# 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/Methyltr_RsmB-F.hmm.txt # target sequence database: proteomes/Petromyzon_marinus.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Methyltr_RsmB-F [M=200] Accession: PF01189.16 Description: 16S rRNA methyltransferase RsmB/F 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-78 262.6 0.0 2.4e-78 262.0 0.0 1.2 1 tr|S4RYQ4|S4RYQ4_PETMA NOP2 nucleolar protein homolog (yeast 1.7e-78 262.4 0.0 2.4e-78 262.0 0.0 1.2 1 tr|S4RYQ5|S4RYQ5_PETMA NOP2 nucleolar protein homolog (yeast 6.4e-43 146.3 0.0 1e-42 145.7 0.0 1.3 1 tr|S4RE18|S4RE18_PETMA NOL1/NOP2/Sun domain family, member 6 1.6e-22 79.7 0.3 4.3e-22 78.4 0.3 1.7 1 tr|S4RVL0|S4RVL0_PETMA NOL1/NOP2/Sun domain family, member 4 2.1e-19 69.6 0.0 6.8e-19 67.9 0.0 1.7 1 tr|S4RD16|S4RD16_PETMA NOP2/Sun RNA methyltransferase family 8.5e-08 31.7 0.0 1.1e-07 31.3 0.0 1.1 1 tr|S4R5X4|S4R5X4_PETMA Uncharacterized protein OS=Petromyzon ------ inclusion threshold ------ 0.077 12.2 0.0 0.2 10.9 0.0 1.6 2 tr|S4R827|S4R827_PETMA Protein-L-isoaspartate (D-aspartate) Domain annotation for each sequence (and alignments): >> tr|S4RYQ4|S4RYQ4_PETMA NOP2 nucleolar protein homolog (yeast) OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.0 0.0 1.2e-81 2.4e-78 1 200 [] 187 395 .. 187 395 .. 0.94 Alignments for each domain: == domain 1 score: 262.0 bits; conditional E-value: 1.2e-81 HHHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE CS Methyltr_RsmB-F 1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 +++Lapqe+e++lD+caaPGgKT++ a+lm+n+g +vA+d+n+eRlk+v+ nl+rLgvtn iv+++D+r kv++g fDr+LlDa tr|S4RYQ4|S4RYQ4_PETMA 187 VMALAPQENEKLLDMCAAPGGKTSYAAQLMRNTGAIVANDVNSERLKSVVGNLHRLGVTNSIVCNYDGRALAKVMSG--FDRVLLDA 271 589*************************************************************************9..******** PP --CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTS CS Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsep 170 PCsgtg+i++dp+vk++++ekdi ++a+lqk+ll +aid l +gG+lvY+TCsv+veEne+v+++aL+kr +v+lv+t l tr|S4RYQ4|S4RYQ4_PETMA 272 PCSGTGIISKDPSVKTSKDEKDILRCAHLQKQLLLTAIDCLdaasTTGGFLVYCTCSVTVEENEWVVDYALRKR-NVKLVPTGLDF- 356 *****************************************99999****************************.9******6543. PP TTSSECEEC..............T-EEE-TTTTS.-SEEEEEEE CS Methyltr_RsmB-F 171 kglklgeea..............gtlrllPhtenkdgffiaklk 200 g+e t+r++Pht+n+dgff++k+k tr|S4RYQ4|S4RYQ4_PETMA 357 -----GKEGftrfkerrfhpslkLTRRFYPHTHNMDGFFVSKFK 395 .....3333333445689****99******************96 PP >> tr|S4RYQ5|S4RYQ5_PETMA NOP2 nucleolar protein homolog (yeast) OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.0 0.0 1.2e-81 2.4e-78 1 200 [] 178 386 .. 178 386 .. 0.94 Alignments for each domain: == domain 1 score: 262.0 bits; conditional E-value: 1.2e-81 HHHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE CS Methyltr_RsmB-F 1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 +++Lapqe+e++lD+caaPGgKT++ a+lm+n+g +vA+d+n+eRlk+v+ nl+rLgvtn iv+++D+r kv++g fDr+LlDa tr|S4RYQ5|S4RYQ5_PETMA 178 VMALAPQENEKLLDMCAAPGGKTSYAAQLMRNTGAIVANDVNSERLKSVVGNLHRLGVTNSIVCNYDGRALAKVMSG--FDRVLLDA 262 589*************************************************************************9..