# 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/SpoU_methylase.hmm.txt
# target sequence database: proteomes/Danio_rerio.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: SpoU_methylase [M=142]
Accession: PF00588.18
Description: SpoU rRNA Methylase family
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1e-30 107.3 0.0 3.7e-30 105.5 0.0 2.0 1 tr|F1R356|F1R356_DANRE Si:dkey-85a20.4 OS=Danio rerio OX=795
1.7e-30 106.5 0.0 2e-30 106.3 0.0 1.1 1 tr|F1QG96|F1QG96_DANRE Mitochondrial rRNA methyltransferase
9.1e-24 84.8 0.0 3.8e-23 82.7 0.0 1.9 1 sp|Q566V3|MRM3A_DANRE rRNA methyltransferase 3A, mitochondr
5.5e-23 82.2 0.0 9e-21 75.0 0.0 2.5 1 sp|A1L2E4|MRM3B_DANRE rRNA methyltransferase 3B, mitochondr
------ inclusion threshold ------
0.11 13.2 0.1 0.14 12.8 0.1 1.2 1 tr|Q6PBL4|Q6PBL4_DANRE Polymerase (DNA directed), epsilon 3
0.26 11.9 0.0 3.2 8.4 0.0 2.2 2 tr|Q66ID3|Q66ID3_DANRE SPOUT domain-containing methyltransfe
Domain annotation for each sequence (and alignments):
>> tr|F1R356|F1R356_DANRE Si:dkey-85a20.4 OS=Danio rerio OX=7955 GN=si:dkey-85a20.4 PE=1 SV=4
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 105.5 0.0 8.7e-34 3.7e-30 2 140 .. 1424 1564 .. 1423 1565 .. 0.94
Alignments for each domain:
== domain 1 score: 105.5 bits; conditional E-value: 8.7e-34
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEEST. CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatsl. 83
l vv i++p+NlG ++Rt+++fga++lvl + r+ ++++++++++++++ +l++ +v ++l+++l+ k eg++++++++
tr|F1R356|F1R356_DANRE 1424 LLVVASLIDKPTNLGGLCRTCEIFGAKALVLDSLRH--VNDKQFQALSVSSELWLPMMEVkpAELSDFLQLKKSEGYWVIGVEQt 1506
6799999************************66666..59****************888856799*****************998 PP
.T-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHH CS
SpoU_methylase 84 .kgkslseidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvail 140
+++sl++++++ek +l++GnE++G++ ++l+l+d +v+Ip+ g ++SLNv+v++a+l
tr|F1R356|F1R356_DANRE 1507 sNSQSLQDYTFPEKSLLLLGNEREGIPANVLQLLDVCVEIPQFGVTRSLNVHVSAALL 1564
8999999************************************************985 PP
>> tr|F1QG96|F1QG96_DANRE Mitochondrial rRNA methyltransferase 1 homolog (S. cerevisiae) OS=Danio rerio OX=7955 GN=mrm1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 106.3 0.0 4.8e-34 2e-30 2 142 .] 37 188 .. 36 188 .. 0.90
Alignments for each domain:
== domain 1 score: 106.3 bits; conditional E-value: 4.8e-34
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-S CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl..kgk 86
l +vl++++dp+NlGai+R+a+ +g++++v + ++s +l+p++ +a+ag ev+++ ++l++++k eeg+++v+t + +g+
tr|F1QG96|F1QG96_DANRE 37 LWLVLDGVQDPMNLGAILRSAYYLGVDRIVSSINNSC-PLTPTVSKASAGVMEVMDVFGCSNLKRMIKVKVEEGWQVVGTVGleEGS 122
679***************************9887777.9*****************************************8876444 PP
EGC......CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE--....--TTSSS--HHHHHHHHHH CS
SpoU_methylase 87 sls......eidlkekvalvfGnEdkGlsnelleladrlvkIp....msgeveSLNvavAvailly 142
s s +++++++++l++G E++Gls el++l+d l++Ip m++ veSLNv+vA++ill+
tr|F1QG96|F1QG96_DANRE 123 SQSnvlscsDFKMSRPTLLLMGGEGDGLSSELRQLCDVLITIPprrhMHPGVESLNVSVATGILLH 188
33323445577888****************************98888899*************985 PP
>> sp|Q566V3|MRM3A_DANRE rRNA methyltransferase 3A, mitochondrial OS=Danio rerio OX=7955 GN=mrm3a PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 82.7 0.0 9e-27 3.8e-23 2 142 .] 229 413 .. 228 413 .. 0.85
Alignments for each domain:
== domain 1 score: 82.7 bits; conditional E-value: 9e-27
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89
l++++++++d+gNlG+i+R+a+a+g ++++l+k ++d ++p+++r+a+ga++ l++ +++++ k+l ++ + + +++++++s++
sp|Q566V3|MRM3A_DANRE 229 LFLICDNVRDAGNLGTILRCAAAAGGDRVLLSK-GCVDAWEPKVLRSAMGAHFRLPVFPNLDWDDISKHLPKN-VIVHVADNYSTSTK 314
7899***************************76.*************************************99.88888888888888 PP
CS.................HHH..........................TTEEEEEEBTTTBS-HHHHCTSS....EEEE----TTSSS CS
