.8 (0.001) Passed Fwd filter: 4 (0.000269705); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.24 # Mc/sec: 3621.84 // Query: gi|332010591|gb|AED97974.1| [L=391] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-41 139.4 4.0 1.6e-28 99.3 0.5 2.9 3 mTERF mTERF ------ inclusion threshold ------ 0.035 13.8 0.0 8.6 6.1 0.0 3.2 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, olig Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1.7 0.0 0.0097 72 179 203 .. 42 66 .. 39 73 .. 0.88 2 ! 38.5 0.0 6.7e-14 5e-10 2 98 .. 76 173 .. 75 180 .. 0.88 3 ! 99.3 0.5 2.1e-32 1.6e-28 175 344 .. 181 356 .. 166 357 .. 0.89 Alignments for each domain: == domain 1 score: 1.7 bits; conditional E-value: 0.0097 HHHHHHHTT--HHHHHHHHHTTTGG CS mTERF 179 vevlkslGfskedvwailkkcPell 203 ve+l++ Gf+k ai +++P+l gi|332010591|gb|AED97974.1| 42 VEFLRDNGFQKPLAIAIAMRYPNLK 66 89********************975 PP == domain 2 score: 38.5 bits; conditional E-value: 6.7e-14 HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-H CS mTERF 2 sllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiivad 83 ++l+s+ f+d++i++ ir +p++++ ++ek l pkl f + +g s l+k++s + +++g + vk++ + +++lk+i+ + gi|332010591|gb|AED97974.1| 76 QMLKSYSFSDTQIQKSIRVHPRMMFYNVEKILEPKLRFFKDIGFTGSGLGKFVSQNSSVVGVSLVKKLIPTVEILKSIVAPK 157 599***************************************************************************9865 PP .HHHHHHHHH-SHHHH CS mTERF 84 .kDksskleklpeslp 98 +D + +l + ++l+ gi|332010591|gb|AED97974.1| 158 hEDLPVILSRCGWLLL 173 1466666666666665 PP == domain 3 score: 99.3 bits; conditional E-value: 2.1e-32 HHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T............................THHHHHHHHHHHHHHTTT- CS mTERF 175 ikpnvevlkslGfskedvwailkkcPellglsekkklqt.keilltrvlvedesvikkapqivslseekilnkiefllglGf 255 + pn+ +l++ G+ +++ ++l ++P++++lse+k ++l ++++++ +++ + + slse++ k+ + Gf gi|332010591|gb|AED97974.1| 181 LLPNISYLETCGIVGSQLASLLRRQPRIFNLSEEKLRGYvSRALDLGFTLNSRMLVHAVISLSSLSEKTFDRKVKLFMANGF 262 689*******************************965541555666666666699999999999****************** PP -HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TT...T..GGGGGS CS mTERF 256 sreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskg...k..sillsl 332 s++ei +++r+P l+ s++k+ +eF++k m ++l + P+vl+y+LEkr++PR v++ l +kg k ++ + gi|332010591|gb|AED97974.1| 263 SEDEITDIIRRSPGLIRCSEDKLTLGFEFYLKRMGLEREALAKRPCVLSYNLEKRVIPRLKVLQILREKGlllKeeKKKKNM 344 **********************************************************************865367888999 PP -HHHHHHHHHHT CS mTERF 333 sevlkcsdeefl 344 ++++++e fl gi|332010591|gb|AED97974.1| 345 VGIVEMTEEAFL 356 999999999998 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 6.1 0.0 0.0012 8.6 55 84 .. 67 94 .. 55 105 .. 0.81 2 ? 0.5 0.0 0.065 4.8e+02 59 89 .. 105 135 .. 97 153 .. 0.74 3 ? 2.8 0.0 0.012 90 46 91 .. 235 280 .. 221 303 .. 0.80 Alignments for each domain: == domain 1 score: 6.1 bits; conditional E-value: 0.0012 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakllgv 84 + e+ +++++ +K++ fsD+qi k ++v gi|332010591|gb|AED97974.1| 67 S--LEQPRSVIQMLKSYSFSDTQIQKSIRV 94 3..56777799*************998765 PP == domain 2 score: 0.5 bits; conditional E-value: 0.065 CPSase_L_D3 59 elleellreaKklGfsDaqiakllgvteeev 89 + le lr +K Gf+ + + k+++++++ v gi|332010591|gb|AED97974.1| 105 KILEPKLRFFKDIGFTGSGLGKFVSQNSSVV 135 556668999************9987755444 PP == domain 3 score: 2.8 bits; conditional E-value: 0.012 CPSase_L_D3 46 iveleeelkkkaeelleellreaKklGfsDaqiakllgvteeevrk 91 +v++ +l++ +e++ ++ ++ + +Gfs+ +i ++++++ +r gi|332010591|gb|AED97974.1| 235 LVHAVISLSSLSEKTFDRKVKLFMANGFSEDEITDIIRRSPGLIRC 280 5555666777677777888999999*********999887776665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (391 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 396 (0.0267008); expected 296.6 (0.02) Passed bias filter: 343 (0.0231272); expected 296.6 (0.02) Passed Vit filter: 25 (0.00168566); expected 14.8 (0.001) Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.24 # Mc/sec: 4252.67 // Query: gi|332658065|gb|AEE83465.1| [L=493] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-48 164.3 1.0 5.8e-30 104.0 0.0 2.3 2 mTERF mTERF ------ inclusion threshold ------ 0.05 13.3 0.0 45 3.8 0.0 4.2 5 HHH_4 Helix-hairpin-helix containing domain Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 104.0 0.0 7.8e-34 5.8e-30 145 314 .. 202 375 .. 192 377 .. 0.89 2 ! 59.2 0.1 3.4e-20 2.5e-16 248 344 .. 377 468 .. 375 469 .. 0.89 Alignments for each domain: == domain 1 score: 104.0 bits; conditional E-value: 7.8e-34 HHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T................. CS mTERF 145 klvelgvdpktlkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede 226 +l +lg+ +++k + k + ++s+d +ikp+ve+l +lG+ k+d ++il+k+P++ g+s+ +l+ ++l + ++ gi|332658065|gb|AEE83465.1| 202 YLLDLGLNLEQIKTITRKFAAFPYYSLDGKIKPVVEFLLDLGIPKSDIPTILCKRPQICGISLTDNLKPTMAFLETLGIDKN 283 56667777777777777777788********************************************988877765555544 PP .............THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHH.CSGGGG CS mTERF 227 ...svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelv.efPqvl 303 ++i ++p i+ +s++k+ ++efl + G ++e+i + r+P+++++sve +++ +e++ + + ++ l + Pq + gi|332658065|gb|AEE83465.1| 284 qwaKIISRFPAILTYSRQKLTSTVEFLSQTGLTEEQIGRILTRCPNIMSYSVEDkLRPTMEYF-RSLNVDVAVLLhRCPQTF 364 5****************************************************99*******9.68999999865279**** PP GS-HHHHHHHH CS mTERF 304 gySLEkrikPR 314 g+S+E+ +kP gi|332658065|gb|AEE83465.1| 365 GLSIESNLKPV 375 **********6 PP == domain 2 score: 59.2 bits; conditional E-value: 3.4e-20 HHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTTGG CS mTERF 248 efllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgksi 328 ef+l+ Gf +ei m+ r+ +l ++s++ v +k ++++ m p +elv+fPq++gySL rikPR ++ ++ g gi|332658065|gb|AEE83465.1| 377 EFFLEKGFGLDEIGIMISRYGALYTFSLKEnVMPKWDYFQ-TMDYPKSELVKFPQFFGYSLQERIKPR---YELVQRSG--V 452 9***************************999******997.5**************************...77777777..7 PP GGGS-HHHHHHHHHHT CS mTERF 329 llslsevlkcsdeefl 344 +l l++vl+ s ef+ gi|332658065|gb|AEE83465.1| 453 RLLLNQVLSLSGIEFE 468 7777877777777776 PP >> HHH_4 Helix-hairpin-helix containing domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.2 0.0 0.11 8.2e+02 4 31 .. 64 91 .. 61 99 .. 0.83 2 ? -1.4 0.0 0.26 1.9e+03 12 33 .. 200 221 .. 191 225 .. 0.84 3 ? 3.8 0.0 0.0061 45 7 32 .. 267 292 .. 262 296 .. 0.89 4 ? 2.7 0.0 0.014 1e+02 6 30 .. 301 325 .. 297 328 .. 0.87 5 ? -3.7 0.0 1.4 1e+04 8 41 .. 372 405 .. 369 407 .. 0.70 Alignments for each domain: == domain 1 score: -0.2 bits; conditional E-value: 0.11 HHH_4 4 eqrelrelleflqeygisaklaekiykk 31 ++++ + l f+++ g+s++l +++++k gi|332658065|gb|AEE83465.1| 64 KEEAKAVLTLFFKKQGLSNSLSSRLINK 91 55666778899***********999875 PP == domain 2 score: -1.4 bits; conditional E-value: 0.26 HHH_4 12 leflqeygisaklaekiykkYg 33 +l ++g++ +++++i +k+ gi|332658065|gb|AEE83465.1| 200 TLYLLDLGLNLEQIKTITRKFA 221 5689999**********99985 PP == domain 3 score: 3.8 bits; conditional E-value: 0.0061 HHH_4 7 elrelleflqeygisaklaekiykkY 32 +l+ +++fl+ +gi +++ ki+ ++ gi|332658065|gb|AEE83465.1| 267 NLKPTMAFLETLGIDKNQWAKIISRF 292 67889*****************9987 PP == domain 4 score: 2.7 bits; conditional E-value: 0.014 HHH_4 6 relrelleflqeygisaklaekiyk 30 ++l ++efl++ g++++++ +i++ gi|332658065|gb|AEE83465.1| 301 QKLTSTVEFLSQTGLTEEQIGRILT 325 667889****************986 PP == domain 5 score: -3.7 bits; conditional E-value: 1.4 HHH_4 8 lrelleflqeygisaklaekiykkYgeeaievik 41 l+ + ef+ e g++ + ++ +Yg+ +k gi|332658065|gb|AEE83465.1| 372 LKPVTEFFLEKGFGLDEIGIMISRYGALYTFSLK 405 5667788888888888888888888876555555 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (493 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 320 (0.0215764); expected 296.6 (0.02) Passed bias filter: 300 (0.0202279); expected 296.6 (0.02) Passed Vit filter: 25 (0.00168566); expected 14.8 (0.001) Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.25 # Mc/sec: 5147.57 // Query: gi|332003686|gb|AED91069.1| [L=1141] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-51 174.1 17.3 1.2e-15 56.9 0.5 6.1 6 mTERF mTERF 0.0024 18.0 0.3 0.61 10.2 0.0 4.3 6 RuvA_C RuvA, C-terminal domain ------ inclusion threshold ------ 0.011 15.6 0.2 26 4.7 0.0 3.2 3 T6SS_Vgr Putative type VI secretion system Rhs element Vgr Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.7 0.0 1.7e-06 0.0083 108 193 .. 173 259 .. 154 265 .. 0.88 2 ! 26.3 0.0 4.8e-10 2.4e-06 2 106 .. 277 380 .. 276 397 .. 0.81 3 ! 54.5 1.4 1.3e-18 6.5e-15 205 343 .. 422 560 .. 417 562 .. 0.90 4 ! 22.7 0.0 6.1e-09 3e-05 111 272 .. 695 855 .. 669 860 .. 0.92 5 ! 9.6 0.0 6.2e-05 0.3 18 93 .. 847 922 .. 844 942 .. 0.84 6 ! 56.9 0.5 2.5e-19 1.2e-15 207 344 .. 981 1118 .. 975 1119 .. 0.91 Alignments for each domain: == domain 1 score: 14.7 bits; conditional E-value: 1.7e-06 HHHHHHHTT--HHHHHHHHHH-CHHHHS-..HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT CS mTERF 108 nvsvlrelgvtrkllislliselqpvlgk..evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGf 187 n vl +gv +k i+ + e + v++ v+ ++k ++lg+++ l ++i pr+l+ + ++ ++v+ l+slGf gi|332003686|gb|AED91069.1| 173 NHHVLCYSGVDPK-RIGKIFKEAREVFSYetGVLASKIKAYEDLGFSRLFLSKLIVCSPRVLMGHTNIELVQVVKTLQSLGF 253 6678888999999.888899999999988677999*********************************************** PP --HHHH CS mTERF 188 skedvw 193 ++e v gi|332003686|gb|AED91069.1| 254 EFEWVM 259 998775 PP == domain 2 score: 26.3 bits; conditional E-value: 4.8e-10 HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-H CS mTERF 2 sllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiivad 83 sllr f + ir+ p+ll++++ k + + f + gas+sel + +++ P i +k v+++++ flk+i ++d gi|332003686|gb|AED91069.1| 277 SLLREICFDEEKLYGLIRNCPSLLFENSGKWTGILVGFETKLGASRSELCSLFQKFPLIQVEKCVSNLRQCFLFLKEIEMED 358 56777777777777779***************************************************************85 PP HHHHHHHHH-SHHHHS---HHHH CS mTERF 84 kDksskleklpeslpqsleenke 106 +++ +++ ++ l+ + +k gi|332003686|gb|AED91069.1| 359 DEIHKVFRSHSWWLGS-CKLKKT 380 5555555555555544.333333 PP == domain 3 score: 54.5 bits; conditional E-value: 1.3e-18 GGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 205 lsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 ++++ k + + ll ++ +e+ ++ a + + + +++ + + l +lGf+++++ mvk +P +l+ + + + k+ +l+ gi|332003686|gb|AED91069.1| 422 VDIESKSMKTQFLLDLGYKENSEEMETAMKNFRGKGSELRERFNVLVSLGFTKKDVKDMVKACPTMLSQTCDILESKVNYLI 503 5666666667888888888888777777888888999999****************************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHH CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeef 343 ke pl+ lv+fP l++ L r+k R ++ l+ +gk ++ +s +l csd+ f gi|332003686|gb|AED91069.1| 504 KELGYPLSTLVDFPSCLKFTLQ-RMKLRFAMFSWLQARGKvDRKIKVSTMLACSDKIF 560 *********************6.777788**********9999************988 PP == domain 4 score: 22.7 bits; conditional E-value: 6.1e-09 HHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH CS mTERF 111 vlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked 191 +l +lg++++ ++s li + +++l+ + e + + g+ +++++++ + r + + + +++ +++lGfsk gi|332003686|gb|AED91069.1| 695 FLESLGLKPS-EFSHLIPCDKMFLNEdAFLLENYHVFWNYGIGREKMGKIFKEA-REVFGYETGVLASKIKSYEDLGFSKLF 774 899*******.