# 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/Ciona_intestinalis.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.7e-74 249.7 0.2 4.8e-74 248.2 0.0 1.8 2 tr|H2XZT6|H2XZT6_CIOIN Uncharacterized protein OS=Ciona inte
2.9e-39 134.7 0.0 1.4e-38 132.4 0.0 2.1 1 tr|F6XKA2|F6XKA2_CIOIN Uncharacterized protein OS=Ciona inte
2.7e-34 118.4 0.1 4.5e-34 117.7 0.1 1.3 1 tr|H2XZ35|H2XZ35_CIOIN Uncharacterized protein OS=Ciona inte
5.3e-31 107.7 0.1 8.6e-31 107.0 0.1 1.3 1 tr|H2XS72|H2XS72_CIOIN Uncharacterized protein OS=Ciona inte
3e-16 59.6 0.0 4.6e-16 59.0 0.0 1.3 1 tr|F6ZY66|F6ZY66_CIOIN Uncharacterized protein OS=Ciona inte
1.1e-14 54.4 0.0 1.5e-14 54.0 0.0 1.5 1 tr|F7AFH3|F7AFH3_CIOIN Uncharacterized protein OS=Ciona inte
6.2e-05 22.6 0.0 0.00011 21.8 0.0 1.4 1 tr|F6QVW6|F6QVW6_CIOIN Uncharacterized protein OS=Ciona inte
------ inclusion threshold ------
0.018 14.6 0.0 0.041 13.4 0.0 1.5 1 tr|F6TIA8|F6TIA8_CIOIN Uncharacterized protein OS=Ciona inte
0.025 14.1 0.0 0.041 13.4 0.0 1.3 1 tr|F7A5J2|F7A5J2_CIOIN rRNA 2'-O-methyltransferase fibrillar
Domain annotation for each sequence (and alignments):
>> tr|H2XZT6|H2XZT6_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.4 0.2 1.5 2.8e+03 97 129 .. 37 71 .. 32 106 .. 0.68
2 ! 248.2 0.0 2.6e-77 4.8e-74 1 200 [] 380 588 .. 380 588 .. 0.94
Alignments for each domain:
== domain 1 score: -2.4 bits; conditional E-value: 1.5
T-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE..E CS
Methyltr_RsmB-F 97 rdpdvklrrkekdiaqlaklqkellsaaidll..k 129
++p+ k++ + k a+ l+k+ll+++++ k
tr|H2XZT6|H2XZT6_CIOIN 37 QEPNKKISSRAKVRAKKRDLKKQLLTSLVEAKaeK 71
56666777777777777889999999988765333 PP
== domain 2 score: 248.2 bits; conditional E-value: 2.6e-77
HHHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE CS
Methyltr_RsmB-F 1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87
+++Lapq++e++lD+caaPGgKTt+ia+lmkn+g ++ +d+nk Rlk+v+ n++r+gv n ++++Dar +++++g+ f r+LlDa
tr|H2XZT6|H2XZT6_CIOIN 380 VMALAPQPGERVLDMCAAPGGKTTYIAQLMKNSGFIFVNDINKARLKAVVGNMHRMGVSNSVISNYDARSFPTIMGN--FSRVLLDA 464
589*************************************************************************8..******** PP
--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTS CS
Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsep 170
PCsgtgvi++dp+vk++++++di+++++lqkel+ aaid+ ++gG++vY+TCsv veEneev+++aLkkr +v+lv+t l+ +
tr|H2XZT6|H2XZT6_CIOIN 465 PCSGTGVISKDPSVKTSKDDSDITKCSHLQKELILAAIDSCnaqaQNGGYIVYCTCSVMVEENEEVVNYALKKR-NVKLVQTGLEFG 550
****************************************999999***************************9.9******66544 PP
TTSSECEEC........T-EEE-TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 171 kglklgeea........gtlrllPhtenkdgffiaklk 200
++ ++ + +t+r++Ph++n+dgff+ak+k
tr|H2XZT6|H2XZT6_CIOIN 551 VEGFCKYRQyrfhpslkQTRRFYPHSHNMDGFFVAKFK 588
433333333789999999******************96 PP
>> tr|F6XKA2|F6XKA2_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 132.4 0.0 7.8e-42 1.4e-38 2 200 .] 136 392 .. 135 392 .. 0.92
Alignments for each domain:
== domain 1 score: 132.4 bits; conditional E-value: 7.8e-42
HHH---TT-EEEECS-TT-HHHHHHHHHTTT.......TSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.... CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmkn.......kgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.... 77
llL+ + + ++lD+caaPG+KT+ i el++ +g vA+d++++R +++ + rL +t +++ Da++++++ +
tr|F6XKA2|F6XKA2_CIOIN 136 LLLDVHSHHKVLDMCAAPGSKTAQIVELLHRdennsipEGICVANDKDNKRCYMLVHQIGRLHSPSTLIVNHDASNFPEIFIKnddg 222
57999***********************76412222225678*************************************99888999 PP
....--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-.TT CS
