# hmmsearch :: search profile(s) against a sequence database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: pfam_list/TYW3.hmm.txt # target sequence database: proteomes/Anolis_carolinensis.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TYW3 [M=214] Accession: PF02676.13 Description: Methyltransferase TYW3 Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-59 199.4 0.0 7.6e-59 198.7 0.0 1.3 1 tr|H9GHH2|H9GHH2_ANOCA tRNA-yW synthesizing protein 3 homolo 0.0008 18.9 36.6 2.4 7.5 0.2 9.3 10 tr|H9GH12|H9GH12_ANOCA Uncharacterized protein OS=Anolis car ------ inclusion threshold ------ 4.2 6.7 9.5 0.37 10.1 4.6 1.7 2 tr|G1KTW8|G1KTW8_ANOCA General transcription factor IIA subu Domain annotation for each sequence (and alignments): >> tr|H9GHH2|H9GHH2_ANOCA tRNA-yW synthesizing protein 3 homolog OS=Anolis carolinensis OX=28377 GN=TYW3 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 198.7 0.0 1.2e-62 7.6e-59 13 213 .. 13 201 .. 6 202 .. 0.91 Alignments for each domain: == domain 1 score: 198.7 bits; conditional E-value: 1.2e-62 ..HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE...............EESSTT-STT-EEEEEESS---HHHHHHHHC CS TYW3 13 pdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrk...saeaeekaaksggkkgggkwlfvsHdpvkeeellaele 96 ++ d s+kGsvDe+i l++++n +e+++TtSSCsGRv+v+ + + ++++ + +k++++wl+v+H+ ++ e++l++l+ tr|H9GHH2|H9GHH2_ANOCA 13 SRADGSRKGSVDEPIEGLVRLLNGREGFCTTSSCSGRVVVLEQP-PqprPPPRGQATTGFEVQKQNCTWLMVTHQICTIEDVLTALQ 98 33799************************************333.2465344677778888899*********************** PP S--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEEEEE---EEEEEEESST.S-- CS TYW3 97 gleeeeesaksseseeeerlivfkfePmILhvlcrslehAqkllsaAlsaGfreSGivslkkkkvivairsglklevpigrkk.llv 182 + + + vfkfeP++Lhv+cr+l++Aq l+++A++aGfr+SGi+ +k+k+i+a+rs+++levp+++k l+v tr|H9GHH2|H9GHH2_ANOCA 99 KAK---------------EDAVFKFEPFVLHVQCRELQDAQLLHTVAIEAGFRNSGITVGRKGKIIMAVRSTHCLEVPLSQKGkLMV 170 *95...............5789**********************************************************6555*** PP -HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS TYW3 183 seeylkllvklanerfeenkkrierfeealk 213 seey++++v++an+++een++ri+rf+++l+ tr|H9GHH2|H9GHH2_ANOCA 171 SEEYVDFVVRVANQKMEENRRRIDRFYSSLQ 201 ***************************9996 PP >> tr|H9GH12|H9GH12_ANOCA Uncharacterized protein OS=Anolis carolinensis OX=28377 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.8 0.2 0.13 8e+02 46 59 .. 38 73 .. 36 123 .. 0.68 2 ! 6.7 0.4 0.00067 4.1 42 59 .. 137 162 .. 130 234 .. 0.66 3 ? 2.7 0.2 0.012 72 46 59 .. 248 266 .. 247 315 .. 0.73 4 ? -2.0 0.1 0.3 1.9e+03 46 54 .. 383 391 .. 381 424 .. 0.78 5 ! 5.2 0.1 0.0019 12 43 54 .. 486 497 .. 464 544 .. 0.80 6 ! 3.3 0.1 0.0072 45 44 54 .. 592 602 .. 586 634 .. 0.83 7 ? 1.0 0.0 0.036 2.2e+02 45 55 .. 696 706 .. 688 751 .. 0.78 8 ! 7.5 0.2 0.00038 2.4 40 59 .. 931 958 .. 921 1026 .. 0.65 9 ! 5.3 0.1 0.0018 11 43 58 .. 1039 1054 .. 1027 1117 .. 0.84 10 ! 6.8 0.2 0.00062 3.9 42 56 .. 1155 1169 .. 1144 1242 .. 0.73 Alignments for each domain: == domain 1 score: -0.8 bits; conditional E-value: 0.13 ES-EEEEE............................ CS TYW3 46 CsGRvsvflegrk......................s 59 CsGRv ++l+g tr|H9GH12|H9GH12_ANOCA 38 CSGRVEMLLNGLWgtvcddgwdlsdaqvvcrelgcG 73 ********9887666666666665555555555443 PP == domain 2 score: 6.7 bits; conditional E-value: 0.00067 EEEEES-EEEEE................ CS TYW3 42 TtSSCsGRvsvflegrk..........s 59 tS CsGRv vf + + tr|H9GH12|H9GH12_ANOCA 137 GTSPCSGRVEVFHN--DawgticdagwD 162 69**********32..124555555551 PP == domain 3 score: 2.7 bits; conditional E-value: 0.012 ES-EEEEE........... CS TYW3 46 CsGRvsvflegrk.....s 59 CsGRv vf+ g+ + tr|H9GH12|H9GH12_ANOCA 248 CSGRVEVFISGEWtsvcdD 266 ********99876555540 PP == domain 4 score: -2.0 bits; conditional E-value: 0.3 ES-EEEEE. CS TYW3 46 CsGRvsvfl 54 C GRv vf tr|H9GH12|H9GH12_ANOCA 383 CTGRVEVFH 391 ********3 PP == domain 5 score: 5.2 bits; conditional E-value: 0.0019 EEEES-EEEEE. CS TYW3 43 tSSCsGRvsvfl 54 +S CsGRv vf tr|H9GH12|H9GH12_ANOCA 486 SSNCSGRVEVFH 497 688********3 PP == domain 6 score: 3.3 bits; conditional E-value: 0.0072 EEES-EEEEE. CS TYW3 44 SSCsGRvsvfl 54 S CsGR+ vf tr|H9GH12|H9GH12_ANOCA 592 SRCSGRIEVFQ 602 88********3 PP == domain 7 score: 1.0 bits; conditional E-value: 0.036 EES-EEEEE.. CS TYW3 45 SCsGRvsvfle 55 CsGRv +f + tr|H9GH12|H9GH12_ANOCA 696 RCSGRVELFHN 706 6********32 PP == domain 8 score: 7.5 bits; conditional E-value: 0.00038 EEEEEEES-EEEEE.............. CS TYW3 40 lvTtSSCsGRvsvflegrk........s 59 l tS CsGRv vf + + + tr|H9GH12|H9GH12_ANOCA 931 LNGTSPCSGRVEVFHNDTWgticdagwD 958 5679**********43322555555551 PP == domain 9 score: 5.3 bits; conditional E-value: 0.0018 EEEES-EEEEE..... CS TYW3 43 tSSCsGRvsvflegrk 58 t CsGRv vfl+g+ tr|H9GH12|H9GH12_ANOCA 1039 TNGCSGRVEVFLNGEW 1054 667*********9986 PP == domain 10 score: 6.8 bits; conditional E-value: 0.00062 EEEEES-EEEEE... CS TYW3 42 TtSSCsGRvsvfleg 56 tS CsGRv vf + tr|H9GH12|H9GH12_ANOCA 1155 GTSPCSGRVEVFHND 1169 69**********432 PP >> tr|G1KTW8|G1KTW8_ANOCA General transcription factor IIA subunit 1 OS=Anolis carolinensis OX=28377 GN=GTF2A1 PE=4 SV= # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.1 4.6 6e-05 0.37 69 184 .. 68 193 .. 26 200 .. 0.66 2 ? -2.1 0.2 0.33 2e+03 61 97 .. 296 332 .. 257 359 .. 0.68 Alignments for each domain: == domain 1 score: 10.1 bits; conditional E-value: 6e-05 STT-STT-EEEEEESS---HHHHHHHHCS--.......................SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHC CS TYW3 69 sggkkgggkwlfvsHdpvkeeellaelegleeeeesaksseseee.........erlivfkfePmILhvlcrslehAqkllsaAlsa 146 +++++++ + + ++H+ ++++++ ++ ++++++ +++++++ ++ v ++ +h ++ +++A++ ++Al a tr|G1KTW8|G1KTW8_ANOCA 68 AQQQQQQQQQHHQQHQHHPPQQHVHHHHHPPQQQQQTVQQSQAQQvlipatqqaPQQQVIVPDSKLMHMNTSGMSAAATAATLALPA 154 22222333444555555544555555544444444444444444355666666655555667999********************** PP T-TT-EEEEECTTEEEEEEE---EEEEEEE.SSTS---H CS TYW3 147 GfreSGivslkkkkvivairsglklevpig.rkkllvse 184 G + +++++++ +r+ + + +i +++++ ++ tr|G1KTW8|G1KTW8_ANOCA 155 GVTPVQQILTNSGQILQVVRAANGAQYIIQpQQQVVLQQ 193 *99888888888788888889888888888543455554 PP == domain 2 score: -2.1 bits; conditional E-value: 0.33 .....EESSTT-STT-EEEEEESS---HHHHHHHHCS CS TYW3 61 eaeekaaksggkkgggkwlfvsHdpvkeeellaeleg 97 e +++++++++k gg+ v+ +p+++e+ ++ eg tr|G1KTW8|G1KTW8_ANOCA 296 EDYDDDEEEDKEKDGGEDGQVEEEPLNSEDDVSDEEG 332 3334444555555566666666666666666555555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (214 nodes) Target sequences: 18528 (9796552 residues searched) Passed MSV filter: 755 (0.0407491); expected 370.6 (0.02) Passed bias filter: 394 (0.0212651); expected 370.6 (0.02) Passed Vit filter: 26 (0.00140328); expected 18.5 (0.001) Passed Fwd filter: 6 (0.000323834); expected 0.2 (1e-05) Initial search space (Z): 18528 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.19u 0.01s 00:00:00.20 Elapsed: 00:00:00.07 # Mc/sec: 29949.46 // [ok]