SpoU_methylase 90 ei.................dlk..........................ekvalvfGnEdkGlsnellelad....rlvkIpmsgeveS 130
++ + + +++alv+G E++Gls e+l+la+ + + +pm++ veS
sp|Q566V3|MRM3A_DANRE 315 QLvsgqtenvssddysesdS-DddddeeededslphvkpqvyhecwaqRSAALVIGGETHGLSVEALRLAEetdgKRLFVPMAPGVES 401
66666666666665555550.0555556667777788888999999999******************9887433558*********** PP
--HHHHHHHHHH CS
SpoU_methylase 131 LNvavAvailly 142
LN a+A++ill+
sp|Q566V3|MRM3A_DANRE 402 LNSAMAAGILLF 413
*********985 PP
>> sp|A1L2E4|MRM3B_DANRE rRNA methyltransferase 3B, mitochondrial OS=Danio rerio OX=7955 GN=rnmtl1b PE=2 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 75.0 0.0 2.1e-24 9e-21 2 142 .] 231 431 .. 230 431 .. 0.82
Alignments for each domain:
== domain 1 score: 75.0 bits; conditional E-value: 2.1e-24
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89
l+++++ ++dpgNlG+++R+a+a+g++ ++l+k ++d+++ +++raa+ga++ l++ ++ ++ ++l ++ ++ +++++++++
sp|A1L2E4|MRM3B_DANRE 231 LTLICDTVRDPGNLGSVLRSAAAAGCHSVLLTK-GCVDIWELKVLRAAMGAHFRLPIIPNLTWTDISNHLPKT-STVHVADNHSTTMG 316
7899***************************88.*************************************99.67766666666555 PP
CS......................HHH.....................................TTEEEEEEBTTTBS-HHHHCTSS. CS
SpoU_methylase 90 ei......................dlk.....................................ekvalvfGnEdkGlsnellelad. 117
+ + +++ l++G E++Gls+e+l+la+
sp|A1L2E4|MRM3B_DANRE 317 KHndnttpqkhrrpsdygwvkghqY-QskahddddandlcsledycdensksletqlyytdwvaGHTSLIIGGETHGLSREALQLAEr 403
3333344555566666666666650.1556666666677777777788888889999999999*********************9994 PP
...EEEE----TTSSS--HHHHHHHHHH CS
SpoU_methylase 118 ...rlvkIpmsgeveSLNvavAvailly 142
r + Ipm v+SLN a A+++ll+
sp|A1L2E4|MRM3B_DANRE 404 tsgRRLLIPMVDGVDSLNSAIAAGVLLF 431
3344899******************985 PP
>> tr|Q6PBL4|Q6PBL4_DANRE Polymerase (DNA directed), epsilon 3 (p17 subunit) OS=Danio rerio OX=7955 GN=pole3 PE=1 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.8 0.1 3.3e-05 0.14 13 86 .. 27 99 .. 16 116 .. 0.82
Alignments for each domain:
== domain 1 score: 12.8 bits; conditional E-value: 3.3e-05
HHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-S CS
SpoU_methylase 13 gNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgk 86
N+++ aR a as vl ++ +a+ + +akr +++a +v+ + + +++e++l+ l+e+ ++ + +kgk
tr|Q6PBL4|Q6PBL4_DANRE 27 VNVSKEARRAISQAASVFVLYATSCANSFAMKAKRKTLNAGDVMSAMEEMEFERFLQPLREA-LEAYKKGQKGK 99
5888888888888899999999***************************************9.77776666444 PP
>> tr|Q66ID3|Q66ID3_DANRE SPOUT domain-containing methyltransferase 1 OS=Danio rerio OX=7955 GN=spout1 PE=1 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 8.4 0.0 0.00075 3.2 16 40 .. 101 125 .. 100 161 .. 0.72
2 ? 0.8 0.0 0.17 7.1e+02 69 102 .. 278 315 .. 253 331 .. 0.81
Alignments for each domain:
== domain 1 score: 8.4 bits; conditional E-value: 0.00075
HHHHHHHHHTT-SEEEEESGSSCTC CS
SpoU_methylase 16 GaiaRtakafgaselvlvkprsadl 40
G iaR++++f ++e+v+ ++ ++d
tr|Q66ID3|Q66ID3_DANRE 101 GQIARACAVFCVDEVVIFDELGEDA 125
99***************99866654 PP
== domain 2 score: 0.8 bits; conditional E-value: 0.17
HHHCCC.TEEE.EEESTT-SEGCCSHHH..TTEEEEEE CS
SpoU_methylase 69 kelkee.gfal.vatslkgkslseidlk..ekvalvfG 102
+e+ + g++l ++ts+kg++++ ++l+ +++++vfG
tr|Q66ID3|Q66ID3_DANRE 278 SECPYKeGYDLtIGTSEKGQNTDHVTLPafRHMLVVFG 315
55554436777588999***999998888899999999 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (142 nodes)
Target sequences: 25687 (13798380 residues searched)
Passed MSV filter: 591 (0.0230077); expected 513.7 (0.02)
Passed bias filter: 528 (0.0205551); expected 513.7 (0.02)
Passed Vit filter: 35 (0.00136256); expected 25.7 (0.001)
Passed Fwd filter: 6 (0.000233581); expected 0.3 (1e-05)
Initial search space (Z): 25687 [actual number of targets]
Domain search space (domZ): 6 [number of targets reported over threshold]
# CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.08
# Mc/sec: 24492.12
//
[ok]