Methyltr_RsmB-F 78 ....elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkr.ed 159
+DriL D+PCsg g++r++ dv ++ ++++ ++l++ q ++l ++ll +gG lvYsTCs+++ E+e+v+++a+++
tr|F6XKA2|F6XKA2_CIOIN 223 kdilLRYDRILCDVPCSGDGTMRKNTDVWVKWNQANAIYLHRTQYRILLRGLELLASGGQLVYSTCSLNPIEDEAVVAAAIHHCgGA 309
999889**********************9999999********************************************99986258 PP
EEEESSBSTTSTTSSECEEC...........................................T-EEE-TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 160 velvetelsepkglklgeea...........................................gtlrllPhtenkdgffiaklk 200
velv+++l + + + g+ + +rllPh++++ gff+a l+
tr|F6XKA2|F6XKA2_CIOIN 310 VELVSVSLPG-LKWSPGVSSwrvmdsdmnwydthdqvpekkknisysmfppggqdvmeamhleRCMRLLPHQQDTGGFFVAVLR 392
99***98887.777788888999**************************************99999***************885 PP
>> tr|H2XZ35|H2XZ35_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 117.7 0.1 2.5e-37 4.5e-34 2 199 .. 207 410 .. 206 411 .. 0.82
Alignments for each domain:
== domain 1 score: 117.7 bits; conditional E-value: 2.5e-37
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87
+L+p ++ +++D+caaPG KT+h++++m+n+g+++A+d+++eR++ +++ lk+ +v+n v++ D + + + ++++ iL+D
tr|H2XZ35|H2XZ35_CIOIN 207 FVLNPSPNSHVIDACAAPGNKTSHLSAIMNNTGKLFAIDRSSERIEVMKKQLKKASVKNCEVINSDFLILKPTDEKfKQVEYILVDP 293
69****************************************************************97775555555789******* PP
--CCGGGTTT-TTH...HHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESS..BSTT CS
Methyltr_RsmB-F 88 PCsgtgvirrdpdv...klrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvet..else 169
C+g g+i+r+ + k ++ k + +l+k q ++l+ a+ + +vYsTCs++ eEne ++ a +++ + l+++ ++++
tr|H2XZ35|H2XZ35_CIOIN 294 SCTGSGIISRQLEHteeKDSKCSKRLESLSKFQLKVLNHALSFP-NVKRVVYSTCSIHEEENELIVKLAVEQNSNFDLKKVlpKWHN 379
**********7665111556666777778888888888776543.33469*************************999987334444 PP
STTS.SECEECT-EEE-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 170 pkgl.klgeeagtlrllPhtenkdgffiakl 199
+ + + ++ +r P+ + ++gff+a +
tr|H2XZ35|H2XZ35_CIOIN 380 RGLIsDSFNAEKCVRCDPNVDFTNGFFVALF 410
33220222333699**************987 PP
>> tr|H2XS72|H2XS72_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 107.0 0.1 4.6e-34 8.6e-31 2 171 .. 155 335 .. 154 373 .. 0.86
Alignments for each domain:
== domain 1 score: 107.0 bits; conditional E-value: 4.6e-34
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH.....HTT--.SEEEEES-CCCCHHHHCC--EEE CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk.....rLgvt.ntivleaDarkidkvlggelfDr 82
l L+pq+++ ilD+c+aPGgK +++ + ++g++vA+d+n++R+ rv++ k +++v+ +++++ Da++ ++ ++ +D+
tr|H2XS72|H2XS72_CIOIN 155 LSLDPQPGDSILDMCSAPGGKLNVMMQAIGDSGRIVANDINTKRVTRVKNVYKeyipkQFSVEkFVKIVKFDATQWTEIETE-AYDK 240
679******************************************9999876511111566664589*********888885.9999 PP
E.EEEE--C....CGGGTTT-TT.HHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEE CS
Methyltr_RsmB-F 83 i.LlDaPCs....gtgvirrdpd.vklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelv 163
+ L+D+PC+ ++ v +r+ d + + ++++ aql +lq +ll+ ai +++G++vYsTC+ + ne v+++a ++ d +++
tr|H2XS72|H2XS72_CIOIN 241 VvLVDVPCTndrhSLYVSDRETDnIFSTLRKRERAQLPHLQCQLLKNAILACRPNGTIVYSTCTASPLQNEFVVQYAVQELMDQHSI 327
5489****93333467888887636566677889***********************************************999999 PP
SSBSTTST CS
Methyltr_RsmB-F 164 etelsepk 171
+ e+++++
tr|H2XS72|H2XS72_CIOIN 328 SCEVQNTR 335
99888754 PP
>> tr|F6ZY66|F6ZY66_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 59.0 0.0 2.5e-19 4.6e-16 3 56 .. 187 240 .] 185 240 .] 0.96
Alignments for each domain:
== domain 1 score: 59.0 bits; conditional E-value: 2.5e-19
