# 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/Strongylocentrotus_purpuratus.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.4e-74 250.7 0.0 2.7e-74 249.8 0.0 1.5 1 tr|W4Y3J6|W4Y3J6_STRPU Uncharacterized protein OS=Strongyloc
1.9e-33 116.5 0.0 5.7e-33 114.9 0.0 1.8 2 tr|W4XEF7|W4XEF7_STRPU Uncharacterized protein OS=Strongyloc
1.3e-30 107.3 0.5 3.1e-30 106.0 0.0 1.9 2 tr|W4XRY6|W4XRY6_STRPU Uncharacterized protein OS=Strongyloc
1.1e-27 97.6 0.1 1.3e-27 97.4 0.1 1.0 1 tr|H3HGK6|H3HGK6_STRPU Uncharacterized protein OS=Strongyloc
1.2e-23 84.4 0.0 1.9e-23 83.8 0.0 1.2 1 tr|W4XX51|W4XX51_STRPU Uncharacterized protein OS=Strongyloc
2.6e-06 27.9 0.1 4.1e-06 27.2 0.1 1.3 1 tr|W4YR02|W4YR02_STRPU Uncharacterized protein OS=Strongyloc
3.3e-06 27.5 0.0 0.13 12.5 0.0 2.4 2 tr|W4Y7A2|W4Y7A2_STRPU Uncharacterized protein OS=Strongyloc
0.00024 21.5 0.3 0.0031 17.8 0.3 2.2 1 tr|W4X9M2|W4X9M2_STRPU Uncharacterized protein OS=Strongyloc
------ inclusion threshold ------
0.018 15.4 0.0 0.027 14.8 0.0 1.2 1 tr|W4XVH0|W4XVH0_STRPU Uncharacterized protein OS=Strongyloc
0.033 14.5 0.0 0.058 13.7 0.0 1.4 1 tr|W4ZAS4|W4ZAS4_STRPU Uncharacterized protein OS=Strongyloc
Domain annotation for each sequence (and alignments):
>> tr|W4Y3J6|W4Y3J6_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 249.8 0.0 9.3e-78 2.7e-74 1 200 [] 697 905 .. 697 905 .. 0.94
Alignments for each domain:
== domain 1 score: 249.8 bits; conditional E-value: 9.3e-78
HHHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE CS
Methyltr_RsmB-F 1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87
+++Lap+e+e+ilD+ca+PG+KTt+ia+lmkn+g ++A+dank+R+++++ nl+r g+tnt +++ D++ ++kv+gg fDr+LlDa
tr|W4Y3J6|W4Y3J6_STRPU 697 VMALAPHEGEKILDMCASPGSKTTYIAALMKNTGMLFANDANKKRVSALVGNLHRCGITNTVICNEDGKSFPKVMGG--FDRVLLDA 781
589*************************************************************************9..******** PP
--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTS CS
Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsep 170
PCsgtgvi +d +vkl+++e di+++++lqkel+ aaid++ k+gG+lvYsTCs+ veEne+v+++aLkkr +v+lv+t +
tr|W4Y3J6|W4Y3J6_STRPU 782 PCSGTGVIAKDTAVKLSKDEGDIQRCSHLQKELILAAIDSIdansKTGGYLVYSTCSIMVEENEWVVDYALKKR-NVRLVPTGIDF- 866
*************************************************************************9.9******5543. PP
TTSSECEEC..............T-EEE-TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 171 kglklgeea..............gtlrllPhtenkdgffiaklk 200
g++ +r++Pht+n+dgf+ aklk
tr|W4Y3J6|W4Y3J6_STRPU 867 -----GQDGfsrfkarhfhpslkLSRRIYPHTHNMDGFYFAKLK 905
.....33323333357899999999*****************96 PP
>> tr|W4XEF7|W4XEF7_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -3.5 0.0 3.8 1.1e+04 4 17 .. 91 104 .. 90 105 .. 0.89
2 ! 114.9 0.0 2e-36 5.7e-33 21 167 .. 224 381 .. 217 434 .. 0.86
Alignments for each domain:
== domain 1 score: -3.5 bits; conditional E-value: 3.8
H---TT-EEEECS- CS
Methyltr_RsmB-F 4 LapqeeetilDlca 17
L+p +e i+Dl++
tr|W4XEF7|W4XEF7_STRPU 91 LKPDSKEVIVDLAC 104
8999*******998 PP