******999999999556678889999**********988777.5677777899***************** PP HHHHHHHTTTGGGGGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGG CS mTERF 192 vwailkkcPellglsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllg 272 + +++ + P++l+ + + l + +l+ + + v + + vs++ +++ + fl +l ++e ++++++P l++ gi|332003686|gb|AED91069.1| 775 LSKLIVCSPSILIGDMNVGLAKVMEMLKAIGFGVDWVTENLSEEVSYDWSSMHRCLSFLRDLYVDENELCELIRKMPRLIF 855 ******************99999999999999999*******************************************996 PP == domain 5 score: 9.6 bits; conditional E-value: 6.2e-05 HH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGG.S-.HHHHHHHHHHHTTTSS-HHHHHHHHHH- CS mTERF 18 irsyplllvadaekslqpklqfLesrgaskseltkilstvPkilg.kkkvksissvydflkkiivadkDkssklekl 93 ir++p+l+++d+ + f + g+s+sel + +++ P+ + +k v +++ flk+i + d+D++ k ++l gi|332003686|gb|AED91069.1| 847 IRKMPRLIFEDSGEWTLILAGFEAKLGSSRSELSSLFQKFPQCQSlGKFVLNLRHCFLFLKDIEM-DDDEIGKIFRL 922 68899*******999999***********************9854256699************99.56666666655 PP == domain 6 score: 56.9 bits; conditional E-value: 2.5e-19 S-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 207 ekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 k k+ + + ll ++ +e+ +++a + + + +++ + + l ++G +++++ mvk +P +l+ + + + k+ +lv gi|332003686|gb|AED91069.1| 981 TKSKTMKTQFLLDLGYKENSEEMERALKNFRGKGSELRERFNVLVSFGLTEKDVKDMVKACPSILTQACDILESKVNYLV 1060 444555558899999999998889999999999*********************************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 ke pl+ lv fP+ l+y L r+k R ++ l+ +gk +l +s +l csd+ f+ gi|332003686|gb|AED91069.1| 1061 KELGYPLSTLVTFPTCLKYTLQ-RMKLRFSMFSWLQDRGKaDPKLQVSTILVCSDKFFA 1118 *********************6.777788**********8899************9886 PP >> RuvA_C RuvA, C-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.4 0.0 0.07 3.5e+02 5 15 .. 243 253 .. 241 254 .. 0.91 2 ? -2.1 0.1 0.91 4.5e+03 10 17 .. 434 441 .. 434 442 .. 0.85 3 ! 10.2 0.0 0.00012 0.61 10 27 .. 467 484 .. 465 495 .. 0.90 4 ? -3.5 0.1 2.3 1.2e+04 10 19 .. 696 705 .. 696 705 .. 0.90 5 ? -1.4 0.0 0.53 2.6e+03 10 18 .. 991 999 .. 991 1012 .. 0.82 6 ? -2.1 0.0 0.89 4.4e+03 11 27 .. 1025 1041 .. 1024 1047 .. 0.81 Alignments for each domain: == domain 1 score: 1.4 bits; conditional E-value: 0.07 HCCHHHHHCT- CS RuvA_C 5 daveALlaLGY 15 ++v +L +LG+ gi|332003686|gb|AED91069.1| 243 QVVKTLQSLGF 253 79********9 PP == domain 2 score: -2.1 bits; conditional E-value: 0.91 HHHCT--C CS RuvA_C 10 LlaLGYke 17 Ll LGYke gi|332003686|gb|AED91069.1| 434 LLDLGYKE 441 788****8 PP == domain 3 score: 10.2 bits; conditional E-value: 0.00012 HHHCT--CCCCHHHHHHC CS RuvA_C 10 LlaLGYkekeAekAvakv 27 L++LG+++k+++ +v++ gi|332003686|gb|AED91069.1| 467 LVSLGFTKKDVKDMVKAC 484 9**************986 PP == domain 4 score: -3.5 bits; conditional E-value: 2.3 HHHCT--CCC CS RuvA_C 10 LlaLGYkeke 19 L++LG k++e gi|332003686|gb|AED91069.1| 696 LESLGLKPSE 705 89****9987 PP == domain 5 score: -1.4 bits; conditional E-value: 0.53 HHHCT--CC CS RuvA_C 10 LlaLGYkek 18 Ll LGYke+ gi|332003686|gb|AED91069.1| 991 LLDLGYKEN 999 788***985 PP == domain 6 score: -2.1 bits; conditional E-value: 0.89 HHCT--CCCCHHHHHHC CS RuvA_C 11 laLGYkekeAekAvakv 27 ++ G +ek+++ +v++ gi|332003686|gb|AED91069.1| 1025 VSFGLTEKDVKDMVKAC 1041 56689999**9999986 PP >> T6SS_Vgr Putative type VI secretion system Rhs element Vgr # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.3 0.0 0.03 1.5e+02 25 88 .. 22 85 .. 17 101 .. 0.84 2 ? 4.5 0.0 0.0061 30 25 58 .. 424 461 .. 419 466 .. 0.75 3 ? 4.7 0.0 0.0052 26 26 58 .. 984 1018 .. 975 1023 .. 0.74 Alignments for each domain: == domain 1 score: 2.3 bits; conditional E-value: 0.03 T6SS_Vgr 25 LasehaksqLnlGylvdqkdngrgekrGeGfeLrTdawgavRAgkGlllstearakasgeqldm 88 L+++ + s G+l + +++ r+ + +G e+ +++ + R +G ++ + r+ a++ +ld gi|332003686|gb|AED91069.1| 22 LETQLKPSISGTGFLLRCAQTPRSFATVTGNEVCSEKSKVKRTRNGFKITPNVRKLAEEAMLDY 85 5566666666689999999999999999***************************999999986 PP == domain 2 score: 4.5 bits; conditional E-value: 0.0061 T6SS_Vgr 25 Lasehaksq..LnlGylvdq..kdngrgekrGeGfeLr 58 ++s++ k+q L lGy ++ +++ +++rG+G eLr gi|332003686|gb|AED91069.1| 424 IESKSMKTQflLDLGYKENSeeMETAMKNFRGKGSELR 461 55555555543899**8887546677899********8 PP == domain 3 score: 4.7 bits; conditional E-value: 0.0052 T6SS_Vgr 26 asehaksqLnlGylvdq..kdngrgekrGeGfeLr 58 ++ +++ L lGy ++ +++ +++rG+G eLr gi|332003686|gb|AED91069.1| 984 KTMKTQFLLDLGYKENSeeMERALKNFRGKGSELR 1018 4445555699***9888435566689********8 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (1141 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 307 (0.0206999); expected 296.6 (0.02) Passed Vit filter: 26 (0.00175308); expected 14.8 (0.001) Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.27 # Mc/sec: 11031.07 // Query: gi|332658810|gb|AEE84210.1| [L=575] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-17 63.7 3.0 2.5e-08 32.8 0.2 4.1 3 mTERF mTERF Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.7 0.0 2e-09 3e-05 75 271 .. 103 292 .. 99 302 .. 0.79 2 ! 5.9 0.4 0.00026 3.8 43 136 .. 310 400 .. 303 414 .. 0.76 3 ! 32.8 0.2 1.7e-12 2.5e-08 206 344 .. 415 553 .. 374 554 .. 0.72 Alignments for each domain: == domain 1 score: 22.7 bits; conditional E-value: 2e-09 HHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHH CS mTERF 75 flkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpkt 155 +l+ki+ +kD+s+ l k ++ e++ + +lg+++ +++ + +++l+ +++e l + g+++ + gi|332658810|gb|AEE84210.1| 103 LLSKIDDNQKDVSKGLTKFLRY----NPI-NEFE-PFFESLGLCPY-EFETFLPRKLMFLSDdGIMFENFHALCNYGIPRGK 177 5666666666666665543333....332.1222.36679999999.9999999988888887899**************** PP HHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T............................ CS mTERF 156 lkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede..svikkapqi 235 ++r+ + r + + + +++ +++lG+sk v +++ +cP ll+ + ++ + ++ ++++++ + + gi|332658810|gb|AEE84210.1| 178 IGRMYKEA-REIFRYESGMLAMKLRGYENLGLSKATVIKLVTSCPLLLVGGIDAEFSS--VVDKLKGLQVGcdWLGRYLSDR 256 ****9988.6788888899******************************999984444..4444444443354555555577 PP .THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGG CS mTERF 236 vslseekilnkiefllglGfsreeiakmvkrfPqll 271 +s + il++iefl ++G+ +e + k +P+l gi|332658810|gb|AEE84210.1| 257 KTYSWRRILETIEFLDKVGCKEEKLSSLLKTYPALV 292 89*******************************985 PP == domain 2 score: 5.9 bits; conditional E-value: 0.00026 TT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHH CS mTERF 43 rgaskseltkilstvPkilgkkkvksissvydflkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrkllis 124 g++ e+ + +P+ l+ k vk+i++ +dfl i ++ + + ++l+ e+ + + + l +l v+++ l++ gi|332658810|gb|AEE84210.1| 310 AGLQVNEIYRLFIDNPEMLSDKCVKNIQKTLDFLIAIRMETQFITKILLSHMELIGSCSLP--APRTACL-SLNVKQDELCK 388 5666667777788899999999999999999999999999888888888888776654443..4455556.78999999999 PP HHHH-CHHHHS- CS mTERF 125 lliselqpvlgk 136 +l e++ ++++ gi|332658810|gb|AEE84210.1| 389 ILKKEPLRLFCF 400 998888877776 PP == domain 3 score: 32.8 bits; conditional E-value: 1.7e-12 GS-T............................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHH CS mTERF 206 sekkklqtkeilltrvlvede.svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlv 286 + k l++ e ll+++ ve+ ++k a + + + +++ + + l + G + + +++++ P +l ls + + kk+ l gi|332658810|gb|AEE84210.1| 415 DSRKYLEKTEFLLRLGYVENSdEMVK-ALKQFRGRGDQLQERFDCLVKAGLNYNVVTEIIRHAPMILNLSKDVIEKKIHSLT 495 22333444444444444444465555.455556778888899999999********************************** PP HCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 287 kemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 + p+++lv+fP++l y + +ri R ++ l ++ ls s +l+c d +f gi|332658810|gb|AEE84210.1| 496 ELLGYPIESLVRFPAYLCYDM-QRIHHRFSMYLWLRERDAaKPMLSPSTILTCGDARFV 553 *********************.5899998999999999955777788999999999996 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (575 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 310 (0.0209022); expected 296.6 (0.02) Passed Vit filter: 24 (0.00161823); expected 14.8 (0.001) Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.26 # Mc/sec: 5772.85 // Query: gi|332009269|gb|AED96652.1| [L=496] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-39 135.2 3.0 1.4e-21 76.4 0.1 2.2 2 mTERF mTERF ------ inclusion threshold ------ 0.049 13.7 16.3 0.085 13.0 11.3 1.3 1 SPT6_acidic Acidic N-terminal SPT6 0.48 8.5 3.0 0.68 8.0 2.1 1.1 1 DUF2151 Cell cycle and development regulator 0.48 8.8 6.2 0.65 8.4 4.3 1.1 1 Daxx Daxx Family 0.77 8.7 11.5 1.1 8.2 8.0 1.1 1 BUD22 BUD22 1.4 8.7 7.4 0.38 10.5 2.4 1.9 2 RXT2_N RXT2-like, N-terminal 2.3 7.7 9.2 3.9 7.0 6.3 1.3 1 YL1 YL1 nuclear protein Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 76.4 0.1 6.6e-25 1.4e-21 111 276 .. 190 362 .. 163 366 .. 0.89 2 ! 59.5 0.3 9.1e-20 1.9e-16 244 344 .. 366 465 .. 362 466 .. 