HH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHT CS
Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrL 56
+L+pqe++ +lD+caaPGgKT+hi l++ +g++vAvd+++++++++++n +L
tr|F6ZY66|F6ZY66_CIOIN 187 VLNPQEGDIVLDMCAAPGGKTSHIVSLLRGRGRLVAVDRSSSKVEKIKQNAAKL 240
8*************************************************9876 PP
>> tr|F7AFH3|F7AFH3_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 54.0 0.0 8.1e-18 1.5e-14 108 185 .. 2 75 .. 1 136 [. 0.87
Alignments for each domain:
== domain 1 score: 54.0 bits; conditional E-value: 8.1e-18
CHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEECT-EEE- CS
Methyltr_RsmB-F 108 kdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeeagtlrll 185
k+i+++ lq++l+++a+ llk+gG+lvYsTC+ +v+Ene +e aL k++ +l++ p++ +g+++ +l
tr|F7AFH3|F7AFH3_CIOIN 2 KNIKSYPALQRQLFNTAVRLLKPGGTLVYSTCTTTVDENEGLVEWALDKHPCLKLSQH---TPHIGGTGRQE-VTNLS 75
68999************************************************99987...34455555555.44444 PP
>> tr|F6QVW6|F6QVW6_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=3 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 21.8 0.0 6.1e-08 0.00011 4 92 .. 13 104 .. 10 118 .. 0.86
Alignments for each domain:
== domain 1 score: 21.8 bits; conditional E-value: 6.1e-08
H---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.....--EEEEEE CS
Methyltr_RsmB-F 4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.....elfDriLl 85
L+ + ++ i+D+ + Gg T +i+e ++ +v+A+d++++ + ++ k++ + +i l + ++ dk l++ + + +Ll
tr|F6QVW6|F6QVW6_CIOIN 13 LNIKRGDVIIDMTFGAGGHTKFIMEN-YKHCKVIALDRDEKAFEIAQDLSKKFKGR-IIPLLGKFSELDKLLSEngiveNSLNAALL 97
89999********************8.6678899****998777666666666666.888999999999999998898899****** PP
EE--CCG CS
Methyltr_RsmB-F 86 DaPCsgt 92
Da Cs++
tr|F6QVW6|F6QVW6_CIOIN 98 DAGCSSM 104
*****86 PP
>> tr|F6TIA8|F6TIA8_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.4 0.0 2.2e-05 0.041 7 73 .. 330 395 .. 325 413 .. 0.88
Alignments for each domain:
== domain 1 score: 13.4 bits; conditional E-value: 2.2e-05
-TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHH CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidk 73
+e++ ++D c++ G +a+l + +++ v++++e l+r ++ ++ L+++n+++ + + ++ k
tr|F6TIA8|F6TIA8_CIOIN 330 EEGDVLVDFCSGGGHVGIVLAHL-LPLCKIILVENKEESLERAMQRIQELNLKNIMIYQCNLDQFMK 395
688999****9988888888888.67889999**************************999988855 PP
>> tr|F7A5J2|F7A5J2_CIOIN rRNA 2'-O-methyltransferase fibrillarin isoform X1 OS=Ciona intestinalis OX=7719 GN=LOC100186
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.4 0.0 2.2e-05 0.041 6 87 .. 144 224 .. 140 235 .. 0.78
Alignments for each domain:
== domain 1 score: 13.4 bits; conditional E-value: 2.2e-05
--TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS
Methyltr_RsmB-F 6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87
+++ ++l l aa G +h+++++ ++g v+Av+ +++ + +++ k+ tn+i + Dar+++k+ ++D i D+
tr|F7A5J2|F7A5J2_CIOIN 144 IKPGSKVLYLGAASGTTVSHVSDIVGPEGLVYAVEFSHRSGRDLINVAKK--RTNIIPIIEDARHPHKYRMLvGMVDTIFADV 224
567788999**************************987665555544433..3456777889999988754335788887775 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (200 nodes)
Target sequences: 16678 (5370518 residues searched)
Passed MSV filter: 580 (0.0347764); expected 333.6 (0.02)
Passed bias filter: 400 (0.0239837); expected 333.6 (0.02)
Passed Vit filter: 39 (0.00233841); expected 16.7 (0.001)
Passed Fwd filter: 9 (0.000539633); expected 0.2 (1e-05)
Initial search space (Z): 16678 [actual number of targets]
Domain search space (domZ): 9 [number of targets reported over threshold]
# CPU time: 0.11u 0.00s 00:00:00.11 Elapsed: 00:00:00.04
# Mc/sec: 26852.59
//
[ok]