# 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/Homo_sapiens.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-55 190.5 0.3 2.1e-55 189.6 0.3 1.4 1 sp|Q6IPR3|TYW3_HUMAN tRNA wybutosine-synthesizing protein 2.4e-41 143.7 0.3 5.6e-22 80.4 0.1 2.2 2 sp|Q6IPR3-2|TYW3_HUMAN Isoform 2 of tRNA wybutosine-synthesi 1.5e-28 101.9 0.4 1.3e-13 53.1 0.0 2.2 2 tr|B4DFU6|B4DFU6_HUMAN cDNA FLJ50478 OS=Homo sapiens GN=TYW3 ------ inclusion threshold ------ 0.032 15.8 0.1 0.11 14.1 0.1 1.7 1 tr|E5RIY1|E5RIY1_HUMAN Serine/threonine-protein phosphatase 0.1 14.2 0.1 0.16 13.6 0.1 1.3 1 sp|Q8N7H5-2|PAF1_HUMAN Isoform 2 of RNA polymerase II-associ 0.11 14.1 0.1 0.17 13.4 0.1 1.2 1 tr|F8W9Q2|F8W9Q2_HUMAN Peroxisome biogenesis factor 2 OS=Hom 0.12 13.9 0.1 0.19 13.3 0.1 1.2 1 tr|M0QX35|M0QX35_HUMAN Paf1, RNA polymerase II associated fa Domain annotation for each sequence (and alignments): >> sp|Q6IPR3|TYW3_HUMAN tRNA wybutosine-synthesizing protein 3 homolog OS=Homo sapiens GN=TYW3 PE=2 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.6 0.3 1.7e-59 2.1e-55 3 213 .. 11 193 .. 9 194 .. 0.94 Alignments for each domain: == domain 1 score: 189.6 bits; conditional E-value: 1.7e-59 HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEESS---HHHH CS TYW3 3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeekaaksggkkgggkwlfvsHdpvkeeel 91 Ka++L++ d+s+kGsvDe+++el++ +n +++++TtSSC+GR+ ++ ++ + + +k+++ wl+v+H+ + ++++ sp|Q6IPR3|TYW3_HUMAN 11 KAQCLSK-----ADLSRKGSVDEDVVELVQFLNMRDQFFTTSSCAGRILLL---------DRGINGFEVQKQNCCWLLVTHKLCVKDDV 85 6777776.....6**************************************.........6778889999999**************** PP HHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEEEEE---EEEEEEESST. CS TYW3 92 laelegleeeeesaksseseeeerlivfkfePmILhvlcrslehAqkllsaAlsaGfreSGivslkkkkvivairsglklevpigrkk. 179 + +l++ + + ++kfeP++Lhv+cr+l++Aq l+s+A+++Gfr+SGi+ k++k ++a+rs+++levp+++k sp|Q6IPR3|TYW3_HUMAN 86 IVALKKAN---------------GDATLKFEPFVLHVQCRQLQDAQILHSMAIDSGFRNSGITVGKRGKTMLAVRSTHGLEVPLSHKGk 159 *****994...............6789**********************************************************5555 PP S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS TYW3 180 llvseeylkllvklanerfeenkkrierfeealk 213 l+v+eey+++l+++an+++eenkkrierf++ l+ sp|Q6IPR3|TYW3_HUMAN 160 LMVTEEYIDFLLNVANQKMEENKKRIERFYNCLQ 193 ******************************9987 PP >> sp|Q6IPR3-2|TYW3_HUMAN Isoform 2 of tRNA wybutosine-synthesizing protein 3 homolog OS=Homo sapiens GN=TYW3 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 62.7 0.0 1.2e-20 1.5e-16 3 90 .. 11 84 .. 9 87 .. 0.89 2 ! 80.4 0.1 4.5e-26 5.6e-22 138 213 .. 84 160 .. 82 161 .. 