# 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_savignyi.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.3e-55 187.6 0.0 2.5e-55 186.6 0.0 1.5 1 tr|H2ZRD3|H2ZRD3_CIOSA Uncharacterized protein OS=Ciona savi
6.3e-40 136.3 0.2 8e-39 132.7 0.0 2.5 2 tr|H2YC22|H2YC22_CIOSA Uncharacterized protein OS=Ciona savi
2.9e-36 124.4 0.2 5.2e-36 123.6 0.2 1.4 1 tr|H2Z203|H2Z203_CIOSA Uncharacterized protein OS=Ciona savi
2.3e-30 105.1 0.0 4.2e-30 104.3 0.0 1.4 1 tr|H2YUK6|H2YUK6_CIOSA Uncharacterized protein OS=Ciona savi
------ inclusion threshold ------
0.013 14.5 0.0 0.021 13.8 0.0 1.3 1 tr|H2YWU1|H2YWU1_CIOSA Uncharacterized protein OS=Ciona savi
0.016 14.2 0.0 0.024 13.7 0.0 1.3 1 tr|H2YFA0|H2YFA0_CIOSA Uncharacterized protein OS=Ciona savi
0.039 13.0 0.0 0.048 12.7 0.0 1.1 1 tr|H2YK86|H2YK86_CIOSA Uncharacterized protein OS=Ciona savi
Domain annotation for each sequence (and alignments):
>> tr|H2ZRD3|H2ZRD3_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 186.6 0.0 1.5e-58 2.5e-55 30 200 .] 1 180 [. 1 180 [. 0.93
Alignments for each domain:
== domain 1 score: 186.6 bits; conditional E-value: 1.5e-58
TTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHH CS
Methyltr_RsmB-F 30 mknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlakl 116
mkn+g ++ +d+nk Rl++v+ nl+r+gv n+ v+++Dar +++++g+ f r+LlDaPCsgtgvi++dp+vk++++++di+++++l
tr|H2ZRD3|H2ZRD3_CIOSA 1 MKNSGFIFVNDVNKDRLRAVVGNLHRMGVSNAVVSNYDARSFPTIMGN--FSRVLLDAPCSGTGVISKDPSVKTNKDDSDITKCSHL 85
7999*******************************************8..************************************* PP
HHHHHHHHHHHE....EEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEEC..............T-EEE- CS
Methyltr_RsmB-F 117 qkellsaaidll....kkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeea..............gtlrll 185
qkel+ +aid+ +gG++vY+TCsv veEneev+++aLkkr +v+lv+t l+ +g+e t+r++
tr|H2ZRD3|H2ZRD3_CIOSA 86 QKELILSAIDSCnaqaANGGYIVYCTCSVMVEENEEVVNYALKKR-NVKLVQTGLE------FGVEGfcryrqyrfhpslkLTRRFY 165
***********9888789**************************9.9*****9554......4444444444579999*999***** PP
TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 186 Phtenkdgffiaklk 200
Pht+n+dgf++ak+k
tr|H2ZRD3|H2ZRD3_CIOSA 166 PHTHNMDGFYVAKFK 180
*************96 PP
>> tr|H2YC22|H2YC22_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 132.7 0.0 4.9e-42 8e-39 2 200 .] 135 392 .. 134 392 .. 0.91
2 ? -3.0 0.0 1.9 3.1e+03 110 133 .. 478 503 .. 470 513 .. 0.56
Alignments for each domain:
== domain 1 score: 132.7 bits; conditional E-value: 4.9e-42
HHH---TT-EEEECS-TT-HHHHHHHHHTTTT.......SEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.... CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknk.......gtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.... 77
llL+ + + ++lD+caaPG+KT+ i el++ g vA+d++++R +++ + rL +ti+++ Da++++++l +
tr|H2YC22|H2YC22_CIOSA 135 LLLDVRSHHKVLDMCAAPGSKTAQIVELLHRDennaipdGICVANDKDNKRCYMLVHQIGRLHSPSTIIVNHDASNFPEILVKndvg 221
579999**********************754311122225689************************************99988999 PP
....--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-T.T CS
Methyltr_RsmB-F 78 ....elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkre.d 159
+Dr+L D+PCsg g++r++ dv ++ ++++ ++l++ q ++l ++ll +gG lvYsTCs+++ E+e+v+++a+++