0.89 Alignments for each domain: == domain 1 score: 76.4 bits; conditional E-value: 6.6e-25 HHHHTT--HHHHHHHHHH-CHHHHS-HHH..HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--H CS mTERF 111 vlrelgvtrkllislliselqpvlgkevf..eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfske 190 +l+ g++++ + + ++ p l+ vf +e++++l ++gv+ ++kr++ ++p++l + +++++k+ + +l +lG+ ++ gi|332009269|gb|AED96652.1| 190 YLSTFGLKES-HFVQMYERHMPSLQINVFsaQERLDYLLSVGVKHRDIKRMLLRQPQILQYTVENNLKAHISFLMGLGIPNS 270 6677777777.66677777777777755522689************************************************ PP HHHHHHHHTTTGGGGGS-T...............................THHHHHHHHHHHHHHT..TT--HHHHHHHHHT CS mTERF 191 dvwailkkcPellglsekkklq.tkeilltrvlvede...svikkapqivslseekilnkiefllg..lGfsreeiakmvkr 266 + +i++ +P+l+ +s+++ l t ++l v+ +++ +v++ pqi++ + + + n+ ++l+ lG r+ ++kmvk+ gi|332009269|gb|AED96652.1| 271 KIGQIVAATPSLFSYSVENSLRpTIRYLIEEVGIKETdvgKVVQLSPQILVQRLDITWNTRYMFLSkeLGAPRDSVVKMVKK 352 *******************9865888888887777777***********************9999999************** PP SGGGGGS-HH CS mTERF 267 fPqllglsve 276 Pqll +s++ gi|332009269|gb|AED96652.1| 353 HPQLLHYSID 362 ********98 PP == domain 2 score: 59.5 bits; conditional E-value: 9.1e-20 HHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--T CS mTERF 244 lnkiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallsk 324 l+ i+fl ++G+ +i k + q+l+ls+e +k+k+ +lv+e + ++ l ++P +l++SL++ri PR ++ l++ gi|332009269|gb|AED96652.1| 366 LPRINFLRSIGMCNSDILKVLTSLTQVLSLSLEDnLKPKYMYLVNELNNEVHILTKYPMYLSLSLDQRIRPR---HRFLVEL 444 789******************************99*************************************...9999998 PP TT..GGGGGS-HHHHHHHHHHT CS mTERF 325 gk..sillslsevlkcsdeefl 344 k +ls+ l +de+f+ gi|332009269|gb|AED96652.1| 445 KKvrKGPFPLSS-LVPNDESFC 465 865455566665.556777776 PP >> SPT6_acidic Acidic N-terminal SPT6 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.0 11.3 4e-05 0.085 2 79 .. 74 152 .. 73 165 .. 0.64 Alignments for each domain: == domain 1 score: 13.0 bits; conditional E-value: 4e-05 SPT6_acidic 2 DsseEeddddDeeeark.vreGFIvddedeeeeeeeeskrrrkkkkrkrrereeeeealdedDleL.ieentgvkekree 79 Ds+e++ddddD+++++ ++F + e+++ +++k+ +kk k+ + ee + dedDl+L i n+ ++k+e+ gi|332009269|gb|AED96652.1| 74 DSDEDDDDDDDDDDDDWlLNDDFAEV-TEYEKKKPKSHKQTIAKKSVKKGIVKPEESETDEDDLDLgISPNATSEKKKES 152 67666655555555543356666654.3334555556667777788888888889999********66666666555543 PP >> DUF2151 Cell cycle and development regulator # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.0 2.1 0.00032 0.68 601 692 .. 78 177 .. 48 179 .. 0.53 Alignments for each domain: == domain 1 score: 8.0 bits; conditional E-value: 0.00032 DUF2151 601 eraksvsdeeeeeleese.............aitdspdspeilekkkkvkiee..skkkeakkgevsllsllssriekaesk 667 + +++ d+++ + + +p+s +++ +kk+vk + +e+++ +++l ek+++ gi|332009269|gb|AED96652.1| 78 DDDDD-DDDDD------DdwllnddfaevteYEKKKPKSHKQTIAKKSVKKGIvkPEESETDEDDLDLGISPNATSEKKKES 152 11111.12222......13433334554433222233333333233333322222333333333334322222335999999 PP DUF2151 668 krreFvGRlesvgniAkLYpqlaek 692 r + G+++s + kLYp lae+ gi|332009269|gb|AED96652.1| 153 WRLDGRGKMSSRKYVEKLYPRLAEE 177 9**********************97 PP >> Daxx Daxx Family # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.4 4.3 0.00031 0.65 428 524 .. 56 151 .. 31 169 .. 0.67 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 0.00031 Daxx 428 stesPllasqeseeeekaekeedeeddekeeedkseeeeeeeeeeeeeeeadneeeedleassegegddeeeeedeekndev 509 + +P ++s+ +++ + +++ed++dd+++++d+ +++ e e e+++ + +++ + ++s ++g ++ee e+++d+ gi|332009269|gb|AED96652.1| 56 KIINPKKKSRYGQTLSPYDSDEDDDDDDDDDDDDWLLNDDFAEVTEYEKKKPKSHKQTIAKKSVKKGIVKPEES-ETDEDDL 136 55688889999999999999999999888888876666666666666666666666666666666665555444.3446777 PP Daxx 510 akgirvseeqqkres 524 gi + k+++ gi|332009269|gb|AED96652.1| 137 DLGISPNATSEKKKE 151 788854444444433 PP >> BUD22 BUD22 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.2 8.0 0.00051 1.1 238 335 .. 75 174 .. 56 179 .. 0.69 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 0.00051 BUD22 238 esesesdeeeeedsds.rsvsdseeseppskkaKkkkaktsstfLPsLmggyfsgsedeeeede...dvapddvvkekt.kk 314 ++e ++d+++++d+d +++ +e +e ++kk+K++k +++ + s ++g ++++e+e +ed+ + p+ ++++k+ gi|332009269|gb|AED96652.1| 75 SDEDDDDDDDDDDDDWlLNDDFAEVTEYEKKKPKSHK---QTIAKKSVKKGIVKPEESETDEDDldlGISPNATSEKKKeSW 153 2222222222222222023444455667777777777...99999999***********99998988778888777777688 PP BUD22 315 rKNRrGQraRqkiwekKYGsk 335 r rG+ +k ek Y + gi|332009269|gb|AED96652.1| 154 RLDGRGKMSSRKYVEKLYPRL 174 999999999999999988665 PP >> RXT2_N RXT2-like, N-terminal # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.5 2.4 0.00018 0.38 25 70 .. 41 88 .. 35 106 .. 0.59 2 ? -1.1 0.2 0.65 1.4e+03 41 61 .. 113 135 .. 91 152 .. 0.46 Alignments for each domain: == domain 1 score: 10.5 bits; conditional E-value: 0.00018 RXT2_N 25 kslkekvveYnGserkvlsrkrkkk..kkepridedenelddededde 70 ++++ vv Y+ s+ k+++ k+k ++ +d+de+++dd+d+dd+ gi|332009269|gb|AED96652.1| 41 RKTRGFVVTYAHSNPKIINPKKKSRygQTLSPYDSDEDDDDDDDDDDD 88 5667779************33332234333333433333332222222 PP == domain 2 score: -1.1 bits; conditional E-value: 0.65 RXT2_N 41 vlsrkrkkk..kkepridedene 61 + +k++kk k+++++ de++ gi|332009269|gb|AED96652.1| 113 TIAKKSVKKgiVKPEESETDEDD 135 22223333322222222222222 PP >> YL1 YL1 nuclear protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 7.0 6.3 0.0018 3.9 57 149 .. 74 168 .. 56 181 .. 0.43 Alignments for each domain: == domain 1 score: 7.0 bits; conditional E-value: 0.0018 YL1 57 Dsdfddseddeeesddeeegekele.keekekkkkrkkkkaykeplkkkkkkkkkaakkkeaaaeekk.......kkkeeks 130 Dsd dd++dd+ ++dd ++ e e ++kk k + +++++kk kk +k +e++++e+ + ++ek+ gi|332009269|gb|AED96652.1| 74 DSDEDDDDDDDDDDDDWLLNDDFAEvTEYEKKKPK------SHKQTIAKKSVKKGIVKPEESETDEDDldlgispNATSEKK 149 23333333322222222222222222222222222......22222222222222233223322222222233332333333 PP YL1 131 eaetlldkkrRkSsRsstv 149 ++ +ld+ + SsR+ + gi|332009269|gb|AED96652.1| 150 KESWRLDGRGKMSSRKYVE 168 3444455567888887765 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (496 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 676 (0.0455802); expected 296.6 (0.02) Passed bias filter: 439 (0.0296002); expected 296.6 (0.02) Passed Vit filter: 59 (0.00397815); expected 14.8 (0.001) Passed Fwd filter: 8 (0.000539411); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.26 # Mc/sec: 4979.71 // Query: gi|332661488|gb|AEE86888.1| [L=378] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-45 153.0 0.9 7.4e-37 126.7 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.11 11.8 0.0 0.17 11.2 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.11 12.1 0.0 15 5.4 0.0 3.4 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 26.9 0.0 3.3e-10 1.6e-06 181 285 .. 12 121 .. 9 123 .. 0.72 2 ! 126.7 0.3 1.5e-40 7.4e-37 140 344 .. 115 321 .. 112 322 .. 0.93 Alignments for each domain: == domain 1 score: 26.9 bits; conditional E-value: 3.3e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661488|gb|AEE86888.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665577888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661488|gb|AEE86888.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888877676666666 PP == domain 2 score: 126.7 bits; conditional E-value: 1.5e-40 HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T........... CS mTERF 140 eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeillt 219 ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l++ gi|332661488|gb|AEE86888.1| 115 CPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLKS 196 56788899****************************************9986268**************9998747777888 PP ....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHH CS mTERF 220 rvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkel 296 +v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e+ gi|332661488|gb|AEE86888.1| 197 SVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDEV 278 88888889******************9862689************************************************* PP HCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 297 vefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661488|gb|AEE86888.1| 279 ASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 ******************...*9999999..***************96 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.2 0.0 3.4e-05 0.17 34 134 .. 219 328 .. 180 336 .. 0.78 Alignments for each domain: == domain 1 score: 11.2 bits; conditional E-value: 3.4e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661488|gb|AEE86888.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666556667788887777888888888888888888888777788887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPe 134 +++ Csl+e ++++++F e+fG e gi|332661488|gb|AEE86888.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSE 328 8899*********************765 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.5 0.0 0.047 2.3e+02 31 60 .. 93 122 .. 84 124 .. 0.75 2 ? -0.2 0.0 0.16 7.8e+02 16 52 .. 188 224 .. 181 241 .. 0.69 3 ? 5.4 0.0 0.0029 15 20 52 .. 265 297 .. 263 307 .. 0.92 Alignments for each domain: == domain 1 score: 1.5 bits; conditional E-value: 0.047 Fe_dep_repr_C 31 eevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661488|gb|AEE86888.1| 93 REVASAITKFPPILSHSVEEKLCPLLAFFQ 122 55555556666799***********99875 PP == domain 2 score: -0.2 bits; conditional E-value: 0.16 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrl 52 r +FL + +g++++ ++ + ++ +l ++ + l gi|332661488|gb|AEE86888.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKIL 224 55689********999988777766665555555555 PP == domain 3 score: 5.4 bits; conditional E-value: 0.0029 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661488|gb|AEE86888.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (378 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 382 (0.0257569); expected 296.6 (0.02) Passed bias filter: 348 (0.0234644); expected 296.6 (0.02) Passed Vit filter: 31 (0.00209022); expected 14.8 (0.001) Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.24 # Mc/sec: 4111.27 // Query: gi|332661487|gb|AEE86887.1| [L=363] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-45 153.2 1.0 5.6e-37 127.1 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.089 12.1 0.0 0.13 11.5 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.094 12.4 0.0 14 5.4 0.0 3.5 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di 0.16 11.7 0.0 1.7 8.4 0.0 2.5 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, ol Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.0 0.0 4e-10 1.5e-06 181 285 .. 12 121 .. 8 123 .. 0.73 2 ! 127.1 0.3 1.5e-40 5.6e-37 139 344 .. 114 321 .. 111 322 .. 0.93 Alignments for each domain: == domain 1 score: 27.0 bits; conditional E-value: 4e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661487|gb|AEE86887.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665577888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661487|gb|AEE86887.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888877676666666 PP == domain 2 score: 127.1 bits; conditional E-value: 1.5e-40 HHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T.......... CS mTERF 139 feesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeill 218 + ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l+ gi|332661487|gb|AEE86887.1| 114 LCPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLK 195 56788999*****************************************9986268**************999874777788 PP .....