# 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/Danio_rerio.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-59 201.2 1.0 3.5e-59 200.2 1.0 1.5 1 sp|Q6DHJ1|TYW3_DANRE tRNA wybutosine-synthesizing protein 6.7e-05 22.8 61.6 3.5 7.4 0.8 15.3 17 tr|F6PCI1|F6PCI1_DANRE Si:dkey-14d8.20 OS=Danio rerio OX=795 0.0022 17.9 41.5 4.3 7.1 0.2 10.0 11 tr|F1QTA3|F1QTA3_DANRE Si:dkey-21h14.12 OS=Danio rerio OX=79 Domain annotation for each sequence (and alignments): >> sp|Q6DHJ1|TYW3_DANRE tRNA wybutosine-synthesizing protein 3 homolog OS=Danio rerio OX=7955 GN=tyw3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 200.2 1.0 4.1e-63 3.5e-59 3 213 .. 10 192 .. 7 193 .. 0.93 Alignments for each domain: == domain 1 score: 200.2 bits; conditional E-value: 4.1e-63 HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEESS---HHHH CS TYW3 3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeekaaksggkkgggkwlfvsHdpvkeeel 91 K+++L++ +d s+kGsvDe+i ++++ ins+++++TtSSCsGR+ +f ++ ++ + +k++++wlfv+H++++ e++ sp|Q6DHJ1|TYW3_DANRE 10 KNQCLNK-----CDFSKKGSVDEDISHVVSFINSQDRYFTTSSCSGRIILF---------DAVSDCPDVQKQNCSWLFVTHQKCQMEDV 84 4555554.....8**************************************.........56677788888999*************** PP HHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEEEEE---EEEEEEESST. CS TYW3 92 laelegleeeeesaksseseeeerlivfkfePmILhvlcrslehAqkllsaAlsaGfreSGivslkkkkvivairsglklevpigrkk. 179 ++ le++ + +fkfeP++Lhv+c++le+Aq l+++A+++Gfr+SGi+ kk+k+i+a+rs+++levp+++++ sp|Q6DHJ1|TYW3_DANRE 85 VRGLEKSV---------------GDATFKFEPFVLHVQCKQLEDAQLLHTVAINSGFRNSGITVGKKGKIIMAVRSTHCLEVPLSHRSh 158 ***99996...............6789**********************************************************6566 PP S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS TYW3 180 llvseeylkllvklanerfeenkkrierfeealk 213 +lv+++yl++lv +an+++een kri+rf+e l+ sp|Q6DHJ1|TYW3_DANRE 159 VLVTHQYLDFLVGVANQKMEENLKRIQRFSECLQ 192 ******************************9997 PP >> tr|F6PCI1|F6PCI1_DANRE Si:dkey-14d8.20 OS=Danio rerio OX=7955 GN=si:dkey-14d8.20 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 3.5 0.1 0.0063 54 45 54 .. 32 41 .. 26 83 .. 0.81 2 ? 0.4 0.1 0.056 4.8e+02 45 58 .. 140 153 .. 134 200 .. 0.73 3 ? 1.1 0.1 0.034 2.9e+02 45 54 .. 243 252 .. 241 285 .. 0.88 4 ! 6.7 0.2 0.00065 5.6 45 59 .. 328 348 .. 326 385 .. 0.74 5 ! 7.1 0.1 0.00052 4.4 45 103 .. 430 509 .. 427 526 .. 0.65 6 ! 5.1 0.1 0.0021 18 45 58 .. 531 544 .. 523 594 .. 0.77 7 ? 0.9 0.1 0.039 3.3e+02 46 58 .. 635 647 .. 633 691 .. 0.75 8 ! 5.5 0.1 0.0016 14 43 53 .. 744 754 .. 740 788 .. 0.87 9 ! 