tr|H2YC22|H2YC22_CIOSA 222 eeipLRYDRVLCDVPCSGDGTMRKNTDVWVKWNQANAIYLHRTQYRILLRGLELLGSGGQLVYSTCSLNPIEDEAVVAAAIQHCGgA 308
998889**********************9999999**********************************************997426 PP
EEEESSBSTTSTTSSECEEC............................................T-EEE-TTTTS.-SEEEEEEE CS
Methyltr_RsmB-F 160 velvetelsepkglklgeea............................................gtlrllPhtenkdgffiaklk 200
ve+++ +l + + + g+ + +rllPh++++ gff+a l+
tr|H2YC22|H2YC22_CIOSA 309 VEVIDADLPG-LKWSPGVSKwrvmdrdmnwyethdevpenkkknlsysmfppggqdvmekmhleRCMRLLPHQQDTGGFFVAVLR 392
7888887777.66677777789999************************************999999***************885 PP
== domain 2 score: -3.0 bits; conditional E-value: 1.9
HCCHHHHHHHHHHHHHHHEE..EEEE CS
Methyltr_RsmB-F 110 iaqlaklqkellsaaidllk..kgGv 133
+ ++kl k+++++ id++k + Gv
tr|H2YC22|H2YC22_CIOSA 478 LYFVSKLVKNIVETNIDHVKviNTGV 503
55556666666666666665223344 PP
>> tr|H2Z203|H2Z203_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 123.6 0.2 3.1e-39 5.2e-36 2 199 .. 209 407 .. 208 408 .. 0.81
Alignments for each domain:
== domain 1 score: 123.6 bits; conditional E-value: 3.1e-39
HHH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS
Methyltr_RsmB-F 2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87
+L+p ++ +++D+caaPG KT+h+a++m+n+g+++Avd+++ R+k +++ l++ +v+n +++ D k + + + ++++ iL+D
tr|H2Z203|H2Z203_CIOSA 209 FVLDPAPHTHVIDACAAPGNKTSHLAAIMNNTGKLFAVDRDRDRVKIMERQLQKANVQNCEIINSDFMKLNPTDPKfQKVECILVDP 295
68****************************************************************99987665556999******* PP
--CCGGGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESS.BSTTSTTS CS
Methyltr_RsmB-F 88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvet.elsepkgl 173
Csg g+++rd + + +++++ + l k l + +vYsTCs++ eEne v+++aLk+++ +l e+ ++ +g+
tr|H2Z203|H2Z203_CIOSA 296 SCSGSGIVSRDLENQKD-TNAEVLKRLALSKFLKLKF--YAWTSCRVVYSTCSIHQEENEDVVKSALKQNPFFKLLEVmPAWTNRGI 379
**********9998444.4444444444444332222..23456679*************************999876222222333 PP
S..ECEECT-EEE-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 174 k..lgeeagtlrllPhtenkdgffiakl 199
k + e+++ +r P + ++gff+a +
tr|H2Z203|H2Z203_CIOSA 380 KmvNYETQKCIRCDPAVNCTNGFFVALF 407
30033344599**************987 PP
>> tr|H2YUK6|H2YUK6_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=3 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 104.3 0.0 2.6e-33 4.2e-30 3 169 .. 203 379 .. 201 407 .. 0.84
Alignments for each domain:
== domain 1 score: 104.3 bits; conditional E-value: 2.6e-33
HH---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH.....HTT--.SEEEEES-CCCCHHHHCC--EEEE CS
Methyltr_RsmB-F 3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk.....rLgvt.ntivleaDarkidkvlggelfDri 83
L+pq++++ilD+c+aPGgK i++ + ++g++vA+d++++Rl r+++ k +++v+ ++ ++ D+r+ ++ + + +D++
tr|H2YUK6|H2YUK6_CIOSA 203 SLDPQPGDHILDMCSAPGGKLNIIMQAIGDSGRIVANDVDSKRLTRIKNVYKeyipkQFSVEeFIKFVQFDGREWTEIET-NAYDKV 288
79******************************************999987651111156666457899*******88887.59**** PP
EEEE--CC....GGGTTT-TT.HHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESS CS
Methyltr_RsmB-F 84 LlDaPCsg....tgvirrdpd.vklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvet 165
L+D+PC+ + + +rd d + + ++++ aql + q ell+ ai +++G++vYsTC+ + n+ v+++a ++ + + ++