0.95 Alignments for each domain: == domain 1 score: 62.7 bits; conditional E-value: 1.2e-20 HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEESS---HHH CS TYW3 3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeekaaksggkkgggkwlfvsHdpvkeee 90 Ka++L++ d+s+kGsvDe+++el++ +n +++++TtSSC+GR+ ++ ++ + + +k+++ wl+v+H+ + +++ sp|Q6IPR3-2|TYW3_HUMAN 11 KAQCLSK-----ADLSRKGSVDEDVVELVQFLNMRDQFFTTSSCAGRILLL---------DRGINGFEVQKQNCCWLLVTHKLCVKDD 84 6777776.....6**************************************.........6778889999999********9986665 PP == domain 2 score: 80.4 bits; conditional E-value: 4.5e-26 HHHHHHHHCT-TT-EEEEECTTEEEEEEE---EEEEEEESST.S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS TYW3 138 kllsaAlsaGfreSGivslkkkkvivairsglklevpigrkk.llvseeylkllvklanerfeenkkrierfeealk 213 +++s+A+++Gfr+SGi+ k++k ++a+rs+++levp+++k l+v+eey+++l+++an+++eenkkrierf++ l+ sp|Q6IPR3-2|TYW3_HUMAN 84 DVHSMAIDSGFRNSGITVGKRGKTMLAVRSTHGLEVPLSHKGkLMVTEEYIDFLLNVANQKMEENKKRIERFYNCLQ 160 6899***********************************5555******************************9987 PP >> tr|B4DFU6|B4DFU6_HUMAN cDNA FLJ50478 OS=Homo sapiens GN=TYW3 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 53.1 0.0 1e-17 1.3e-13 3 53 .. 11 56 .. 9 59 .. 0.90 2 ! 47.2 0.1 6.3e-16 8e-12 164 213 .. 59 109 .. 58 110 .. 0.93 Alignments for each domain: == domain 1 score: 53.1 bits; conditional E-value: 1e-17 HHHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE CS TYW3 3 KakiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvf 53 Ka++L++ d+s+kGsvDe+++el++ +n +++++TtSSC+GR+ ++ tr|B4DFU6|B4DFU6_HUMAN 11 KAQCLSK-----ADLSRKGSVDEDVVELVQFLNMRDQFFTTSSCAGRILLL 56 6777777.....6***********************************987 PP == domain 2 score: 47.2 bits; conditional E-value: 6.3e-16 EEE---EEEEEEESST.S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS TYW3 164 airsglklevpigrkk.llvseeylkllvklanerfeenkkrierfeealk 213 a+rs+++levp+++k l+v+eey+++l+++an+++eenkkrierf++ l+ tr|B4DFU6|B4DFU6_HUMAN 59 AVRSTHGLEVPLSHKGkLMVTEEYIDFLLNVANQKMEENKKRIERFYNCLQ 109 79***********5555******************************9987 PP >> tr|E5RIY1|E5RIY1_HUMAN Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform OS=Homo sap # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 14.1 0.1 8.7e-06 0.11 19 94 .. 17 98 .. 9 122 .. 0.72 Alignments for each domain: == domain 1 score: 14.1 bits; conditional E-value: 8.7e-06 HCCHC-GGGH..HHHHHH..HC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEESS--.......-HHHHHHH CS TYW3 19 pkGsvDekir..elidei..nsledlvTtSSCsGRvsvflegrksaeaeekaaksggkkgggkwlfvsHdpv.......keeellae 94 kG vD +++ ++i+++ n+ +l t GRv++f ++e+e+k ++++ + + f+sH+p + ee +++ tr|E5RIY1|E5RIY1_HUMAN 17 VKGAVDDDVAeaDIISTVefNHSGELLATGDKGGRVVIF-----QQEQENKIQSHSRGEYNVYSTFQSHEPEfdylkslEIEEKINK 98 5899999996336887543389999**************.....55666666666666677789******98777766544444444 PP >> sp|Q8N7H5-2|PAF1_HUMAN Isoform 2 of RNA polymerase II-associated factor 1 homolog OS=Homo sapiens GN=PAF1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.6 0.1 1.2e-05 0.16 62 160 .. 299 419 .. 279 470 .. 