******** PP --CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTS CS Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsep 170 PCsgtg+i++dp+vk++++ekdi ++a+lqk+ll +aid l +gG+lvY+TCsv+veEne+v+++aL+kr +v+lv+t l tr|S4RYQ5|S4RYQ5_PETMA 263 PCSGTGIISKDPSVKTSKDEKDILRCAHLQKQLLLTAIDCLdaasTTGGFLVYCTCSVTVEENEWVVDYALRKR-NVKLVPTGLDF- 347 *****************************************99999****************************.9******6543. PP TTSSECEEC..............T-EEE-TTTTS.-SEEEEEEE CS Methyltr_RsmB-F 171 kglklgeea..............gtlrllPhtenkdgffiaklk 200 g+e t+r++Pht+n+dgff++k+k tr|S4RYQ5|S4RYQ5_PETMA 348 -----GKEGftrfkerrfhpslkLTRRFYPHTHNMDGFFVSKFK 386 .....3333333445689****99******************96 PP >> tr|S4RE18|S4RE18_PETMA NOL1/NOP2/Sun domain family, member 6 OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 145.7 0.0 5.2e-46 1e-42 3 168 .. 234 412 .. 232 445 .. 0.88 Alignments for each domain: == domain 1 score: 145.7 bits; conditional E-value: 5.2e-46 HH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC............ CS Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg............ 77 +L+ +++ ++lD+caaPGgKTthia lm ++g+++A+d+ + +++++++n +rL++++++ ++ D ++ g tr|S4RE18|S4RE18_PETMA 234 VLDVRPGLRVLDMCAAPGGKTTHIATLMGDTGEIIALDKTAAKVQKIQNNASRLNLKSIQTFCCDSTQAIAS--Gphtgkgllwwvg 318 688899999********************************************************9998432..2345678999999 PP ......--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-T CS Methyltr_RsmB-F 78 ......elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkre 158 e fDr+LlDaPCs++g ++p + + + ++++++a lq++ll aa++ll++gGvl+Y+TCsv+ +Ene +++ aL++ + tr|S4RE18|S4RE18_PETMA 319 hppfpeEYFDRVLLDAPCSALG---KRPCLGFPASLRQLQSYAPLQRKLLAAAVALLRPGGVLLYTTCSVASAENERQVAWALRTFP 402 *******************987...99************************************************************ PP TEEEESSBST CS Methyltr_RsmB-F 159 dvelvetels 168 + +lv e + tr|S4RE18|S4RE18_PETMA 403 QLHLVAQEPH 412 *999987544 PP >> tr|S4RVL0|S4RVL0_PETMA NOL1/NOP2/Sun domain family, member 4 OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 78.4 0.3 2.2e-25 4.3e-22 2 169 .. 167 343 .. 166 384 .. 0.75 Alignments for each domain: == domain 1 score: 78.4 bits; conditional E-value: 2.2e-25 HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--..........SEEEEES-CCCCHHHHCC. CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt..........ntivleaDarkidkvlgg. 77 l+L+ q + ++lDlcaaPGgKT +++ ++ +++ +d++++R+ r+++ l+ + + v + D+ k + tr|S4RVL0|S4RVL0_PETMA 167 LALDVQLGHRVLDLCAAPGGKTLALLQT-ACCDQLTSNDVSASRTGRLQRVLRTYVPRdaeeagvpagGVSVRTRDGIFWLKSAEEr 252 68999999*******************9.999***********99888877765433312111111223444455554443333336 PP --EEEEEEEE--CCG..GGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEE CS Methyltr_RsmB-F 78 elfDriLlDaPCsgt..gvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162 ++Dr+L+DaPC+ + ++++ r + k+ +ql lq +ll a ++gGv+vYsTCs+ n+ v+e+aL+ + tr|S4RVL0|S4RVL0_PETMA 253 GVYDRVLVDAPCTNDrhSLHEEENNIFSRSRMKERQQLPALQTQLLLLA---CRPGGVVVYSTCSLSQLQNSCVVEAALSLATTNHN 336 79***********852156677788888888999***********9876...59*************************97665555 PP ESSBSTT CS Methyltr_RsmB-F 163 vetelse 169 v+ ++ + tr|S4RVL0|S4RVL0_PETMA 337 VDAQACD 343 5555544 PP >> tr|S4RD16|S4RD16_PETMA NOP2/Sun RNA methyltransferase family member 2 OS=Petromyzon marinus OX=7757 GN=NSUN2 PE=3 SV # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 67.9 0.0 3.5e-22 6.8e-19 2 105 .. 