# 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]