tr|H2YUK6|H2YUK6_CIOSA 289 LVDVPCTNdrhsLYTSDRDADnIFSNLRKRERAQLPHVQCELLKNAILACRPNGIVVYSTCTASPLQNQFVVQYAVQELLEQHNITC 375
******96222255677776426667788999*******************************************998777666666 PP
BSTT CS
Methyltr_RsmB-F 166 else 169
++++
tr|H2YUK6|H2YUK6_CIOSA 376 QVED 379
6655 PP
>> tr|H2YWU1|H2YWU1_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 13.8 0.0 1.3e-05 0.021 7 74 .. 379 445 .. 373 455 .. 0.85
Alignments for each domain:
== domain 1 score: 13.8 bits; conditional E-value: 1.3e-05
-TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHH CS
Methyltr_RsmB-F 7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkv 74
++++ i+D c++ G +a l ++ +v+ v++++e l+r ++ ++ L ++n+++ + + +++k+
tr|H2YWU1|H2YWU1_CIOSA 379 KKDDVIVDFCSGGGHVGIVLAYL-LPSCKVILVENKEESLDRAYQRIQTLKLKNIMLYQCNLDQFSKD 445
78999*****9966666666666.777888899*************************9999999775 PP
>> tr|H2YFA0|H2YFA0_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 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 1.5e-05 0.024 5 87 .. 141 222 .. 137 232 .. 0.78
Alignments for each domain:
== domain 1 score: 13.7 bits; conditional E-value: 1.5e-05
---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.--EEEEEEEE CS
Methyltr_RsmB-F 5 apqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.elfDriLlDa 87
+ +++ ++l l aa G +h+++++ ++g v+Av+ +++ + +++ k+ tn+i + Dar+++k+ ++D i D+
tr|H2YFA0|H2YFA0_CIOSA 141 HIKPGSKVLYLGAASGTTVSHVSDIVGPEGLVYAVEFSHRSGRDLINVAKK--RTNIIPIIEDARHPHKYRMLvGMVDTIFADV 222
567788999***************************987665555544433..3456777889999988754335788887775 PP
>> tr|H2YK86|H2YK86_CIOSA Uncharacterized protein OS=Ciona savignyi OX=51511 PE=4 SV=1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.7 0.0 2.9e-05 0.048 18 146 .. 12 147 .. 6 182 .. 0.73
Alignments for each domain:
== domain 1 score: 12.7 bits; conditional E-value: 2.9e-05
TT-HHHHHHHHH.TTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC.....--EEEEEEEE--CCGGGTTT- CS
Methyltr_RsmB-F 18 aPGgKTthiael.mknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg.....elfDriLlDaPCsgtgvirrd 98
a G+ + ia+ k+++++ + ++ e+l+ va+ k Lg ++++v+ aD++k ++ + e+f ri + + +g v +
tr|H2YK86|H2YK86_CIOSA 12 ASGSFGSAIAQQfSKESANIALTGRSLEKLNGVANKCKALGSKKVTVIVADLSKKEDLSHVirsttEKFARIDVLVNNAGFYVHQNL 98
667777888876478899999999*****************************9977655466788999999888888888888888 PP
TTHHHH.-CCHHCCHHHHHHHHHHHHHHHE.EEEEEEEEEES---CTCT CS
Methyltr_RsmB-F 99 pdvklrrkekdiaqlaklqkellsaaidll.kkgGvlvYsTCsvlveEn 146
+v ++ + ++ +k l + a++ l + G +v ve n
tr|H2YK86|H2YK86_CIOSA 99 CKVEWEDIDDTFDLNVKAPLILSKLAMPFLqETKGCIVNISSVTPVEQN 147
8888877766665555555545555566664456666654433333444 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (200 nodes)
Target sequences: 11592 (4231397 residues searched)
Passed MSV filter: 377 (0.0325224); expected 231.8 (0.02)
Passed bias filter: 247 (0.0213078); expected 231.8 (0.02)
Passed Vit filter: 27 (0.00232919); expected 11.6 (0.001)
Passed Fwd filter: 7 (0.000603865); expected 0.1 (1e-05)
Initial search space (Z): 11592 [actual number of targets]
Domain search space (domZ): 7 [number of targets reported over threshold]
# CPU time: 0.08u 0.00s 00:00:00.08 Elapsed: 00:00:00.03
# Mc/sec: 28209.31
//
[ok]