140 271 .. 139 276 .. 0.87 Alignments for each domain: == domain 1 score: 67.9 bits; conditional E-value: 3.5e-22 HHH---TT-EEEECS-TT-HHHHHHHHHTT.......TTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.... CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmk.......nkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.... 77 llL+ +++ ++lD+caaPG+KT+ + e+++ + g ++A+d +++R +++ krL +iv++ Da + tr|S4RD16|S4RD16_PETMA 140 LLLKVEPHHKVLDMCAAPGSKTAQLIEMLHsdmstplPDGFIIANDSDNKRCYLLVHQSKRLHSPCVIVCNHDAGSLPLLQMTpats 226 579999*********************97622222223689********************************99988766656678 PP ..................--EEEEEEEE--CCGGGTTT-TTHHHH. CS Methyltr_RsmB-F 78 ..................elfDriLlDaPCsgtgvirrdpdvklrr 105 fDriL D+PCsg g++r++ dv +++ tr|S4RD16|S4RD16_PETMA 227 aaageaaatataattrrfLRFDRILADVPCSGDGTLRKNIDV-WKK 271 88999**********99889*********************9.554 PP >> tr|S4R5X4|S4R5X4_PETMA Uncharacterized protein OS=Petromyzon marinus OX=7757 PE=3 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 31.3 0.0 5.6e-11 1.1e-07 2 52 .. 127 176 .. 126 201 .. 0.88 Alignments for each domain: == domain 1 score: 31.3 bits; conditional E-value: 5.6e-11 HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHH CS Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaen 52 l+L + +e++lD+caaPGgKT i++ ++ + ++A++ ++ R +r+ tr|S4R5X4|S4R5X4_PETMA 127 LALGVRSGERVLDMCAAPGGKTLGILQC-AQPSLLCANEPDEVRRRRLLLA 176 5788899********************9.778899********99988655 PP >> tr|S4R827|S4R827_PETMA Protein-L-isoaspartate (D-aspartate) O-methyltransferase OS=Petromyzon marinus OX=7757 PE=4 S # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.9 0.0 0.0001 0.2 8 71 .. 80 148 .. 73 174 .. 0.80 2 ? -1.3 0.0 0.55 1.1e+03 122 135 .. 169 182 .. 149 184 .. 0.85 Alignments for each domain: == domain 1 score: 10.9 bits; conditional E-value: 0.0001 TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.....SEEEEES-CCCC CS Methyltr_RsmB-F 8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.....ntivleaDarki 71 e+ +lD+ ++ G T+ ia ++ ++g+v+ +d+ +e +++ ++n+++ + +++++ +D+r+ tr|S4R827|S4R827_PETMA 80 EGASVLDVGSGSGYLTACIARMVGSSGKVFGIDHIQELVDEAIKNVNKDDMSllssgQVTLVVGDGRQG 148 56789******************************9999999998887444333444778888888876 PP == domain 2 score: -1.3 bits; conditional E-value: 0.55 HHHHHHEEEEEEEE CS Methyltr_RsmB-F 122 saaidllkkgGvlv 135 +a+id+lk+gG l+ tr|S4R827|S4R827_PETMA 169 QALIDQLKPGGRLI 182 7899*******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (200 nodes) Target sequences: 13539 (5048892 residues searched) Passed MSV filter: 343 (0.0253342); expected 270.8 (0.02) Passed bias filter: 259 (0.0191299); expected 270.8 (0.02) Passed Vit filter: 21 (0.00155107); expected 13.5 (0.001) Passed Fwd filter: 7 (0.000517025); expected 0.1 (1e-05) Initial search space (Z): 13539 [actual number of targets] Domain search space (domZ): 7 [number of targets reported over threshold] # CPU time: 0.10u 0.00s 00:00:00.10 Elapsed: 00:00:00.04 # Mc/sec: 25244.46 // [ok]