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHH CS mTERF 219 trvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplke 295 ++v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e gi|332661487|gb|AEE86887.1| 196 SSVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDE 277 888888889******************9862689************************************************ PP HHCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 296 lvefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 + ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661487|gb|AEE86887.1| 278 VASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 *******************...*9999999..***************96 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.5 0.0 3.6e-05 0.13 34 135 .. 219 329 .. 180 347 .. 0.79 Alignments for each domain: == domain 1 score: 11.5 bits; conditional E-value: 3.6e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661487|gb|AEE86887.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666556667788887777888888888888888888888777788887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPel 135 +++ Csl+e ++++++F e+fG e+ gi|332661487|gb|AEE86887.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSEV 329 8899*********************7665 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.6 0.0 0.06 2.2e+02 31 60 .. 93 122 .. 84 124 .. 0.75 2 ? -0.1 0.0 0.19 7.1e+02 16 52 .. 188 224 .. 180 241 .. 0.70 3 ? 5.4 0.0 0.0037 14 20 52 .. 265 297 .. 263 307 .. 0.92 Alignments for each domain: == domain 1 score: 1.6 bits; conditional E-value: 0.06 Fe_dep_repr_C 31 eevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661487|gb|AEE86887.1| 93 REVASAITKFPPILSHSVEEKLCPLLAFFQ 122 55555556666799***********99875 PP == domain 2 score: -0.1 bits; conditional E-value: 0.19 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrl 52 r +FL + +g++++ ++ + ++ +l ++ + l gi|332661487|gb|AEE86887.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKIL 224 56789********999988777766666555555555 PP == domain 3 score: 5.4 bits; conditional E-value: 0.0037 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661487|gb|AEE86887.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.4 0.0 0.48 1.8e+03 67 84 .. 12 29 .. 3 45 .. 0.68 2 ? 8.4 0.0 0.00045 1.7 55 90 .. 218 254 .. 205 267 .. 0.71 3 ? -0.2 0.0 0.21 7.9e+02 4 55 .. 255 301 .. 252 328 .. 0.66 Alignments for each domain: == domain 1 score: -1.4 bits; conditional E-value: 0.48 CPSase_L_D3 67 eaKklGfsDaqiakllgv 84 ++ +Gf D i k+l++ gi|332661487|gb|AEE86887.1| 12 FFRDKGFDDPSIDKMLRK 29 567788888888888643 PP == domain 2 score: 8.4 bits; conditional E-value: 0.00045 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakll.gvteeevr 90 + ++ l+ + ++K+ Gf D+qia ++ g + ++ gi|332661487|gb|AEE86887.1| 218 RDVNKILKPNYDYLKECGFGDSQIATMVtGYPQILIK 254 4456677778899************886255554444 PP == domain 3 score: -0.2 bits; conditional E-value: 0.21 CPSase_L_D3 4 klkkptderlfaiaealrrgvsveeiheltkidpwFleklkeiveleeelkk 55 ++k+ + r+ +++ + rg++ e+ ++ ++F + lk+ ve +l k gi|332661487|gb|AEE86887.1| 255 SVKNSLQPRIRFLVQVMGRGMD-----EVASYPEFFHHGLKKKVESRFKLVK 301 5666677777778888877775.....5666778888888887777766665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (363 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 390 (0.0262963); expected 296.6 (0.02) Passed bias filter: 328 (0.0221158); expected 296.6 (0.02) Passed Vit filter: 30 (0.00202279); expected 14.8 (0.001) Passed Fwd filter: 4 (0.000269705); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.24 # Mc/sec: 3948.13 // Query: gi|332661486|gb|AEE86886.1| [L=333] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-45 153.8 0.9 5.1e-37 127.2 0.3 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.066 12.9 0.0 12 5.6 0.0 3.5 3 Fe_dep_repr_C Iron dependent repressor, metal binding and di 0.077 12.3 0.0 0.12 11.7 0.0 1.3 1 dTMP_synthase Thymidylate synthase 0.12 12.1 0.0 1.4 8.6 0.0 2.6 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, ol Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 27.3 0.0 3.4e-10 1.2e-06 181 285 .. 12 121 .. 8 123 .. 0.73 2 ! 127.2 0.3 1.4e-40 5.1e-37 140 344 .. 115 321 .. 112 322 .. 0.93 Alignments for each domain: == domain 1 score: 27.3 bits; conditional E-value: 3.4e-10 HHHHHTT--HHHHHHHHHTTTGGGGGS-T..............................THH.HHHHHHHHHHHHTTT--HH CS mTERF 181 vlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede...svikkapqivsls.eekilnkiefllglGfsre 258 ++++ Gf+ + +++l kc +l++ + + + +l v+ ++ ++ + p+i+ l+ e +++ +e l +lG + gi|332661486|gb|AEE86886.1| 12 FFRDKGFDDPSIDKMLRKCKQLEKAQSDVASENWDYLSNIVGIQERklpYIVSRCPKILTLRlDERLIPMVECLSSLGRNPR 93 6677788888888888888888887777777777777777666665677888888888887734567888888888888888 PP HHHHHHHTSGGGGGS-HHH..HHHHHHH CS mTERF 259 eiakmvkrfPqllglsvek.vkkkteFl 285 e+a + +fP++l+ sve + + + F+ gi|332661486|gb|AEE86886.1| 94 EVASAITKFPPILSHSVEEkLCPLLAFF 121 8888888888888888887676666666 PP == domain 2 score: 127.2 bits; conditional E-value: 1.4e-40 HHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HH.HHHHHHHTTTGGGGGS-T........... CS mTERF 140 eesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfsked.vwailkkcPellglsekkklq.tkeillt 219 ++++ ++ lgv++++l+++i ++prl+ +s d ++ v +l slG++++ ++l k+P l+g+s+ k l t e l++ gi|332661486|gb|AEE86886.1| 115 CPLLAFFQALGVPETQLGKMILFNPRLISYSIDTKLTVIVSFLASLGLDQDGmIGKVLVKNPFLMGYSVDKRLRpTTEFLKS 196 56788899****************************************9986268**************9998747777888 PP ....................THHHHHHHH.HHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHH CS mTERF 220 rvlvede...svikkapqivslseekiln.kiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkel 296 +v+++++ sv+ +pq+++ + +kil+ ++l ++Gf +ia+mv +Pq+l+ sv++ +++ + Flv+ m + + e+ gi|332661486|gb|AEE86886.1| 197 SVGLSEDgikSVVMNFPQLLCRDVNKILKpNYDYLKECGFGDSQIATMVTGYPQILIKSVKNsLQPRIRFLVQVMGRGMDEV 278 88888889******************9862689************************************************* PP HCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 297 vefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 ++P+++ +L k++ R +k +++ + i +sl e+l c+ ++f gi|332661486|gb|AEE86886.1| 279 ASYPEFFHHGLKKKVESR---FKLVKKNN--IDCSLREMLDCNTKKFH 321 ******************...*9999999..***************96 PP >> Fe_dep_repr_C Iron dependent repressor, metal binding and dimerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.8 0.0 0.052 1.9e+02 30 60 .. 92 122 .. 83 124 .. 0.76 2 ? 0.1 0.0 0.17 6.3e+02 16 53 .. 188 225 .. 180 241 .. 0.70 3 ? 5.6 0.0 0.0032 12 20 52 .. 265 297 .. 263 308 .. 0.92 Alignments for each domain: == domain 1 score: 1.8 bits; conditional E-value: 0.052 Fe_dep_repr_C 30 weevheeAerlEHvlsdelidrldellgfpe 60 ev ++ +ls++++++l+ ll f++ gi|332661486|gb|AEE86886.1| 92 PREVASAITKFPPILSHSVEEKLCPLLAFFQ 122 555555556666799***********99875 PP == domain 2 score: 0.1 bits; conditional E-value: 0.17 Fe_dep_repr_C 16 rllerFLvevlgvdweevheeAerlEHvlsdelidrld 53 r +FL + +g++++ ++ + ++ +l ++ + l+ gi|332661486|gb|AEE86886.1| 188 RPTTEFLKSSVGLSEDGIKSVVMNFPQLLCRDVNKILK 225 56789********9999887777666665555555555 PP == domain 3 score: 5.6 bits; conditional E-value: 0.0032 Fe_dep_repr_C 20 rFLvevlgvdweevheeAerlEHvlsdelidrl 52 rFLv+v+g +ev e + H l+++++ r gi|332661486|gb|AEE86886.1| 265 RFLVQVMGRGMDEVASYPEFFHHGLKKKVESRF 297 7**************************999886 PP >> dTMP_synthase Thymidylate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 3.1e-05 0.12 34 135 .. 219 329 .. 180 332 .. 0.78 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 3.1e-05 dTMP_synthase 34 eldefieepeelLpe..lpeaDlviaytlhpDlllelaekakekkvkalivpaekpk.......aglrkelkekleelgvev 106 ++++ ++L+e ++ ++ ++t p +l++ ++ + +++l+ ++ ++lk+k+e+ v gi|332661486|gb|AEE86886.1| 219 DVNKILKPNYDYLKEcgFGDSQIATMVTGYPQILIKSVKNSLQPRIRFLVQVMGRGMdevasypEFFHHGLKKKVESRFKLV 300 5666566667888887777888888888888888888888777888887766666656677776678899******988788 PP dTMP_synthase 107 avpkpfCsleeegkpkideFleefGkPel 135 +++ Csl+e ++++++F e+fG e+ gi|332661486|gb|AEE86886.1| 301 KKNNIDCSLREMLDCNTKKFHEKFGFSEV 329 8899*********************8665 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.2 0.0 0.42 1.6e+03 67 84 .. 12 29 .. 3 46 .. 0.68 2 ? 8.6 0.0 0.00038 1.4 55 91 .. 218 255 .. 205 269 .. 0.71 3 ? -0.0 0.0 0.19 6.9e+02 4 55 .. 255 301 .. 252 328 .. 0.67 Alignments for each domain: == domain 1 score: -1.2 bits; conditional E-value: 0.42 CPSase_L_D3 67 eaKklGfsDaqiakllgv 84 ++ +Gf D i k+l++ gi|332661486|gb|AEE86886.1| 12 FFRDKGFDDPSIDKMLRK 29 567788888888888643 PP == domain 2 score: 8.6 bits; conditional E-value: 0.00038 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakll.gvteeevrk 91 + ++ l+ + ++K+ Gf D+qia ++ g + +++ gi|332661486|gb|AEE86886.1| 218 RDVNKILKPNYDYLKECGFGDSQIATMVtGYPQILIKS 255 4456677778899************8863555554544 PP == domain 3 score: -0.0 bits; conditional E-value: 0.19 CPSase_L_D3 4 klkkptderlfaiaealrrgvsveeiheltkidpwFleklkeiveleeelkk 55 ++k+ + r+ +++ + rg++ e+ ++ ++F + lk+ ve +l k gi|332661486|gb|AEE86886.1| 255 SVKNSLQPRIRFLVQVMGRGMD-----EVASYPEFFHHGLKKKVESRFKLVK 301 5666677777788888877775.....5666778888888887777766665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (333 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 463 (0.0312184); expected 296.6 (0.02) Passed bias filter: 443 (0.0298699); expected 296.6 (0.02) Passed Vit filter: 37 (0.00249477); expected 14.8 (0.001) Passed Fwd filter: 4 (0.000269705); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.24 # Mc/sec: 3621.84 // Query: gi|332010591|gb|AED97974.1| [L=391] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-41 139.4 4.0 1.6e-28 99.3 0.5 2.9 3 mTERF mTERF ------ inclusion threshold ------ 0.035 13.8 0.0 8.6 6.1 0.0 3.2 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, olig Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1.7 0.0 0.0097 72 179 203 .. 42 66 .. 39 73 .. 0.88 2 ! 38.5 0.0 6.7e-14 5e-10 2 98 .. 76 173 .. 75 180 .. 0.88 3 ! 99.3 0.5 2.1e-32 1.6e-28 175 344 .. 181 356 .. 166 357 .. 