# 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/Pan_troglodytes.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.5e-30 106.6 0.0 3.8e-30 105.3 0.0 1.7 2 tr|H2Q1D3|H2Q1D3_PANTR TAR (HIV-1) RNA binding protein 1 OS=
3.8e-28 98.8 0.0 5.1e-28 98.4 0.0 1.2 1 tr|H2R9M4|H2R9M4_PANTR MRM1 isoform 1 OS=Pan troglodytes OX=
1.8e-21 77.1 0.0 5.2e-20 72.4 0.0 2.2 1 tr|K7CMU7|K7CMU7_PANTR MRM3 isoform 1 OS=Pan troglodytes OX=
------ inclusion threshold ------
0.016 15.7 0.1 0.021 15.3 0.1 1.1 1 tr|G2HEE7|G2HEE7_PANTR DNA polymerase epsilon 3, accessory s
Domain annotation for each sequence (and alignments):
>> tr|H2Q1D3|H2Q1D3_PANTR TAR (HIV-1) RNA binding protein 1 OS=Pan troglodytes OX=9598 GN=TARBP1 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.4 0.0 2.2 1.3e+04 54 92 .. 983 1021 .. 974 1030 .. 0.80
2 ! 105.3 0.0 6.7e-34 3.8e-30 2 141 .. 1466 1607 .. 1465 1608 .. 0.92
Alignments for each domain:
== domain 1 score: -3.4 bits; conditional E-value: 2.2
HHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSH CS
SpoU_methylase 54 evlelkvvdsleealkelkeegfalvatslkgkslseid 92
+ +l +++l+++++ + ++++ ++a++ kg+ + +i+
tr|H2Q1D3|H2Q1D3_PANTR 983 SNTQLIFWPNLKAFVQFVFDNKVLTIAAKIKGQAYFKIK 1021
556677899999999999999899999988999998774 PP
== domain 2 score: 105.3 bits; conditional E-value: 6.7e-34
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEE..SSHHHHHHHHCCCTEEEEEESTT CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvv..dsleealkelkeegfalvatslk 84
livv i++p+NlG ++Rt+++fgas lv+ + ++ + ++++++++++a+++l+l++v ++l ++l++ k eg++++++++
tr|H2Q1D3|H2Q1D3_PANTR 1466 LIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC--ISDKQFQHLSVSAEQWLPLVEVkpPQLIDYLQQKKTEGYTIIGVEQT 1548
799***********************7777766666..5*****************888856799*******************6 PP
-SEGC..CSHHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHH CS
SpoU_methylase 85 gksls..eidlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvaill 141
++sl+ ++ ++ek +l++GnE++G++ +l++++d +v+Ip++g ++SLNv+v+ a+l+
tr|H2Q1D3|H2Q1D3_PANTR 1549 ARSLDltQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLI 1607
665555599**********************************************9987 PP
>> tr|H2R9M4|H2R9M4_PANTR MRM1 isoform 1 OS=Pan troglodytes OX=9598 GN=MRM1 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 98.4 0.0 8.8e-32 5.1e-28 2 142 .] 146 301 .. 145 301 .. 0.85
Alignments for each domain:
== domain 1 score: 98.4 bits; conditional E-value: 8.8e-32
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST..T-S CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl..kgk 86
l +vl++i+dp+N+Ga++R+a +g+++++ ++++s +l+p + +++aga ev+++ d+l +l+ ++g+ + +t + +++
tr|H2R9M4|H2R9M4_PANTR 146 LWLVLDGIQDPRNFGAVLRSAHFLGVDKVITSRRNSC-PLTPVVSKSSAGAMEVMDVFSTDDLTGFLQTKAQQGWLVAGTVGcpSTE 231
569****************************987776.***********************************99999998876444 PP
EGC..CS........HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE-....---TTSSS--HHHHHHHHHH CS
SpoU_methylase 87 sls..ei........dlkekvalvfGnEdkGlsnelleladrlvkI....pmsgeveSLNvavAvailly 142
+ + ei ++++++lv+GnE++Gls+e+ + ++ l++I + eSLNv+vA++ill+
tr|H2R9M4|H2R9M4_PANTR 232 DPQssEIpimsclefLWERPTLLVLGNEGSGLSQEVQASCQLLLTIlprrQLPPGLESLNVSVAAGILLH 301
444343333333333666***********************999995443346788***********985 PP
>> tr|K7CMU7|K7CMU7_PANTR MRM3 isoform 1 OS=Pan troglodytes OX=9598 GN=MRM3 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 72.4 0.0 9e-24 5.2e-20 2 142 .] 210 400 .. 209 400 .. 0.83
Alignments for each domain:
== domain 1 score: 72.4 bits; conditional E-value: 9e-24
EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST....T CS
SpoU_methylase 2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl....k 84
l +++++++dpgNlG+i+R+a+ +g+s+++l+k ++d ++p+++ra++ga++ +++ ++e + + l ++++++++
tr|K7CMU7|K7CMU7_PANTR 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK-GCVDAWEPKVLRAGMGAHFRMPIINNLEWETVPNYLPPD-TRVYVADNcglyA 294
6799***************************88.**********************99999****99999999.99*9999976642 PP
-SEGC.CS................HHH............................TTEEEEEEBTTTBS-HHHHCTSS....EEEE- CS
SpoU_methylase 85 gksls.ei................dlk............................ekvalvfGnEdkGlsnellelad....rlvkI 122
+ ++s ++ + ++a+v+G E+ G+s e l+la+ + + I
tr|K7CMU7|K7CMU7_PANTR 295 QAEMSnKAsdhgwvcdqrvmkfhkY-EeeedvetgasqdwlphvevqsydsdwteAPAAVVIGGETYGVSLESLQLAEstggKRLLI 380
2233333356677776666666650.15556666677777777788888899999********************99955556899* PP
---TTSSS--HHHHHHHHHH CS
SpoU_methylase 123 pmsgeveSLNvavAvailly 142
p+ + v+SLN a+A++ill+
tr|K7CMU7|K7CMU7_PANTR 381 PVVPGVDSLNSAMAASILLF 400
*****************985 PP
>> tr|G2HEE7|G2HEE7_PANTR DNA polymerase epsilon 3, accessory subunit OS=Pan troglodytes OX=9598 GN=POLE3 PE=2 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 15.3 0.1 3.7e-06 0.021 8 89 .. 22 102 .. 16 118 .. 0.84
Alignments for each domain:
== domain 1 score: 15.3 bits; conditional E-value: 3.7e-06
S-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC CS
SpoU_methylase 8 eiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatslkgksls 89
+ d N+++ aR+a as vl ++ +a+ + + kr +++a +vl + + ++++++++ lke+ ++ + +++kgk+
tr|G2HEE7|G2HEE7_PANTR 22 ALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVLSAMEEMEFQRFVTPLKEA-LEAYRREQKGKKEA 102
55667799999****9999999*********************************************.*****999665433 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (142 nodes)
Target sequences: 23008 (11942255 residues searched)
Passed MSV filter: 416 (0.0180807); expected 460.2 (0.02)
Passed bias filter: 387 (0.0168202); expected 460.2 (0.02)
Passed Vit filter: 33 (0.00143428); expected 23.0 (0.001)
Passed Fwd filter: 4 (0.000173853); expected 0.2 (1e-05)
Initial search space (Z): 23008 [actual number of targets]
Domain search space (domZ): 4 [number of targets reported over threshold]
# CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.08
# Mc/sec: 21197.50
//
[ok]