== domain 2 score: 114.9 bits; conditional E-value: 2e-36
HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC..............--EEEEEEEE--CCGG CS
Methyltr_RsmB-F 21 gKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg..............elfDriLlDaPCsgtg 93
gKTthia lmk++g+v+A+d+ ++++ r+++ L +t + Da+k ++ +fDriLlDaPCsg+g
tr|W4XEF7|W4XEF7_STRPU 224 GKTTHIATLMKDQGRVIALDKASKKIARIEAYAAALHLTCIRAYYFDATKACASESEilkgkedfhppfpeMTFDRILLDAPCSGLG 310
9**************************************9999999*999877666677789********999************98 PP
GTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBS CS
Methyltr_RsmB-F 94 virrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetel 167
++p + + + ++++++ lq++l+s+a+ ll++gG+lvYsTC++++eEne ++ aL+k+++++l++ e
tr|W4XEF7|W4XEF7_STRPU 311 ---QRPMIYNKMSLSEVKSYPALQHKLFSSAVRLLREGGTLVYSTCTITPEENEGLVAWALQKHPQMKLEKQEP 381
...78999999999*******************************************************98753 PP
>> tr|W4XRY6|W4XRY6_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 106.0 0.0 1.1e-33 3.1e-30 2 199 .. 243 452 .. 242 453 .. 0.87
2 ? -2.4 0.3 1.8 5.1e+03 144 168 .. 540 564 .. 518 584 .. 0.59
Alignments for each domain:
== domain 1 score: 106.0 bits; conditional E-value: 1.1e-33
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87
++L +++ +++D+c+aPG KT+h+a l++n ++++ d + +R++ +++ l+r gv ++ ++ D +d + + ++ ++D
tr|W4XRY6|W4XRY6_STRPU 243 YVLSAKPGSHVIDACSAPGNKTSHMASLLRNDAKIYSYDLDPKRISVMNTLLERAGVSAAKTIHQDFLTTDPCSKEnMRVEYTIVDP 329
78999*****************************************************************9988886789******* PP
--CCGGGTTT-TTH...HHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTST CS
Methyltr_RsmB-F 88 PCsgtgvirrdpdv...klrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepk 171
Csg g+ +r+ + ++ + + + +l++lq ++l+ a+ + +vYsTCsv+ eEne v+ ++L++ + +lv++ +
tr|W4XRY6|W4XRY6_STRPU 330 SCSGSGMASRKDYLvddDMQEDRARLRSLHQLQCRILTHALSF-PSVRRVVYSTCSVHREENEDVVRTVLEQSDGFRLVPVMQGTWD 415
*******9998766121355566678889999*9*99988753.344579*****************************99655545 PP
TSSECEEC.........T-EEE-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 172 glklgeea.........gtlrllPhtenkdgffiakl 199
+ l++ + +r Pht+ ++gff+a +
tr|W4XRY6|W4XRY6_STRPU 416 RRGLSTSQdgeedhigeCCVRASPHTDLTNGFFVALF 452
4444444455899999999****************87 PP
== domain 2 score: -2.4 bits; conditional E-value: 1.8
TCTHHHHHHHHHH-TTEEEESSBST CS
Methyltr_RsmB-F 144 eEneevieeaLkkredvelvetels 168
+E + ++++ kk+++ + ++ e
tr|W4XRY6|W4XRY6_STRPU 540 DEISDDVKQIKKKHKKSKNESEESD 564
3334444444444544444444444 PP
>> tr|H3HGK6|H3HGK6_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 97.4 0.1 4.5e-31 1.3e-27 76 144 .. 3 73 .. 1 82 [. 0.94
Alignments for each domain:
== domain 1 score: 97.4 bits; conditional E-value: 4.5e-31
CC--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE....EEEEEEEEEES---CT CS
Methyltr_RsmB-F 76 ggelfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidll....kkgGvlvYsTCsvlve 144
gg fDr+LlDaPCsgtgvi +d +vkl+++e di+++++lqkel+ aaid++ k+gG+lvYsTCs+ v