0.89 Alignments for each domain: == domain 1 score: 1.7 bits; conditional E-value: 0.0097 HHHHHHHTT--HHHHHHHHHTTTGG CS mTERF 179 vevlkslGfskedvwailkkcPell 203 ve+l++ Gf+k ai +++P+l gi|332010591|gb|AED97974.1| 42 VEFLRDNGFQKPLAIAIAMRYPNLK 66 89********************975 PP == domain 2 score: 38.5 bits; conditional E-value: 6.7e-14 HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-H CS mTERF 2 sllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiivad 83 ++l+s+ f+d++i++ ir +p++++ ++ek l pkl f + +g s l+k++s + +++g + vk++ + +++lk+i+ + gi|332010591|gb|AED97974.1| 76 QMLKSYSFSDTQIQKSIRVHPRMMFYNVEKILEPKLRFFKDIGFTGSGLGKFVSQNSSVVGVSLVKKLIPTVEILKSIVAPK 157 599***************************************************************************9865 PP .HHHHHHHHH-SHHHH CS mTERF 84 .kDksskleklpeslp 98 +D + +l + ++l+ gi|332010591|gb|AED97974.1| 158 hEDLPVILSRCGWLLL 173 1466666666666665 PP == domain 3 score: 99.3 bits; conditional E-value: 2.1e-32 HHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T............................THHHHHHHHHHHHHHTTT- CS mTERF 175 ikpnvevlkslGfskedvwailkkcPellglsekkklqt.keilltrvlvedesvikkapqivslseekilnkiefllglGf 255 + pn+ +l++ G+ +++ ++l ++P++++lse+k ++l ++++++ +++ + + slse++ k+ + Gf gi|332010591|gb|AED97974.1| 181 LLPNISYLETCGIVGSQLASLLRRQPRIFNLSEEKLRGYvSRALDLGFTLNSRMLVHAVISLSSLSEKTFDRKVKLFMANGF 262 689*******************************965541555666666666699999999999****************** PP -HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TT...T..GGGGGS CS mTERF 256 sreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskg...k..sillsl 332 s++ei +++r+P l+ s++k+ +eF++k m ++l + P+vl+y+LEkr++PR v++ l +kg k ++ + gi|332010591|gb|AED97974.1| 263 SEDEITDIIRRSPGLIRCSEDKLTLGFEFYLKRMGLEREALAKRPCVLSYNLEKRVIPRLKVLQILREKGlllKeeKKKKNM 344 **********************************************************************865367888999 PP -HHHHHHHHHHT CS mTERF 333 sevlkcsdeefl 344 ++++++e fl gi|332010591|gb|AED97974.1| 345 VGIVEMTEEAFL 356 999999999998 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 6.1 0.0 0.0012 8.6 55 84 .. 67 94 .. 55 105 .. 0.81 2 ? 0.5 0.0 0.065 4.8e+02 59 89 .. 105 135 .. 97 153 .. 0.74 3 ? 2.8 0.0 0.012 90 46 91 .. 235 280 .. 221 303 .. 0.80 Alignments for each domain: == domain 1 score: 6.1 bits; conditional E-value: 0.0012 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakllgv 84 + e+ +++++ +K++ fsD+qi k ++v gi|332010591|gb|AED97974.1| 67 S--LEQPRSVIQMLKSYSFSDTQIQKSIRV 94 3..56777799*************998765 PP == domain 2 score: 0.5 bits; conditional E-value: 0.065 CPSase_L_D3 59 elleellreaKklGfsDaqiakllgvteeev 89 + le lr +K Gf+ + + k+++++++ v gi|332010591|gb|AED97974.1| 105 KILEPKLRFFKDIGFTGSGLGKFVSQNSSVV 135 556668999************9987755444 PP == domain 3 score: 2.8 bits; conditional E-value: 0.012 CPSase_L_D3 46 iveleeelkkkaeelleellreaKklGfsDaqiakllgvteeevrk 91 +v++ +l++ +e++ ++ ++ + +Gfs+ +i ++++++ +r gi|332010591|gb|AED97974.1| 235 LVHAVISLSSLSEKTFDRKVKLFMANGFSEDEITDIIRRSPGLIRC 280 5555666777677777888999999*********999887776665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (391 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 396 (0.0267008); expected 296.6 (0.02) Passed bias filter: 343 (0.0231272); expected 296.6 (0.02) Passed Vit filter: 25 (0.00168566); expected 14.8 (0.001) Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.24 # Mc/sec: 4252.67 // Query: gi|332658065|gb|AEE83465.1| [L=493] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-48 164.3 1.0 5.8e-30 104.0 0.0 2.3 2 mTERF mTERF ------ inclusion threshold ------ 0.05 13.3 0.0 45 3.8 0.0 4.2 5 HHH_4 Helix-hairpin-helix containing domain Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 104.0 0.0 7.8e-34 5.8e-30 145 314 .. 202 375 .. 192 377 .. 0.89 2 ! 59.2 0.1 3.4e-20 2.5e-16 248 344 .. 377 468 .. 375 469 .. 0.89 Alignments for each domain: == domain 1 score: 104.0 bits; conditional E-value: 7.8e-34 HHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T................. CS mTERF 145 klvelgvdpktlkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede 226 +l +lg+ +++k + k + ++s+d +ikp+ve+l +lG+ k+d ++il+k+P++ g+s+ +l+ ++l + ++ gi|332658065|gb|AEE83465.1| 202 YLLDLGLNLEQIKTITRKFAAFPYYSLDGKIKPVVEFLLDLGIPKSDIPTILCKRPQICGISLTDNLKPTMAFLETLGIDKN 283 56667777777777777777788********************************************988877765555544 PP .............THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHH.CSGGGG CS mTERF 227 ...svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelv.efPqvl 303 ++i ++p i+ +s++k+ ++efl + G ++e+i + r+P+++++sve +++ +e++ + + ++ l + Pq + gi|332658065|gb|AEE83465.1| 284 qwaKIISRFPAILTYSRQKLTSTVEFLSQTGLTEEQIGRILTRCPNIMSYSVEDkLRPTMEYF-RSLNVDVAVLLhRCPQTF 364 5****************************************************99*******9.68999999865279**** PP GS-HHHHHHHH CS mTERF 304 gySLEkrikPR 314 g+S+E+ +kP gi|332658065|gb|AEE83465.1| 365 GLSIESNLKPV 375 **********6 PP == domain 2 score: 59.2 bits; conditional E-value: 3.4e-20 HHHHTTT--HHHHHHHHHTSGGGGGS-HHH..HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTTGG CS mTERF 248 efllglGfsreeiakmvkrfPqllglsvek.vkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgksi 328 ef+l+ Gf +ei m+ r+ +l ++s++ v +k ++++ m p +elv+fPq++gySL rikPR ++ ++ g gi|332658065|gb|AEE83465.1| 377 EFFLEKGFGLDEIGIMISRYGALYTFSLKEnVMPKWDYFQ-TMDYPKSELVKFPQFFGYSLQERIKPR---YELVQRSG--V 452 9***************************999******997.5**************************...77777777..7 PP GGGS-HHHHHHHHHHT CS mTERF 329 llslsevlkcsdeefl 344 +l l++vl+ s ef+ gi|332658065|gb|AEE83465.1| 453 RLLLNQVLSLSGIEFE 468 7777877777777776 PP >> HHH_4 Helix-hairpin-helix containing domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.2 0.0 0.11 8.2e+02 4 31 .. 64 91 .. 61 99 .. 0.83 2 ? -1.4 0.0 0.26 1.9e+03 12 33 .. 200 221 .. 191 225 .. 0.84 3 ? 3.8 0.0 0.0061 45 7 32 .. 267 292 .. 262 296 .. 0.89 4 ? 2.7 0.0 0.014 1e+02 6 30 .. 301 325 .. 297 328 .. 0.87 5 ? -3.7 0.0 1.4 1e+04 8 41 .. 372 405 .. 369 407 .. 0.70 Alignments for each domain: == domain 1 score: -0.2 bits; conditional E-value: 0.11 HHH_4 4 eqrelrelleflqeygisaklaekiykk 31 ++++ + l f+++ g+s++l +++++k gi|332658065|gb|AEE83465.1| 64 KEEAKAVLTLFFKKQGLSNSLSSRLINK 91 55666778899***********999875 PP == domain 2 score: -1.4 bits; conditional E-value: 0.26 HHH_4 12 leflqeygisaklaekiykkYg 33 +l ++g++ +++++i +k+ gi|332658065|gb|AEE83465.1| 200 TLYLLDLGLNLEQIKTITRKFA 221 5689999**********99985 PP == domain 3 score: 3.8 bits; conditional E-value: 0.0061 HHH_4 7 elrelleflqeygisaklaekiykkY 32 +l+ +++fl+ +gi +++ ki+ ++ gi|332658065|gb|AEE83465.1| 267 NLKPTMAFLETLGIDKNQWAKIISRF 292 67889*****************9987 PP == domain 4 score: 2.7 bits; conditional E-value: 0.014 HHH_4 6 relrelleflqeygisaklaekiyk 30 ++l ++efl++ g++++++ +i++ gi|332658065|gb|AEE83465.1| 301 QKLTSTVEFLSQTGLTEEQIGRILT 325 667889****************986 PP == domain 5 score: -3.7 bits; conditional E-value: 1.4 HHH_4 8 lrelleflqeygisaklaekiykkYgeeaievik 41 l+ + ef+ e g++ + ++ +Yg+ +k gi|332658065|gb|AEE83465.1| 372 LKPVTEFFLEKGFGLDEIGIMISRYGALYTFSLK 405 5667788888888888888888888876555555 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (493 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 320 (0.0215764); expected 296.6 (0.02) Passed bias filter: 300 (0.0202279); expected 296.6 (0.02) Passed Vit filter: 25 (0.00168566); expected 14.8 (0.001) Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.25 # Mc/sec: 5147.57 // Query: gi|332005852|gb|AED93235.1| [L=457] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-112 373.5 10.0 9.2e-112 373.0 6.9 1.2 1 mTERF mTERF 0.0066 16.4 1.3 28 4.7 0.1 3.9 3 RNA_pol_Rpb4 RNA polymerase Rpb4 ------ inclusion threshold ------ 0.014 15.1 0.2 1.1 9.0 0.0 2.9 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oli 0.034 13.9 0.0 0.55 10.1 0.0 2.7 3 UBA UBA/TS-N domain 0.055 13.0 2.9 7.4 6.2 0.0 4.1 5 UBA_3 Fungal ubiquitin-associated domain Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.0 6.9 3.1e-115 9.2e-112 1 345 [] 91 428 .. 91 428 .. 0.98 Alignments for each domain: == domain 1 score: 373.0 bits; conditional E-value: 3.1e-115 -HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS- CS mTERF 1 esllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiiva 82 ++llrs+gf+ds+is+ii+ yp++l+++ ek+l kl fL++ gas+selt+i+s+vPkilgk++ k is +yd++k+i gi|332005852|gb|AED93235.1| 91 LKLLRSYGFKDSQISSIISTYPRFLIENPEKTLRAKLHFLKLNGASSSELTEIVSKVPKILGKRGGKWISHYYDYVKEILQ- 171 589****************************************************************************99. PP HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHHHHHHHCTT-SSHHHHHHHHHHH- CS mTERF 83 dkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgkevfeesvkklvelgvdpktlkrviakrp 164 d+D+ss+ k+ + n rnvsvlr+lgv+++ll++llis+ +pv+gke feesvkk+ve+g+dpk k+v a+ gi|332005852|gb|AED93235.1| 172 DQDSSSSSSKRKQT-------NRNRNVSVLRKLGVPQRLLLNLLISRAKPVCGKERFEESVKKIVEMGFDPKSPKFVNALY- 245 8*****99877666.......5568********************************************************. PP GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T.............................THHHHHHH CS mTERF 165 rllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede..svikkapqivslseekil 244 + + sdkti+++v+ + +lG+s+++vwa++kk+P l++sek+++q++e+l++ +l ++e v+kk+p++v +seeki+ gi|332005852|gb|AED93235.1| 246 -VFYELSDKTIEEKVNAYIRLGLSVNEVWAVFKKWPFSLKYSEKNIIQKFETLKRVGLTKEEvcLVVKKYPECVGTSEEKIV 326 .********************************************************************************* PP HHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT CS mTERF 245 nkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk 326 +++ ++l+lGf+++e+ +++kr Pq++gl+++ vkkkteFlvk m wplk + + P vlg+SLEk + PRcnv+kal+s g gi|332005852|gb|AED93235.1| 327 KSVKTFLELGFTKDEVLMIIKRHPQCIGLAADSVKKKTEFLVKTMGWPLKVVASTPIVLGFSLEKFVLPRCNVIKALMSNGL 408 *********************************************************************************8 PP .GGGGGS-HHHHHHHHHHTC CS mTERF 327 .sillslsevlkcsdeeflk 345 + +++s+vl++ + +flk gi|332005852|gb|AED93235.1| 409 iGEMPAISSVLTSPKLKFLK 428 789999************86 PP >> RNA_pol_Rpb4 RNA polymerase Rpb4 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 4.1 0.0 0.014 42 40 85 .. 68 113 .. 16 118 .. 0.82 2 ! 4.7 0.1 0.0095 28 37 82 .. 253 313 .. 165 319 .. 0.75 3 ? 4.0 0.0 0.015 45 55 85 .. 321 351 .. 313 356 .. 