4.5 0.1 0.0033 28 45 56 .. 849 860 .. 842 915 .. 0.82 10 ? -1.6 0.0 0.23 2e+03 45 55 .. 952 962 .. 950 982 .. 0.82 11 ? -1.8 0.0 0.27 2.3e+03 45 54 .. 1176 1185 .. 1175 1201 .. 0.86 12 ? -0.2 0.1 0.087 7.4e+02 46 54 .. 1278 1286 .. 1272 1326 .. 0.81 13 ? 2.2 0.1 0.016 1.4e+02 46 95 .. 1380 1452 .. 1377 1477 .. 0.75 14 ! 5.0 0.3 0.0022 19 44 55 .. 1581 1592 .. 1576 1710 .. 0.82 15 ! 4.6 0.4 0.0029 25 45 58 .. 1792 1805 .. 1789 1875 .. 0.72 16 ? -1.9 0.1 0.29 2.5e+03 45 57 .. 1891 1903 .. 1888 1940 .. 0.80 17 ! 7.4 0.8 0.00041 3.5 43 59 .. 1992 2030 .. 1990 2128 .. 0.74 Alignments for each domain: == domain 1 score: 3.5 bits; conditional E-value: 0.0063 EES-EEEEE. CS TYW3 45 SCsGRvsvfl 54 SCsGRv vf+ tr|F6PCI1|F6PCI1_DANRE 32 SCSGRVEVFF 41 9********5 PP == domain 2 score: 0.4 bits; conditional E-value: 0.056 EES-EEEEE..... CS TYW3 45 SCsGRvsvflegrk 58 CsGRv v+ +g+ tr|F6PCI1|F6PCI1_DANRE 140 PCSGRVEVLNDGQW 153 6********88875 PP == domain 3 score: 1.1 bits; conditional E-value: 0.034 EES-EEEEE. CS TYW3 45 SCsGRvsvfl 54 SCsGRv ++ tr|F6PCI1|F6PCI1_DANRE 243 SCSGRVEIYY 252 9*******94 PP == domain 4 score: 6.7 bits; conditional E-value: 0.00065 EES-EEEEE............ CS TYW3 45 SCsGRvsvflegrk......s 59 SCsGRv vf++g+ + tr|F6PCI1|F6PCI1_DANRE 328 SCSGRVEVFFDGQWgtvcddN 348 9*********99975565541 PP == domain 5 score: 7.1 bits; conditional E-value: 0.00052 EES-EEEEE..................................EESSTT-STT-EEEEEESS---HHHHHHHHCS--.... CS TYW3 45 SCsGRvsvflegrk......................saeaeekaaksggkkgggkwlfvsHdpvkeeellaelegleeeee 103 SCsGRv vfl ++ ++a++k++ g+ g+g+ + + + v +e++l+ e+l+++++ tr|F6PCI1|F6PCI1_DANRE 430 SCSGRVEVFLHSQWatvyddgwdlsdaavvcremgcGDAAQAKSNAYFGQ-GTGQTYMSNVNCVGNESSLSVCESLKPKST 509 9********87766788888888887777777776532333333333333.445556666666666666666666665554 PP == domain 6 score: 5.1 bits; conditional E-value: 0.0021 EES-EEEEE..... CS TYW3 45 SCsGRvsvflegrk 58 SCsGRv vf g+ tr|F6PCI1|F6PCI1_DANRE 531 SCSGRVEVFYSGQW 544 9********88875 PP == domain 7 score: 0.9 bits; conditional E-value: 0.039 ES-EEEEE..... CS TYW3 46 CsGRvsvflegrk 58 CsGRv v+l+g+ tr|F6PCI1|F6PCI1_DANRE 635 CSGRVEVLLNGQW 647 ********99986 PP == domain 8 score: 5.5 bits; conditional E-value: 0.0016 EEEES-EEEEE CS TYW3 43 tSSCsGRvsvf 53 +SSCsGRv v+ tr|F6PCI1|F6PCI1_DANRE 744 SSSCSGRVQVL 754 6*********9 PP == domain 9 score: 4.5 bits; conditional E-value: 0.0033 EES-EEEEE... CS TYW3 45 SCsGRvsvfleg 56 SCsGRv vf +g tr|F6PCI1|F6PCI1_DANRE 849 SCSGRVEVFHNG 860 9********766 PP == domain 10 score: -1.6 bits; conditional E-value: 0.23 EES-EEEEE.. CS