tr|H3HGK6|H3HGK6_STRPU 3 GG--FDRVLLDAPCSGTGVIAKDTAVKLSKDEGDIQRCSHLQKELILAAIDSIdansKTGGYLVYSTCSIMVS 73
55..******************************************************************986 PP
>> tr|W4XX51|W4XX51_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 83.8 0.0 6.7e-27 1.9e-23 2 168 .. 276 448 .. 275 468 .. 0.77
Alignments for each domain:
== domain 1 score: 83.8 bits; conditional E-value: 6.7e-27
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.......SEEEEES-CCCCHHHHCC--EE CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.......ntivleaDarkidkvlggelfD 81
l+++ + ++ +lDlca+PGgK i++ m +t++A+++ +R +r++e l L + + v+ D+ + ++ +D
tr|W4XX51|W4XX51_STRPU 276 LAMDVRTDDVVLDLCAGPGGKSVAILQTM-LISTLTANEKVLSRKRRLQEVLG-LCLPrsirtsgAIRVSGLDGCEWGQIEP-MAYD 359
5678899********************96.56899****98888888877653.2222112233456778888888866655.79** PP
EEEEEE--CCGGGTTT-TT...HHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESS CS
Methyltr_RsmB-F 82 riLlDaPCsgtgvirrdpd...vklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvet 165
++L+D+PCs+ v + d k++r ++ l +lq +ll a ++ +k+gG++vYsTC++ + n v+++a+ + ++ ++t
tr|W4XX51|W4XX51_STRPU 360 KVLVDVPCSTDRVSATQADnnlFKVSR-SRERWDLPELQTDLLCAGLQAVKPGGTVVYSTCTMSPLQNDGVVQNAITRCQEEFNIST 445
**********99987766612234444.4556789****************************************998776655555 PP
BST CS
Methyltr_RsmB-F 166 els 168
++
tr|W4XX51|W4XX51_STRPU 446 SVA 448
555 PP
>> tr|W4YR02|W4YR02_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 27.2 0.1 1.4e-09 4.1e-06 2 33 .. 223 254 .. 222 258 .. 0.89
Alignments for each domain:
== domain 1 score: 27.2 bits; conditional E-value: 1.4e-09
HHH---TT-EEEECS-TT-HHHHHHHHHTTTT CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknk 33
llL+ +++ ++lD+caaPG+KT+ + e+++ +
tr|W4YR02|W4YR02_STRPU 223 LLLQVKPHHKVLDMCAAPGSKTAQLIEMLHAE 254
579999*********************98765 PP
>> tr|W4Y7A2|W4Y7A2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 12.2 0.0 5.7e-05 0.16 11 83 .. 110 180 .. 102 184 .. 0.88
2 ! 12.5 0.0 4.5e-05 0.13 11 83 .. 274 344 .. 265 348 .. 0.86
Alignments for each domain:
== domain 1 score: 12.2 bits; conditional E-value: 5.7e-05
EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEE CS
Methyltr_RsmB-F 11 tilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83
++lD+ ++ G T +a+ ++++ v vd+ ++ +++ ++ +rLg++n+ +++D++ ++++ + +fD++
tr|W4Y7A2|W4Y7A2_STRPU 110 RMLDVGCGAGLATQILAKK-FPESHFVGVDIAQSMVDEANAEATRLGLKNVSYFRVDGSVMPSDWAS-TFDHA 180
68*******9999988887.7888999********************************99887774.78875 PP
== domain 2 score: 12.5 bits; conditional E-value: 4.5e-05
EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEE CS
Methyltr_RsmB-F 11 tilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDri 83
++lD+ ++ G T +a+ ++++ v vd+ ++ +++ ++ +rLg++n+ +++D++ ++++ + +fD++
tr|W4Y7A2|W4Y7A2_STRPU 274 RVLDVGCGAGLATQILAKK-FPESHFVGVDIAQSIVDEANAEATRLGLKNVSYFRVDGSVMPSDWAS-TFDHA 344
59*******9999988887.7888999********************************99887774.78875 PP
>> tr|W4X9M2|W4X9M2_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.8 0.3 1.1e-06 0.0031 7 152 .. 318 479 .. 314 493 .. 0.72