0.89 Alignments for each domain: == domain 1 score: 4.1 bits; conditional E-value: 0.014 HHHHHHHHHTS-TTSSHHHHHHHHHHHTTSTS-HHHHHHHHHH--S CS RNA_pol_Rpb4 40 lkktleYltkfsrlknqekvrelveelksfeltkaeklqivnllPe 85 + k e ++ +++++++ + +++++l+s++++ ++ +i++ P+ gi|332005852|gb|AED93235.1| 68 TTKLAESISMKANFDEKGNPDSVLKLLRSYGFKDSQISSIISTYPR 113 4444555556999999999*********************999886 PP == domain 2 score: 4.7 bits; conditional E-value: 0.0095 CHHHHHHHHHHHT...............S-TTSSHHHHHHHHHHHTTSTS-HHHHHHHHHH CS RNA_pol_Rpb4 37 nkilkktleYltk...............fsrlknqekvrelveelksfeltkaeklqivnl 82 ++i +k+ Y++ fs ++++++ + +e+lk+ +ltk+e++ +v gi|332005852|gb|AED93235.1| 253 KTIEEKVNAYIRLglsvnevwavfkkwpFSLKYSEKNIIQKFETLKRVGLTKEEVCLVVKK 313 555555555666555566666666668888888888899999*************988765 PP == domain 3 score: 4.0 bits; conditional E-value: 0.015 SHHHHHHHHHHHTTSTS-HHHHHHHHHH--S CS RNA_pol_Rpb4 55 nqekvrelveelksfeltkaeklqivnllPe 85 ++ek+ + v+++ + ++tk e+l+i+ +P+ gi|332005852|gb|AED93235.1| 321 SEEKIVKSVKTFLELGFTKDEVLMIIKRHPQ 351 5788999999999*************88886 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.0 0.0 0.00038 1.1 43 84 .. 71 110 .. 55 131 .. 0.76 2 ? -0.9 0.0 0.41 1.2e+03 56 84 .. 118 146 .. 107 168 .. 0.77 3 ? 2.5 0.0 0.038 1.1e+02 18 83 .. 261 330 .. 251 351 .. 0.62 Alignments for each domain: == domain 1 score: 9.0 bits; conditional E-value: 0.00038 CPSase_L_D3 43 lkeiveleeelkkkaeelleellreaKklGfsDaqiakllgv 84 l e + ++++ ++ + + +++l+ ++++Gf D+qi+ ++++ gi|332005852|gb|AED93235.1| 71 LAESISMKANFDE--KGNPDSVLKLLRSYGFKDSQISSIIST 110 4455555666655..566777****************99765 PP == domain 2 score: -0.9 bits; conditional E-value: 0.41 CPSase_L_D3 56 kaeelleellreaKklGfsDaqiakllgv 84 + e++l++ l+ +K +G s +++ +++++ gi|332005852|gb|AED93235.1| 118 NPEKTLRAKLHFLKLNGASSSELTEIVSK 146 467788889999********999999754 PP == domain 3 score: 2.5 bits; conditional E-value: 0.038 CPSase_L_D3 18 ealrrgvsveeiheltkidpwFle.klkeiveleeelkkkaeelleellreaKkl....GfsDaqiakllg 83 + +r g+sv+e+ + k p+ l+ k+i++ e+lk+ ++ee+ + +Kk+ G s+++i k ++ gi|332005852|gb|AED93235.1| 261 AYIRLGLSVNEVWAVFKKWPFSLKySEKNIIQKFETLKRVG-LTKEEVCLVVKKYpecvGTSEEKIVKSVK 330 56778888888888888888887623467888888888743.33333444444432333777777776644 PP >> UBA UBA/TS-N domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.1 0.0 0.00018 0.55 3 16 .. 222 235 .. 220 236 .. 0.90 2 ? -0.0 0.0 0.28 8.3e+02 7 20 .. 330 343 .. 327 348 .. 0.80 3 ? -2.9 0.0 2.3 6.8e+03 19 26 .. 399 406 .. 398 407 .. 0.73 Alignments for each domain: == domain 1 score: 10.1 bits; conditional E-value: 0.00018 HHHHHHHHHTTS-H CS UBA 3 eeaiqqLreMGfsr 16 ee++++++eMGf+ gi|332005852|gb|AED93235.1| 222 EESVKKIVEMGFDP 235 89**********95 PP == domain 2 score: -0.0 bits; conditional E-value: 0.28 HHHHHTTS-HHHHH CS UBA 7 qqLreMGfsreeak 20 ++ +e+Gf+++e++ gi|332005852|gb|AED93235.1| 330 KTFLELGFTKDEVL 343 555799*****997 PP == domain 3 score: -2.9 bits; conditional E-value: 2.3 HHHHHHHT CS UBA 19 akkALrat 26 ++kAL ++ gi|332005852|gb|AED93235.1| 399 VIKALMSN 406 78999876 PP >> UBA_3 Fungal ubiquitin-associated domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.7 0.0 0.065 1.9e+02 23 35 .. 187 199 .. 185 202 .. 0.87 2 ? 1.8 0.0 0.059 1.8e+02 11 23 .. 223 235 .. 222 245 .. 0.78 3 ? -2.4 0.0 1.2 3.5e+03 11 32 .. 257 278 .. 254 280 .. 0.84 4 ? -3.0 0.1 1.9 5.5e+03 17 26 .. 298 307 .. 287 313 .. 0.49 5 ? 6.2 0.0 0.0025 7.4 12 32 .. 328 348 .. 326 350 .. 0.93 Alignments for each domain: == domain 1 score: 1.7 bits; conditional E-value: 0.065 HHHHHHHHHHS-- CS UBA_3 23 kdkvievLkrLgi 35 +++ + vL++Lg+ gi|332005852|gb|AED93235.1| 187 RNRNVSVLRKLGV 199 78889******98 PP == domain 2 score: 1.8 bits; conditional E-value: 0.059 HHHHHHHHHT--H CS UBA_3 11 dlVdefvsqGFek 23 + V++ v +GF+ gi|332005852|gb|AED93235.1| 223 ESVKKIVEMGFDP 235 789********84 PP == domain 3 score: -2.4 bits; conditional E-value: 1.2 HHHHHHHHHT--HHHHHHHHHH CS UBA_3 11 dlVdefvsqGFekdkvievLkr 32 + V+ + G + v +v+k+ gi|332005852|gb|AED93235.1| 257 EKVNAYIRLGLSVNEVWAVFKK 278 6688888889999999999998 PP == domain 4 score: -3.0 bits; conditional E-value: 1.9 HHHT--HHHH CS UBA_3 17 vsqGFekdkv 26 G k+ v gi|332005852|gb|AED93235.1| 298 KRVGLTKEEV 307 2334444444 PP == domain 5 score: 6.2 bits; conditional E-value: 0.0025 HHHHHHHHT--HHHHHHHHHH CS UBA_3 12 lVdefvsqGFekdkvievLkr 32 V++f GF kd v ++kr gi|332005852|gb|AED93235.1| 328 SVKTFLELGFTKDEVLMIIKR 348 599*************99998 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (457 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 572 (0.0385679); expected 296.6 (0.02) Passed bias filter: 396 (0.0267008); expected 296.6 (0.02) Passed Vit filter: 27 (0.00182051); expected 14.8 (0.001) Passed Fwd filter: 5 (0.000337132); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.24 # Mc/sec: 4970.51 // Query: gi|332003836|gb|AED91219.1| [L=405] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-44 152.1 3.8 4e-25 88.1 0.0 2.1 2 mTERF mTERF ------ inclusion threshold ------ 0.11 11.1 0.0 0.27 9.8 0.0 1.6 1 tRNA-synt_1c tRNA synthetases class I (E and Q), catalytic d Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 88.1 0.0 5.4e-29 4e-25 1 190 [. 105 294 .. 105 295 .. 0.92 2 ! 67.8 0.6 8.1e-23 6e-19 251 344 .. 287 381 .. 277 382 .. 0.93 Alignments for each domain: == domain 1 score: 88.1 bits; conditional E-value: 5.4e-29 -HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS- CS mTERF 1 esllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiiva 82 ++llr +gf+ +is+ ++++p ll+a+ae+ l pkl+f s+g+sks l+ l P il+++ v+++ ++y+flk++ + gi|332003836|gb|AED91219.1| 105 LNLLRDHGFTTAQISSLVKKRPVLLLANAESVLLPKLSFFLSIGVSKSLLARTLASDPTILTRSLVNQLIPSYNFLKSVLDS 186 589******************************************************************************* PP HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHHHHHHHHHH CS mTERF 83 dkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpktlkrviakr 163 d+ ++ l + ++++++ +n+ n+ + e gv++k+ ll+ + v++k f++ +k+ +e+g+ p+++++v+a + gi|332003836|gb|AED91219.1| 187 DEKIVAALRRTTWVFLEDHTKNLVPNINYMAETGVPEKCIKLLLTHFPEAVMQKnHEFQAIAKQAQEMGFNPQKSTFVLAIH 268 **************************************766666666667777777889999******************99 PP -GGGGGS-HHHHHHH.HHHHHHHTT--H CS mTERF 164 prllllssdktikpn.vevlkslGfske 190 l + k i ++ +ev+++ G s++ gi|332003836|gb|AED91219.1| 269 --ALSGKGNKSIWDKcFEVYQRWGWSED 294 ..88888888886653688888887765 PP == domain 2 score: 67.8 bits; conditional E-value: 8.1e-23 HTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGG CS mTERF 251 lglGfsreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sills 331 G s+++i+ +k+ P ++ ls+ k+ + +e++v+em+ +++ + P vl +SLEkri+PRc v k+l+s g + s gi|332003836|gb|AED91219.1| 287 QRWGWSEDDIMCAFKKHPHCMMLSERKINRTMEYFVNEMNMAPRSIAQCPVVLFFSLEKRIIPRCSVTKVLVSNGLvKEDWS 368 5579***********************************************************************7799999 PP S-HHHHHHHHHHT CS mTERF 332 lsevlkcsdeefl 344 l + l ++ fl gi|332003836|gb|AED91219.1| 369 LTSLLVPVEKVFL 381 9999988888886 PP >> tRNA-synt_1c tRNA synthetases class I (E and Q), catalytic domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 9.8 0.0 3.6e-05 0.27 182 266 .. 172 259 .. 157 281 .. 0.71 Alignments for each domain: == domain 1 score: 9.8 bits; conditional E-value: 3.6e-05 TCEE-HHHHHHHHHHHCT-SEEEEEGGGCCCHHHHHHHHHCCT-S-....-EEEEEE--B-CTTSB-SCCCCHHCHHCCCCC CS tRNA-synt_1c 182 dgyPtYdfavvidDalmeiThvlrgeeflantpkyiwllealglev....ppfahlslllnlegkklSKRklsllvdislvk 259 + +P Y+f + D++++i +lr + + +++ +l+ +++ + p+ ll+ + + ++ K ++ + +++ + gi|332003836|gb|AED91219.1| 172 QLIPSYNFLKSVLDSDEKIVAALRRTTWVFLEDHTKNLVPNINYMAetgvPEKCIKLLLTHFPEAVMQKNHEFQA-IAKQAQ 252 568*********************999987777777777766654311225555566666777777777666665.566666 PP CTT-TCC CS tRNA-synt_1c 260 eegdlre 266 e g++++ gi|332003836|gb|AED91219.1| 253 EMGFNPQ 259 6666665 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (405 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 477 (0.0321624); expected 296.6 (0.02) Passed bias filter: 378 (0.0254872); expected 296.6 (0.02) Passed Vit filter: 20 (0.00134853); expected 14.8 (0.001) Passed Fwd filter: 2 (0.000134853); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.25 # Mc/sec: 4228.74 // Query: gi|332646534|gb|AEE80055.1| [L=558] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-23 80.9 0.7 2.9e-12 45.8 0.0 3.9 3 mTERF mTERF Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 11.3 0.1 6e-06 0.089 147 285 .. 136 274 .. 98 276 .. 0.67 2 ! 21.0 0.0 6.9e-09 0.0001 145 210 .. 273 338 .. 270 358 .. 0.90 3 ! 45.8 0.0 2e-16 2.9e-12 227 343 .. 412 529 .. 385 531 .. 0.86 Alignments for each domain: == domain 1 score: 11.3 bits; conditional E-value: 6e-06 CTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T................... CS mTERF 147 velgvdpktlkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede.. 226 + g++ ++l+++ + rl+ + + +i+ ++ +k++Gfs v P+ l + + + +++ + de gi|332646534|gb|AEE80055.1| 136 SGFGFPWNKLGKLYKEE-RLVFVQRPGEIESRLLKFKDIGFSTVAVIGTCLAIPRTLCGGGELGSEIRCLFVKLKRLFDEfd 216 55666666666666666.6777777777777777777777777777777777777776666554444444444444444455 PP ............THHHHHHHHHHHHHHTTT--HHHHHHHH.HTSGGGGGS-HHH.HHHHHHH CS mTERF 227 ..svikkapqivslseekilnkiefllglGfsreeiakmv.krfPqllglsvekvkkkteFl 285 +++ ++ s + ki+++ +lG+ ee+++++ + + l +s+e + +k ++ gi|332646534|gb|AEE80055.1| 217 shHLFEENVD----SWLAVSRKIRIFYDLGCENEEMWELMcRNKSLFLEYSEEALMNKAGYF 274 5655553333....33457789***************96615568889******88777666 PP == domain 2 score: 21.0 bits; conditional E-value: 6.9e-09 HHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T. CS mTERF 145 klvelgvdpktlkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkk 210 ++ gv++++++ +i ++p ++ ++++k + + +lk +G+++++v+a+ k+P ++g++ k+ gi|332646534|gb|AEE80055.1| 273 YFCRFGVSKEDAALLILRNPAIMNFDLEKPVISVTGMLKHFGLRQDEVDAVAQKYPYVFGRNQLKN 338 77889*******************************************************998764 PP == domain 3 score: 45.8 bits; conditional E-value: 2e-16 ..........THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HH CS mTERF 227 svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLE 308 + k+ q v + ++ + ++ll+ G+ i +++++ P++l ++ k+ Fl em +l l fP++l + LE gi|332646534|gb|AEE80055.1| 412 GITMKVLQHVHGTAVELHDRFQILLNSGIIFSKICMLIRSAPKILNQKPHSIQDKLRFLCGEMGDSLDYLEVFPAYLCFDLE 493 5666677777778888888999999********************************************************* PP HHHHHHHHHHHTT--TT.TGGGGGS-HHHHHHHHHH CS mTERF 309 krikPRcnvvkallskg.ksillslsevlkcsdeef 343 ri+PR +k l++kg + + s+++++ s++ f gi|332646534|gb|AEE80055.1| 494 NRISPRFRFHKWLVEKGfSEKSYSIASIVATSEKAF 529 *****************669999**********999 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (558 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 346 (0.0233295); expected 296.6 (0.02) Passed bias filter: 303 (0.0204302); expected 296.6 (0.02) Passed Vit filter: 20 (0.00134853); expected 14.8 (0.001) Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.24 # Mc/sec: 6069.02 // Query: gi|332644702|gb|AEE78223.1| [L=450] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-126 421.3 10.6 2.4e-126 420.9 7.4 1.2 1 mTERF mTERF 0.00075 19.2 0.1 1.9 8.2 0.0 3.3 3 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, ------ inclusion threshold ------ 0.045 13.9 0.0 0.56 10.4 0.0 2.7 3 Acetyltransf_11 Udp N-acetylglucosamine O-acyltransferase; D 0.072 12.9 0.1 1.8 8.4 0.0 3.4 4 UBA UBA/TS-N domain 0.15 11.8 0.0 0.35 10.6 0.0 1.6 1 Bac_chlorC Bacteriochlorophyll C binding protein Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.9 7.4 8.1e-130 2.4e-126 1 345 [] 88 427 .. 