TYW3 45 SCsGRvsvfle 55 SCsG v+vf + tr|F6PCI1|F6PCI1_DANRE 952 SCSGTVAVFHN 962 9********43 PP == domain 11 score: -1.8 bits; conditional E-value: 0.27 EES-EEEEE. CS TYW3 45 SCsGRvsvfl 54 CsGRv ++l tr|F6PCI1|F6PCI1_DANRE 1176 ACSGRVEIYL 1185 5******995 PP == domain 12 score: -0.2 bits; conditional E-value: 0.087 ES-EEEEE. CS TYW3 46 CsGRvsvfl 54 CsGRv +f tr|F6PCI1|F6PCI1_DANRE 1278 CSGRVEIFH 1286 ********3 PP == domain 13 score: 2.2 bits; conditional E-value: 0.016 ES-EEEEE...................................EESSTT-STT-EEEEEESS---HHHHHHHH CS TYW3 46 CsGRvsvflegrk.......................saeaeekaaksggkkgggkwlfvsHdpvkeeellael 95 CsGRv v+ +g ++ + ++++ +k++g+ w + s + +e +l + + tr|F6PCI1|F6PCI1_DANRE 1380 CSGRVEVLYDGYGwgtvyndgwnllggdvickqlscGTALSVTNRSFLKKGKGSIWTYNSACTGTEISLKSCI 1452 ********99998899999999999998888888886667777777888888888888776555555555554 PP == domain 14 score: 5.0 bits; conditional E-value: 0.0022 EEES-EEEEE.. CS TYW3 44 SSCsGRvsvfle 55 SSCsGRv v+ + tr|F6PCI1|F6PCI1_DANRE 1581 SSCSGRVEVLRN 1592 9********933 PP == domain 15 score: 4.6 bits; conditional E-value: 0.0029 EES-EEEEE..... CS TYW3 45 SCsGRvsvflegrk 58 SCsGRv vf g+ tr|F6PCI1|F6PCI1_DANRE 1792 SCSGRVEVFDKGQW 1805 9********65554 PP == domain 16 score: -1.9 bits; conditional E-value: 0.29 EES-EEEEE.... CS TYW3 45 SCsGRvsvflegr 57 CsGRv v ++g tr|F6PCI1|F6PCI1_DANRE 1891 PCSGRVEVRFNGV 1903 5******987775 PP == domain 17 score: 7.4 bits; conditional E-value: 0.00041 EEEES-EEEEE............................ CS TYW3 43 tSSCsGRvsvflegrk......................s 59 +SSCsGRv v+ +g+ tr|F6PCI1|F6PCI1_DANRE 1992 SSSCSGRVEVLHNGTWgtvcddgwdlqdakvvcgeigcG 2030 6**********8887677777766666666666655552 PP >> tr|F1QTA3|F1QTA3_DANRE Si:dkey-21h14.12 OS=Danio rerio OX=7955 GN=si:dkey-21h14.12 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.3 0.0 0.015 1.3e+02 43 58 .. 28 43 .. 23 81 .. 0.81 2 ? 2.8 0.2 0.01 89 38 59 .. 124 153 .. 117 219 .. 0.70 3 ! 6.9 0.3 0.00059 5.1 44 57 .. 233 246 .. 227 308 .. 0.86 4 ? -0.5 0.1 0.11 9.5e+02 40 56 .. 330 346 .. 327 421 .. 0.71 5 ! 7.0 0.3 0.00055 4.7 43 57 .. 436 450 .. 407 474 .. 0.84 6 ? -0.9 0.1 0.14 1.2e+03 40 54 .. 534 548 .. 532 622 .. 0.74 7 ! 7.0 0.2 0.00055 4.7 44 57 .. 641 654 .. 632 718 .. 0.84 8 ? -0.3 0.0 0.095 8.1e+02 40 57 .. 738 755 .. 735 840 .. 0.72 9 ! 7.1 0.2 0.0005 4.3 44 58 .. 845 858 .. 832 932 .. 0.74 10 ! 7.0 0.2 0.00054 4.7 44 57 .. 1048 1061 .. 1038 1119 .. 0.84 11 ? -2.2 0.1 0.36 3e+03 46 57 .. 1477 1488 .. 1476 1517 .. 