Alignments for each domain:
== domain 1 score: 17.8 bits; conditional E-value: 1.1e-06
-TT-EEEECS-TT-HHHHHHHHH.TTTTSEEEEEES.SCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE--.C CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiael.mknkgtvvAvda.nkeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPC.s 90
+e++ i+ + G T+h+a l ++++ t++A + ++e l+ +++ + +L ++n++ ++ D ++ + + ++++ P s
tr|W4X9M2|W4X9M2_STRPU 318 NEGDDIIHTNVGNGWTTAHLATLtNQDNTTIYAFGIkDDEHLEMLEARMGKLRIHNVKFIREDFLLVQPEDKKYKGVKVMMVTPRdS 404
577888889999999********888999****997256899*********************876655555555678888888536 PP
CGGGTT.........T-TTH..HHH.-CCHHCCHHHHHHH...HHHHHHHHEEEEEEEEEEES---CTCTHHHHHH CS
Methyltr_RsmB-F 91 gtgvir.........rdpdv..klrrkekdiaqlaklqke...llsaaidllkkgGvlvYsTCsvlveEneeviee 152
g+i+ dp++ l+++ +d+ ++ +l e ll+ a++ + + +vY+T s+ eEne+v+++
tr|W4X9M2|W4X9M2_STRPU 405 RSGIINpveyilqegEDPSIlrELSQEGQDLDRIDELALEhmdLLKHALKFYRVQ-AVVYATTSIMKEENENVVAK 479
6777752222222224666643345666777766666555111555555555554.689**************986 PP
>> tr|W4XVH0|W4XVH0_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 14.8 0.0 9.5e-06 0.027 4 91 .. 73 161 .. 70 171 .. 0.82
Alignments for each domain:
== domain 1 score: 14.8 bits; conditional E-value: 9.5e-06
H---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC...--EEEEEEEE CS
Methyltr_RsmB-F 4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg...elfDriLlDa 87
apq ++ +D+ + Gg T +++ ++ tv+ +d++ ++++a+ l+ ++ l + +++++ l++ +++D iL+Da
tr|W4XVH0|W4XVH0_STRPU 73 FAPQANQVYIDMTFGGGGHTQALMKC-APGITVYGLDRDPF-AHQIAQKLSLHHKGQLCPLLGKFSEVKDLLSQrevSMVDGILIDA 157
68******************999888.88889999999876.5566666654444456668899999999999888889******** PP
--CC CS
Methyltr_RsmB-F 88 PCsg 91
Cs+
tr|W4XVH0|W4XVH0_STRPU 158 GCSS 161
**97 PP
>> tr|W4ZAS4|W4ZAS4_STRPU Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.7 0.0 2e-05 0.058 7 86 .. 147 225 .. 142 245 .. 0.77
Alignments for each domain:
== domain 1 score: 13.7 bits; conditional E-value: 2e-05
-TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEE CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlD 86
+++ ++l l aa G +h+++l+ ++g v+Av+ +++ + ++ n+ + tn+i + Dar+++k+ ++D + D
tr|W4ZAS4|W4ZAS4_STRPU 147 KPGSKVLYLGAASGTTVSHVSDLVGPEGLVYAVEFSHRSGRDLM-NVAKK-RTNIIPIIEDARHPHKYRMLvGMVDCVFAD 225
66788999**************************9865555554.44443.345777888999998875432466666666 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (200 nodes)
Target sequences: 28594 (14266044 residues searched)
Passed MSV filter: 933 (0.0326292); expected 571.9 (0.02)
Passed bias filter: 645 (0.0225572); expected 571.9 (0.02)
Passed Vit filter: 51 (0.00178359); expected 28.6 (0.001)
Passed Fwd filter: 10 (0.000349724); expected 0.3 (1e-05)
Initial search space (Z): 28594 [actual number of targets]
Domain search space (domZ): 10 [number of targets reported over threshold]
# CPU time: 0.23u 0.01s 00:00:00.24 Elapsed: 00:00:00.09
# Mc/sec: 31702.32
//
[ok]