88 427 .. 0.97 Alignments for each domain: == domain 1 score: 420.9 bits; conditional E-value: 8.1e-130 -HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS- CS mTERF 1 esllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiiva 82 ++llrs gf+ds+is iir yp+llv+daeksl pklqfL+srgas+se+ +i+s+vP il kk+++s+s +ydf+k+i+ gi|332644702|gb|AEE78223.1| 88 LNLLRSNGFKDSQISRIIRAYPRLLVTDAEKSLRPKLQFLKSRGASSSEVIEIVSNVPTILDKKGEESVSLYYDFVKDIMQD 169 589*****************************************************************************94 PP HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHHHHHHHCTT-SSHHHHHHHHHHH- CS mTERF 83 dkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgkevfeesvkklvelgvdpktlkrviakrp 164 s l + s p++ ++n +rn+svlrelgv++kll+sllis++qpv+gke+fees+kk+v++g+dp+++k+v+a++ gi|332644702|gb|AEE78223.1| 170 ---GKS-L---CISCPEGKKGNRIRNISVLRELGVPQKLLFSLLISRYQPVCGKEKFEESLKKVVDMGFDPAKSKFVEALH- 243 ...443.3...5566778999************************************************************. PP GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T.............................THHHHHHH CS mTERF 165 rllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede..svikkapqivslseekil 244 +++ +s+kti+++v+v+k+lGfs+ + wai+kk+P +l++sekk++ +e+l++++lve+e sv+k pq++++se+kil gi|332644702|gb|AEE78223.1| 244 -VVYEMSEKTIEEKVNVYKRLGFSEAEIWAIFKKWPYFLKFSEKKIILMFETLKKCGLVEEEiiSVLKSRPQCIRSSEQKIL 324 .********************************************************************************* PP HHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT CS mTERF 245 nkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk 326 ++ie++lglGfsr+++ +mvkr+P + ++s e+++kk+e lvk m+wpl+++v +P+vlgySLEkri+PR nv+kal+skg gi|332644702|gb|AEE78223.1| 325 DSIEMFLGLGFSRDDFKMMVKRYPCCTAYSGETLRKKFEVLVKMMNWPLEAVVMIPTVLGYSLEKRIVPRSNVIKALMSKGL 406 *********************************************************************************6 PP ..GGGGGS-HHHHHHHHHHTC CS mTERF 327 ..sillslsevlkcsdeeflk 345 s+ +++s+vl c+d+eflk gi|332644702|gb|AEE78223.1| 407 igSENPPISSVLVCTDQEFLK 427 68*****************96 PP >> CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 8.2 0.0 0.00064 1.9 53 84 .. 72 107 .. 57 128 .. 0.70 2 ! 6.4 0.0 0.0023 6.9 55 84 .. 247 276 .. 235 296 .. 0.71 3 ? 0.4 0.0 0.17 5.1e+02 64 94 .. 291 321 .. 280 328 .. 0.80 Alignments for each domain: == domain 1 score: 8.2 bits; conditional E-value: 0.00064 CPSase_L_D3 53 lkkk...aeellee.llreaKklGfsDaqiakllgv 84 ++kk +++++++ +l+ ++++Gf D+qi++++++ gi|332644702|gb|AEE78223.1| 72 ISKKvtfEDKVNPDsVLNLLRSNGFKDSQISRIIRA 107 3333333445555559***************99854 PP == domain 2 score: 6.4 bits; conditional E-value: 0.0023 CPSase_L_D3 55 kkaeelleellreaKklGfsDaqiakllgv 84 + +e++ ee ++ +K+lGfs+a+i +++++ gi|332644702|gb|AEE78223.1| 247 EMSEKTIEEKVNVYKRLGFSEAEIWAIFKK 276 34567788899*************988654 PP == domain 3 score: 0.4 bits; conditional E-value: 0.17 CPSase_L_D3 64 llreaKklGfsDaqiakllgvteeevrklrk 94 +++ +Kk G+ +++i +l+++ + +r+ + gi|332644702|gb|AEE78223.1| 291 MFETLKKCGLVEEEIISVLKSRPQCIRSSEQ 321 67889999*****999999998888887655 PP >> Acetyltransf_11 Udp N-acetylglucosamine O-acyltransferase; Domain 2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.4 0.0 0.00019 0.56 22 72 .. 90 142 .. 87 151 .. 0.83 2 ? -1.9 0.0 1.3 3.9e+03 37 72 .. 207 240 .. 187 255 .. 0.67 3 ? -1.1 0.0 0.72 2.1e+03 24 38 .. 261 275 .. 256 318 .. 0.78 Alignments for each domain: == domain 1 score: 10.4 bits; conditional E-value: 0.00019 Acetyltransf_11 22 glkRrgfskeeikalkkay.kllyrsg.ltleealeeleeelaespeveelld 72 l+ +gf++++i+++ +ay +ll + ++l+ l+ l+++ a+s ev e+++ gi|332644702|gb|AEE78223.1| 90 LLRSNGFKDSQISRIIRAYpRLLVTDAeKSLRPKLQFLKSRGASSSEVIEIVS 142 599****************4445554468999999999998888999999885 PP == domain 2 score: -1.9 bits; conditional E-value: 1.3 Acetyltransf_11 37 kkaykllyrsgltleealeeleeelaespeveelld 72 + y+ + + ++ee+l+++ + ++ +p+ +++++ gi|332644702|gb|AEE78223.1| 207 ISRYQPVC-GKEKFEESLKKVVD-MGFDPAKSKFVE 240 55566666.55688888888877.666666666665 PP == domain 3 score: -1.1 bits; conditional E-value: 0.72 Acetyltransf_11 24 kRrgfskeeikalkk 38 kR gfs++ei a+ k gi|332644702|gb|AEE78223.1| 261 KRLGFSEAEIWAIFK 275 899999999887755 PP >> UBA UBA/TS-N domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 8.4 0.0 0.00062 1.8 3 17 .. 220 234 .. 218 237 .. 0.88 2 ? -2.5 0.0 1.7 5.2e+03 11 18 .. 332 339 .. 325 339 .. 0.74 3 ? -2.4 0.0 1.5 4.5e+03 9 20 .. 365 377 .. 364 378 .. 0.80 4 ? -0.6 0.0 0.43 1.3e+03 15 24 .. 393 402 .. 392 405 .. 0.81 Alignments for each domain: == domain 1 score: 8.4 bits; conditional E-value: 0.00062 HHHHHHHHHTTS-HH CS UBA 3 eeaiqqLreMGfsre 17 ee+++++++MGf+ gi|332644702|gb|AEE78223.1| 220 EESLKKVVDMGFDPA 234 89**********975 PP == domain 2 score: -2.5 bits; conditional E-value: 1.7 HTTS-HHH CS UBA 11 eMGfsree 18 +Gfsr++ gi|332644702|gb|AEE78223.1| 332 GLGFSRDD 339 579***96 PP == domain 3 score: -2.4 bits; conditional E-value: 1.5 HHHT.TS-HHHHH CS UBA 9 LreM.Gfsreeak 20 L++M +++ e+++ gi|332644702|gb|AEE78223.1| 365 LVKMmNWPLEAVV 377 67777**999887 PP == domain 4 score: -0.6 bits; conditional E-value: 0.43 -HHHHHHHHH CS UBA 15 sreeakkALr 24 +r++++kAL gi|332644702|gb|AEE78223.1| 393 PRSNVIKALM 402 7899999996 PP >> Bac_chlorC Bacteriochlorophyll C binding protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.6 0.0 0.00012 0.35 39 70 .. 23 54 .. 16 61 .. 0.89 Alignments for each domain: == domain 1 score: 10.6 bits; conditional E-value: 0.00012 Bac_chlorC 39 tkrlganAYpklygggsssslrgssPevsGya 70 t + +nA+p +++ ss+ ++ ssP+ s + gi|332644702|gb|AEE78223.1| 23 TVSIVQNAFPFTTKSFSSTIAKDSSPKGSTFT 54 66799**********************99885 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (450 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 476 (0.0320949); expected 296.6 (0.02) Passed bias filter: 388 (0.0261614); expected 296.6 (0.02) Passed Vit filter: 42 (0.00283191); expected 14.8 (0.001) Passed Fwd filter: 5 (0.000337132); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 5 [number of targets reported over threshold] # CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.24 # Mc/sec: 4894.37 // Query: gi|332642641|gb|AEE76162.1| [L=274] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-39 135.0 0.1 3e-39 134.6 0.1 1.2 1 mTERF mTERF Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 134.6 0.1 2e-43 3e-39 106 344 .. 37 269 .. 24 270 .. 0.88 Alignments for each domain: == domain 1 score: 134.6 bits; conditional E-value: 2e-43 HHHHHHHHHTT-.-HHHHHHHHHH-CHHHHS-HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-H.HHHHHHHHHHH.H CS mTERF 106 ernvsvlrelgv.trkllislliselqpvlgkevfeesvkklvelgvdpktlkrviakrprllllssd.ktikpnvevlk.s 184 n+ l++lg+ ++ ++ ++l ++l++ v+ l++ g++++++ r+ ++p+l d ++ p++++l + gi|332642641|gb|AEE76162.1| 37 RENLRHLSSLGIvPQNPRLAPPANDLSVILSA------VNLLKSKGISDEDFPRLVFLCPQLFSPTFDiSKLDPVFDFLTgE 112 45777777777513444566666666666666......**********************77776666579********846 PP HTT--HHHHHHHHHTTTGGGGGS-T............................THHHHHHHHHHHHHHTTT--HHHHHHHHH CS mTERF 185 lGfskedvwailkkcPellglsekkklqtkeilltrvlvede.svikkapqivslseekilnkiefllglGfsreeiakmvk 265 lG s e+ ++ cP++l ++++ l + l+ +v + + k + ++++++ ek+ k++fl ++Gf ee a gi|332642641|gb|AEE76162.1| 113 LGASAEESRGLIVNCPNILFSDVEYCLRPTLVYLKELGVRNLnRASKTNAHVLNTRVEKLRAKMRFLKSIGFEHEEAARVCG 194 *************************998776666665555555*************************************** PP TSGGGGGS-HHH..HHHHHHHHHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHHHHHHHHT CS mTERF 266 rfPqllglsvek.vkkkteFlvkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgksillslsevlkcsdeefl 344 r P+++g+sve +++k+eFlv m++ l+el++fPq++++SL kri PR + l++k+ ++sls++l++ d++f gi|332642641|gb|AEE76162.1| 195 RIPAIFGYSVEDnLRPKFEFLVYDMERELEELKKFPQYFAFSLGKRIRPR---HWHLKKKN--VRVSLSRMLMWGDQKFY 269 ***********99*************************************...********..***************96 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (274 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 283 (0.0190817); expected 296.6 (0.02) Passed bias filter: 255 (0.0171937); expected 296.6 (0.02) Passed Vit filter: 22 (0.00148338); expected 14.8 (0.001) Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.30u 0.20s 00:00:00.50 Elapsed: 00:00:00.23 # Mc/sec: 3109.70 // Query: gi|79478031|ref|NP_193700.2| [L=575] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-17 63.7 3.0 2.5e-08 32.8 0.2 4.1 3 mTERF mTERF Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 22.7 0.0 2e-09 3e-05 75 271 .. 103 292 .. 99 302 .. 0.79 2 ! 5.9 0.4 0.00026 3.8 43 136 .. 310 400 .. 303 414 .. 0.76 3 ! 32.8 0.2 1.7e-12 2.5e-08 206 344 .. 415 553 .. 374 554 .. 0.72 Alignments for each domain: == domain 1 score: 22.7 bits; conditional E-value: 2e-09 HHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHH CS mTERF 75 flkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpk 154 +l+ki+ +kD+s+ l k ++ e++ + +lg+++ +++ + +++l+ +++e l + g+++ gi|79478031|ref|NP_193700.2| 103 LLSKIDDNQKDVSKGLTKFLRY----NPI-NEFE-PFFESLGLCPY-EFETFLPRKLMFLSDdGIMFENFHALCNYGIPRG 176 5666666666666665543333....332.1222.36679999999.9999999988888887899*************** PP HHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--HHHHHHHHHTTTGGGGGS-T.......................... CS mTERF 155 tlkrviakrprllllssdktikpnvevlkslGfskedvwailkkcPellglsekkklqtkeilltrvlvede..svikkap 233 +++r+ + r + + + +++ +++lG+sk v +++ +cP ll+ + ++ + ++ ++++++ + + gi|79478031|ref|NP_193700.2| 177 KIGRMYKEA-REIFRYESGMLAMKLRGYENLGLSKATVIKLVTSCPLLLVGGIDAEFSS--VVDKLKGLQVGcdWLGRYLS 254 *****9988.6788888899******************************999984444..44444444433545555555 PP ...THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGG CS mTERF 234 qivslseekilnkiefllglGfsreeiakmvkrfPqll 271 +s + il++iefl ++G+ +e + k +P+l gi|79478031|ref|NP_193700.2| 255 DRKTYSWRRILETIEFLDKVGCKEEKLSSLLKTYPALV 292 7789*******************************985 PP == domain 2 score: 5.9 bits; conditional E-value: 0.00026 TT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHH CS mTERF 43 rgaskseltkilstvPkilgkkkvksissvydflkkiivadkDksskleklpeslpqsleenkernvsvlrelgvtrklli 123 g++ e+ + +P+ l+ k vk+i++ +dfl i ++ + + ++l+ e+ + + + l +l v+++ l+ gi|79478031|ref|NP_193700.2| 310 AGLQVNEIYRLFIDNPEMLSDKCVKNIQKTLDFLIAIRMETQFITKILLSHMELIGSCSLP--APRTACL-SLNVKQDELC 387 5666667777788899999999999999999999999999888888888888776654443..4455556.7899999999 PP HHHHH-CHHHHS- CS mTERF 124 slliselqpvlgk 136 ++l e++ ++++ gi|79478031|ref|NP_193700.2| 388 KILKKEPLRLFCF 400 9998888877776 PP == domain 3 score: 32.8 bits; conditional E-value: 1.7e-12 GS-T............................