0.80 Alignments for each domain: == domain 1 score: 2.3 bits; conditional E-value: 0.015 EEEES-EEEEE..... CS TYW3 43 tSSCsGRvsvflegrk 58 S C+GRv v +g+ tr|F1QTA3|F1QTA3_DANRE 28 HSACAGRVEVHHDGQW 43 599*******988875 PP == domain 2 score: 2.8 bits; conditional E-value: 0.01 SSEEEEEEES-EEEEE............... CS TYW3 38 edlvTtSSCsGRvsvflegrk.........s 59 +lv S CsGR +f + + + tr|F1QTA3|F1QTA3_DANRE 124 VRLVGGSHCSGRLEIFHNQ-TwmsvcdaafD 153 568889**********332.13555544440 PP == domain 3 score: 6.9 bits; conditional E-value: 0.00059 EEES-EEEEE.... CS TYW3 44 SSCsGRvsvflegr 57 SSCsGRv v+ g+ tr|F1QTA3|F1QTA3_DANRE 233 SSCSGRVEVYHRGQ 246 9*********6665 PP == domain 4 score: -0.5 bits; conditional E-value: 0.11 EEEEEEES-EEEEE... CS TYW3 40 lvTtSSCsGRvsvfleg 56 lv S CsGR ++ + tr|F1QTA3|F1QTA3_DANRE 330 LVGGSRCSGRLEILHDH 346 577799*****999433 PP == domain 5 score: 7.0 bits; conditional E-value: 0.00055 EEEES-EEEEE.... CS TYW3 43 tSSCsGRvsvflegr 57 SSCsGRv v+ g+ tr|F1QTA3|F1QTA3_DANRE 436 DSSCSGRVEVYHRGQ 450 5**********6654 PP == domain 6 score: -0.9 bits; conditional E-value: 0.14 EEEEEEES-EEEEE. CS TYW3 40 lvTtSSCsGRvsvfl 54 lv S CsGR ++ tr|F1QTA3|F1QTA3_DANRE 534 LVGGSRCSGRLEILH 548 567799*****9993 PP == domain 7 score: 7.0 bits; conditional E-value: 0.00055 EEES-EEEEE.... CS TYW3 44 SSCsGRvsvflegr 57 SSCsGRv v+ g+ tr|F1QTA3|F1QTA3_DANRE 641 SSCSGRVEVYHRGQ 654 9*********6665 PP == domain 8 score: -0.3 bits; conditional E-value: 0.095 EEEEEEES-EEEEE.... CS TYW3 40 lvTtSSCsGRvsvflegr 57 lv S CsGR ++ + + tr|F1QTA3|F1QTA3_DANRE 738 LVGGSRCSGRLEILHDQT 755 577799******994433 PP == domain 9 score: 7.1 bits; conditional E-value: 0.0005 EEES-EEEEE..... CS TYW3 44 SSCsGRvsvflegrk 58 SSCsGRv v+ g+ tr|F1QTA3|F1QTA3_DANRE 845 SSCSGRVEVY-HGQW 858 **********.5544 PP == domain 10 score: 7.0 bits; conditional E-value: 0.00054 EEES-EEEEE.... CS TYW3 44 SSCsGRvsvflegr 57 SSCsGRv v+ g+ tr|F1QTA3|F1QTA3_DANRE 1048 SSCSGRVEVYHRGQ 1061 9*********6665 PP == domain 11 score: -2.2 bits; conditional E-value: 0.36 ES-EEEEE.... CS TYW3 46 CsGRvsvflegr 57 C+GR vf g+ tr|F1QTA3|F1QTA3_DANRE 1477 CAGRLEVFHSGS 1488 ********7665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (214 nodes) Target sequences: 25687 (13798380 residues searched) Passed MSV filter: 1032 (0.040176); expected 513.7 (0.02) Passed bias filter: 507 (0.0197376); expected 513.7 (0.02) Passed Vit filter: 35 (0.00136256); expected 25.7 (0.001) Passed Fwd filter: 8 (0.000311442); expected 0.3 (1e-05) Initial search space (Z): 25687 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.27u 0.01s 00:00:00.28 Elapsed: 00:00:00.10 # Mc/sec: 29528.53 // [ok]