0.66 Alignments for each domain: == domain 1 score: 13.6 bits; conditional E-value: 1.2e-05 ....EESSTT-STT-EEEEEESS---HHHHHHHHCS--........................SSEEEEEEE--EEEEEESSHHHHHH CS TYW3 62 aeekaaksggkkgggkwlfvsHdpvkeeellaelegleeeeesaksseseee..........erlivfkfePmILhvlcrslehAqk 138 ++++ak+g + g+ l+v+H+ ++e+el a+ ++ + e+++ ++e+eee + +++++ P + + A + sp|Q8N7H5-2|PAF1_HUMAN 299 LSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEARKAQLENHEPEEEEEEEmeteekeaggSVMLILRTMPTLMMRTEDRPKVAVT 385 4567888888989999*********55555544444444433333333333345555689888899999999999888888999*** PP HHHHHHHCT-TT-EEEEECTT.............E CS TYW3 139 llsaAlsaGfreSGivslkkk.............k 160 ++++A++ G SG+ + + sp|Q8N7H5-2|PAF1_HUMAN 386 MIQTAAAMGV-ASGAGATAAApvpspvaastrprR 419 *****99997.456555444445555555554442 PP >> tr|F8W9Q2|F8W9Q2_HUMAN Peroxisome biogenesis factor 2 OS=Homo sapiens GN=PAF1 PE=2 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.4 0.1 1.4e-05 0.17 62 157 .. 299 403 .. 279 451 .. 0.66 Alignments for each domain: == domain 1 score: 13.4 bits; conditional E-value: 1.4e-05 ....EESSTT-STT-EEEEEESS---HHHHHHHHCS--........................SSEEEEEEE--EEEEEESSHHHHHH CS TYW3 62 aeekaaksggkkgggkwlfvsHdpvkeeellaelegleeeeesaksseseee..........erlivfkfePmILhvlcrslehAqk 138 ++++ak+g + g+ l+v+H+ ++e+el a+ ++ + e+++ ++e+eee + +++++ P + + A + tr|F8W9Q2|F8W9Q2_HUMAN 299 LSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEARKAQLENHEPEEEEEEEmeteekeaggSVMLILRTMPTLMMRTEDRPKVAVT 385 4567888888989999*********55555544444444433333333333345555689888899999999998888888999*** PP HHHHHHHCT-TT-EEEEEC CS TYW3 139 llsaAlsaGfreSGivslk 157 ++++A++ G SG+ + tr|F8W9Q2|F8W9Q2_HUMAN 386 MIQTAAAMGV-ASGAGATA 403 ****999997.45555544 PP >> tr|M0QX35|M0QX35_HUMAN Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae), isoform CRA_c OS=Homo sap # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 13.3 0.1 1.5e-05 0.19 62 157 .. 322 426 .. 302 474 .. 0.66 Alignments for each domain: == domain 1 score: 13.3 bits; conditional E-value: 1.5e-05 ....EESSTT-STT-EEEEEESS---HHHHHHHHCS--........................SSEEEEEEE--EEEEEESSHHHHHH CS TYW3 62 aeekaaksggkkgggkwlfvsHdpvkeeellaelegleeeeesaksseseee..........erlivfkfePmILhvlcrslehAqk 138 ++++ak+g + g+ l+v+H+ ++e+el a+ ++ + e+++ ++e+eee + +++++ P + + A + tr|M0QX35|M0QX35_HUMAN 322 LSKRRAKAGVQSGTNALLVVKHRDMNEKELEAQEARKAQLENHEPEEEEEEEmeteekeaggSVMLILRTMPTLMMRTEDRPKVAVT 408 4567888888989999*********55555544444444433333333333345555689888899999999998888888999*** PP HHHHHHHCT-TT-EEEEEC CS TYW3 139 llsaAlsaGfreSGivslk 157 ++++A++ G SG+ + tr|M0QX35|M0QX35_HUMAN 409 MIQTAAAMGV-ASGAGATA 426 ****999997.45555544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (214 nodes) Target sequences: 88473 (35070517 residues searched) Passed MSV filter: 2963 (0.0334904); expected 1769.5 (0.02) Passed bias filter: 1737 (0.0196331); expected 1769.5 (0.02) Passed Vit filter: 154 (0.00174064); expected 88.5 (0.001) Passed Fwd filter: 16 (0.000180846); expected 0.9 (1e-05) Initial search space (Z): 88473 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.63u 0.03s 00:00:00.66 Elapsed: 00:00:00.23 # Mc/sec: 32630.83 // [ok]