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHH CS mTERF 206 sekkklqtkeilltrvlvede.svikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFl 285 + k l++ e ll+++ ve+ ++k a + + + +++ + + l + G + + +++++ P +l ls + + kk+ l gi|79478031|ref|NP_193700.2| 415 DSRKYLEKTEFLLRLGYVENSdEMVK-ALKQFRGRGDQLQERFDCLVKAGLNYNVVTEIIRHAPMILNLSKDVIEKKIHSL 494 22333444444444444444465555.455556778888899999999********************************* PP HHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 286 vkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 + p+++lv+fP++l y + +ri R ++ l ++ ls s +l+c d +f gi|79478031|ref|NP_193700.2| 495 TELLGYPIESLVRFPAYLCYDM-QRIHHRFSMYLWLRERDAaKPMLSPSTILTCGDARFV 553 **********************.5899998999999999955777788999999999996 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (575 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 310 (0.0209022); expected 296.6 (0.02) Passed Vit filter: 24 (0.00161823); expected 14.8 (0.001) Passed Fwd filter: 1 (6.74263e-05); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.25 # Mc/sec: 6003.76 // Query: gi|15240177|ref|NP_196299.1| [L=1141] Description: mitochondrial transcription termination factor family protein [Arabidopsis thaliana] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-51 174.1 17.3 1.2e-15 56.9 0.5 6.1 6 mTERF mTERF 0.0024 18.0 0.3 0.61 10.2 0.0 4.3 6 RuvA_C RuvA, C-terminal domain ------ inclusion threshold ------ 0.011 15.6 0.2 26 4.7 0.0 3.2 3 T6SS_Vgr Putative type VI secretion system Rhs element Vgr Domain annotation for each model (and alignments): >> mTERF mTERF # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 14.7 0.0 1.7e-06 0.0083 108 193 .. 173 259 .. 154 265 .. 0.88 2 ! 26.3 0.0 4.8e-10 2.4e-06 2 106 .. 277 380 .. 276 397 .. 0.81 3 ! 54.5 1.4 1.3e-18 6.5e-15 205 343 .. 422 560 .. 417 562 .. 0.90 4 ! 22.7 0.0 6.1e-09 3e-05 111 272 .. 695 855 .. 669 860 .. 0.92 5 ! 9.6 0.0 6.2e-05 0.3 18 93 .. 847 922 .. 844 942 .. 0.84 6 ! 56.9 0.5 2.5e-19 1.2e-15 207 344 .. 981 1118 .. 975 1119 .. 0.91 Alignments for each domain: == domain 1 score: 14.7 bits; conditional E-value: 1.7e-06 HHHHHHHTT--HHHHHHHHHH-CHHHHS-..HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHT CS mTERF 108 nvsvlrelgvtrkllislliselqpvlgk..evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslG 186 n vl +gv +k i+ + e + v++ v+ ++k ++lg+++ l ++i pr+l+ + ++ ++v+ l+slG gi|15240177|ref|NP_196299.1| 173 NHHVLCYSGVDPK-RIGKIFKEAREVFSYetGVLASKIKAYEDLGFSRLFLSKLIVCSPRVLMGHTNIELVQVVKTLQSLG 252 6678888999999.888899999999988677999********************************************** PP T--HHHH CS mTERF 187 fskedvw 193 f++e v gi|15240177|ref|NP_196299.1| 253 FEFEWVM 259 *998775 PP == domain 2 score: 26.3 bits; conditional E-value: 4.8e-10 HHHHHHHHHTS-HHHHHH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS-.HHHHHHHHHHHTTTSS- CS mTERF 2 sllrslgfldslistiirsyplllvadaekslqpklqfLesrgaskseltkilstvPkilgkkkvksissvydflkkiiva 82 sllr f + ir+ p+ll++++ k + + f + gas+sel + +++ P i +k v+++++ flk+i ++ gi|15240177|ref|NP_196299.1| 277 SLLREICFDEEKLYGLIRNCPSLLFENSGKWTGILVGFETKLGASRSELCSLFQKFPLIQVEKCVSNLRQCFLFLKEIEME 357 56777777777777779***************************************************************8 PP HHHHHHHHHH-SHHHHS---HHHH CS mTERF 83 dkDksskleklpeslpqsleenke 106 d+++ +++ ++ l+ + +k gi|15240177|ref|NP_196299.1| 358 DDEIHKVFRSHSWWLGS-CKLKKT 380 55555555555555544.333333 PP == domain 3 score: 54.5 bits; conditional E-value: 1.3e-18 GGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHH CS mTERF 205 lsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFl 285 ++++ k + + ll ++ +e+ ++ a + + + +++ + + l +lGf+++++ mvk +P +l+ + + + k+ +l gi|15240177|ref|NP_196299.1| 422 VDIESKSMKTQFLLDLGYKENSEEMETAMKNFRGKGSELRERFNVLVSLGFTKKDVKDMVKACPTMLSQTCDILESKVNYL 502 5666666667888888888888777777888888999999***************************************** PP HHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHH CS mTERF 286 vkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeef 343 +ke pl+ lv+fP l++ L r+k R ++ l+ +gk ++ +s +l csd+ f gi|15240177|ref|NP_196299.1| 503 IKELGYPLSTLVDFPSCLKFTLQ-RMKLRFAMFSWLQARGKvDRKIKVSTMLACSDKIF 560 **********************6.777788**********9999************988 PP == domain 4 score: 22.7 bits; conditional E-value: 6.1e-09 HHHHTT--HHHHHHHHHH-CHHHHS-.HHHHHHHHHHCTT-SSHHHHHHHHHHH-GGGGGS-HHHHHHHHHHHHHHTT--H CS mTERF 111 vlrelgvtrkllislliselqpvlgk.evfeesvkklvelgvdpktlkrviakrprllllssdktikpnvevlkslGfske 190 +l +lg++++ ++s li + +++l+ + e + + g+ +++++++ + r + + + +++ +++lGfsk gi|15240177|ref|NP_196299.1| 695 FLESLGLKPS-EFSHLIPCDKMFLNEdAFLLENYHVFWNYGIGREKMGKIFKEA-REVFGYETGVLASKIKSYEDLGFSKL 773 899*******.******999999999556678889999**********988777.5677777899**************** PP HHHHHHHHTTTGGGGGS-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGG CS mTERF 191 dvwailkkcPellglsekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqll 271 + +++ + P++l+ + + l + +l+ + + v + + vs++ +++ + fl +l ++e ++++++P l+ gi|15240177|ref|NP_196299.1| 774 FLSKLIVCSPSILIGDMNVGLAKVMEMLKAIGFGVDWVTENLSEEVSYDWSSMHRCLSFLRDLYVDENELCELIRKMPRLI 854 *******************99999999999999999*******************************************99 PP G CS mTERF 272 g 272 + gi|15240177|ref|NP_196299.1| 855 F 855 6 PP == domain 5 score: 9.6 bits; conditional E-value: 6.2e-05 HH.H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGG.S-.HHHHHHHHHHHTTTSS-HHHHHHHHHH- CS mTERF 18 irsyplllvadaekslqpklqfLesrgaskseltkilstvPkilg.kkkvksissvydflkkiivadkDkssklekl 93 ir++p+l+++d+ + f + g+s+sel + +++ P+ + +k v +++ flk+i + d+D++ k ++l gi|15240177|ref|NP_196299.1| 847 IRKMPRLIFEDSGEWTLILAGFEAKLGSSRSELSSLFQKFPQCQSlGKFVLNLRHCFLFLKDIEM-DDDEIGKIFRL 922 68899*******999999***********************9854256699************99.56666666655 PP == domain 6 score: 56.9 bits; conditional E-value: 2.5e-19 S-T...........................THHHHHHHHHHHHHHTTT--HHHHHHHHHTSGGGGGS-HHH.HHHHHHH CS mTERF 207 ekkklqtkeilltrvlvedesvikkapqivslseekilnkiefllglGfsreeiakmvkrfPqllglsvekvkkkteFl 285 k k+ + + ll ++ +e+ +++a + + + +++ + + l ++G +++++ mvk +P +l+ + + + k+ +l gi|15240177|ref|NP_196299.1| 981 TKSKTMKTQFLLDLGYKENSEEMERALKNFRGKGSELRERFNVLVSFGLTEKDVKDMVKACPSILTQACDILESKVNYL 1059 444555558899999999998889999999999********************************************** PP HHCTT--HHHHHCSGGGGGS-HHHHHHHHHHHHHTT--TTT.GGGGGS-HHHHHHHHHHT CS mTERF 286 vkemkwplkelvefPqvlgySLEkrikPRcnvvkallskgk.sillslsevlkcsdeefl 344 vke pl+ lv fP+ l+y L r+k R ++ l+ +gk +l +s +l csd+ f+ gi|15240177|ref|NP_196299.1| 1060 VKELGYPLSTLVTFPTCLKYTLQ-RMKLRFSMFSWLQDRGKaDPKLQVSTILVCSDKFFA 1118 **********************6.777788**********8899************9886 PP >> RuvA_C RuvA, C-terminal domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 1.4 0.0 0.07 3.5e+02 5 15 .. 243 253 .. 241 254 .. 0.91 2 ? -2.1 0.1 0.91 4.5e+03 10 17 .. 434 441 .. 434 442 .. 0.85 3 ! 10.2 0.0 0.00012 0.61 10 27 .. 467 484 .. 465 495 .. 0.90 4 ? -3.5 0.1 2.3 1.2e+04 10 19 .. 696 705 .. 696 705 .. 0.90 5 ? -1.4 0.0 0.53 2.6e+03 10 18 .. 991 999 .. 991 1012 .. 0.82 6 ? -2.1 0.0 0.89 4.4e+03 11 27 .. 1025 1041 .. 1024 1047 .. 0.81 Alignments for each domain: == domain 1 score: 1.4 bits; conditional E-value: 0.07 HCCHHHHHCT- CS RuvA_C 5 daveALlaLGY 15 ++v +L +LG+ gi|15240177|ref|NP_196299.1| 243 QVVKTLQSLGF 253 79********9 PP == domain 2 score: -2.1 bits; conditional E-value: 0.91 HHHCT--C CS RuvA_C 10 LlaLGYke 17 Ll LGYke gi|15240177|ref|NP_196299.1| 434 LLDLGYKE 441 788****8 PP == domain 3 score: 10.2 bits; conditional E-value: 0.00012 HHHCT--CCCCHHHHHHC CS RuvA_C 10 LlaLGYkekeAekAvakv 27 L++LG+++k+++ +v++ gi|15240177|ref|NP_196299.1| 467 LVSLGFTKKDVKDMVKAC 484 9**************986 PP == domain 4 score: -3.5 bits; conditional E-value: 2.3 HHHCT--CCC CS RuvA_C 10 LlaLGYkeke 19 L++LG k++e gi|15240177|ref|NP_196299.1| 696 LESLGLKPSE 705 89****9987 PP == domain 5 score: -1.4 bits; conditional E-value: 0.53 HHHCT--CC CS RuvA_C 10 LlaLGYkek 18 Ll LGYke+ gi|15240177|ref|NP_196299.1| 991 LLDLGYKEN 999 788***985 PP == domain 6 score: -2.1 bits; conditional E-value: 0.89 HHCT--CCCCHHHHHHC CS RuvA_C 11 laLGYkekeAekAvakv 27 ++ G +ek+++ +v++ gi|15240177|ref|NP_196299.1| 1025 VSFGLTEKDVKDMVKAC 1041 56689999**9999986 PP >> T6SS_Vgr Putative type VI secretion system Rhs element Vgr # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.3 0.0 0.03 1.5e+02 25 88 .. 22 85 .. 17 101 .. 0.84 2 ? 4.5 0.0 0.0061 30 25 58 .. 424 461 .. 419 466 .. 0.75 3 ? 4.7 0.0 0.0052 26 26 58 .. 984 1018 .. 975 1023 .. 0.74 Alignments for each domain: == domain 1 score: 2.3 bits; conditional E-value: 0.03 T6SS_Vgr 25 LasehaksqLnlGylvdqkdngrgekrGeGfeLrTdawgavRAgkGlllstearakasgeqldm 88 L+++ + s G+l + +++ r+ + +G e+ +++ + R +G ++ + r+ a++ +ld gi|15240177|ref|NP_196299.1| 22 LETQLKPSISGTGFLLRCAQTPRSFATVTGNEVCSEKSKVKRTRNGFKITPNVRKLAEEAMLDY 85 5566666666689999999999999999***************************999999986 PP == domain 2 score: 4.5 bits; conditional E-value: 0.0061 T6SS_Vgr 25 Lasehaksq..LnlGylvdq..kdngrgekrGeGfeLr 58 ++s++ k+q L lGy ++ +++ +++rG+G eLr gi|15240177|ref|NP_196299.1| 424 IESKSMKTQflLDLGYKENSeeMETAMKNFRGKGSELR 461 55555555543899**8887546677899********8 PP == domain 3 score: 4.7 bits; conditional E-value: 0.0052 T6SS_Vgr 26 asehaksqLnlGylvdq..kdngrgekrGeGfeLr 58 ++ +++ L lGy ++ +++ +++rG+G eLr gi|15240177|ref|NP_196299.1| 984 KTMKTQFLLDLGYKENSeeMERALKNFRGKGSELR 1018 4445555699***9888435566689********8 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (1141 residues) Target model(s): 14831 (2610332 nodes) Passed MSV filter: 403 (0.0271728); expected 296.6 (0.02) Passed bias filter: 307 (0.0206999); expected 296.6 (0.02) Passed Vit filter: 26 (0.00175308); expected 14.8 (0.001) Passed Fwd filter: 3 (0.000202279); expected 0.1 (1e-05) Initial search space (Z): 14831 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.26 # Mc/sec: 11455.34 //