# 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/FtsJ.hmm.txt
# target sequence database: proteomes/Thermococcus_kodakarensis.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: FtsJ [M=177]
Accession: PF01728.18
Description: FtsJ-like methyltransferase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.1e-07 29.2 0.0 1.8e-07 28.5 0.0 1.3 1 tr|Q5JDP5|Q5JDP5_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1
1.3e-07 29.0 0.0 1.8e-07 28.5 0.0 1.2 1 tr|Q5JI15|Q5JI15_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1
0.00012 19.4 0.0 0.00024 18.4 0.0 1.4 1 tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase
0.00014 19.1 0.0 0.00037 17.8 0.0 1.7 1 tr|Q5JEW7|Q5JEW7_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1
0.00018 18.8 0.0 0.00037 17.7 0.0 1.5 1 tr|Q5JDB4|Q5JDB4_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1
0.00034 17.9 0.0 0.0044 14.3 0.0 2.0 2 tr|Q5JHQ2|Q5JHQ2_THEKO SAM-dependent methyltransferase, UbiE
0.00061 17.0 0.0 0.001 16.3 0.0 1.3 1 tr|Q5JCY9|Q5JCY9_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1
0.0011 16.3 0.0 0.0052 14.0 0.0 1.9 1 tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE
0.006 13.8 0.0 0.0091 13.2 0.0 1.4 1 sp|Q5JFN1|FLPA_THEKO Fibrillarin-like rRNA/tRNA 2'-O-methy
0.0095 13.2 0.0 0.4 7.9 0.0 2.1 2 tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransf
Domain annotation for each sequence (and alignments):
>> tr|Q5JDP5|Q5JDP5_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family OS=Thermococcus kodakarensis (strain AT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 28.5 0.0 7.9e-10 1.8e-07 20 138 .. 249 385 .. 230 399 .. 0.75
Alignments for each domain:
== domain 1 score: 28.5 bits; conditional E-value: 7.9e-10
-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--..---TT-EEE......E--TTSSSHHHHHHHHHHHSSEEEEEE----- CS
FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..aplpgvtti......qgditdpetiekikealserkvdlvvsDgapd 98
kpg+tvvDl+aaPGg + +++ ++++gk++a+D+ + + ++ v + + + + + +++ e+l+e+ +d v+ D
tr|Q5JDP5|Q5JDP5_THEKO 249 KPGETVVDLAAAPGGKTAHMAELMENRGKIYAFDVDSAriKRMKEV--LkrtgveIAEVIKADGRNAP-ELLGEEIADRVLLDAPCT 332
5899********************999********88755333222..12132234455555555544.4789999*******9877 PP
--S-HHHHHHHH...........HHHHHHHHHHHHHHEEEEEEEEEEEE-..S CS
FtsJ 99 vsgvhdldeylq...........sqLllaalelalkllkpggtfvlkifr..g 138
g+ ++ l+ + L + +e a kllkpgg ++ ++
tr|Q5JDP5|Q5JDP5_THEKO 333 SDGTIAKNPELRwrlreknipkvVALQKELMESAWKLLKPGGRLLYSTCSmlP 385
7777555555556999999999889*****************99877666443 PP
>> tr|Q5JI15|Q5JI15_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family OS=Thermococcus kodakarensis (strain AT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 28.5 0.0 7.8e-10 1.8e-07 20 152 .. 111 259 .. 50 272 .. 0.75
Alignments for each domain:
== domain 1 score: 28.5 bits; conditional E-value: 7.8e-10
-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS-----.TT-EEEE--TTSSSHHHHHHHHHHH..SSEEEEEE-------S-. CS
FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.pgvttiqgditdpetiekikealse..rkvdlvvsDgapdvsgv. 102
kpg+ v D +aaPGg + +++q ++++g ++a+D+++ +++ ++++ + +t+ + +++e ++d ++ D sg+
tr|Q5JI15|Q5JI15_THEKO 111 KPGEVVADMAAAPGGKTSYMAQLMENGGIIYAFDVGEDRLReTRLNLSRLGVTNTILFHSSSLHIDElgVEFDKILLDAPCTGSGTi 197
46688*******************999***********888777777755555544444333333333378*******976667764 PP
HHHHHHHH..........HHHHHHHHHHHHHHEEEEEEEEEEEE-..STTHHHHHHHHGGGE CS
FtsJ 103 hdldeylq..........sqLllaalelalkllkpggtfvlkifr..geeteallkqlkkfF 152
h+ +e ++ L ++ le +l++lk+gg++v ++ ee e++++ + F
tr|Q5JI15|Q5JI15_THEKO 198 HKNPERKAnrtmedvkfcQGLQMKLLEKGLSVLKKGGVLVYSTCSlePEENEFVIQWVLDNF 259
55555444888999999668999999999999********9888863444446666655555 PP
>> tr|Q5JJ78|Q5JJ78_THEKO Probable tRNA/rRNA methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 18.4 0.0 1e-06 0.00024 15 138 .. 213 338 .. 203 354 .. 0.81
Alignments for each domain:
== domain 1 score: 18.4 bits; conditional E-value: 1e-06
HH--S-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS-----TT-EEEE--TTSSSHHHHHHHHHHH............SSEE CS
FtsJ 15 kfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealse............rkvd 89
k+ +kpg++v+D+ +Gg++ ++ ga vvavD p a +++++ + + +++k+k ++ +k+d
tr|Q5JJ78|Q5JJ78_THEKO 213 KY--VKPGMRVLDVFTYTGGFAIHAAVA-GA-DEVVAVDKSPWA----INMVKENAKLNGVEDKMKYIVGSafpvmeemikrgEKFD 291
33..68*******************999.87.99******9974....778888888888888888555447777777777789*** PP
EEEE-------S-HHHHHHHHHHHHHHHHHHHHHHEEEEEEEEEEEE-S CS
FtsJ 90 lvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrg 138
+v+ D +v+ +dl+ l++ + + +l+l+k+gg++v+ + +
tr|Q5JJ78|Q5JJ78_THEKO 292 IVILDPPAFVQHEKDLKRGLRA--YFNVNYAGLQLVKEGGILVTASCSQ 338
*****99999998888888775..6677777779999**9999877664 PP
>> tr|Q5JEW7|Q5JEW7_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family, containing RNA-binding PUA domain OS=T
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.8 0.0 1.6e-06 0.00037 23 149 .. 200 340 .. 163 352 .. 0.63
Alignments for each domain:
== domain 1 score: 17.8 bits; conditional E-value: 1.6e-06
-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--.........---..TT-EEEE--TTSSSHHHHHHHHHHHSSEEEEEE----. CS
FtsJ 23 ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgditdpetiekikealserkvdlvvsDgap. 97
+ ++D +aaPGg + ++q ++++g ++a+D + + l ++v++i++d ++ i+ +d ++ D
tr|Q5JEW7|Q5JEW7_THEKO 200 DLIIDMAAAPGGKTSHIAQLMQNRGEIIAIDKSRNrlrkmeeelKRLgvKNVRLIHMDARKLPELG-IE-------ADKILLDAPCt 278
459******************999********8886766565443335567777777777766555.33.......78888886433 PP
.........---S-HHHHHHHH.......HHHHHHHHHHHHHHEEEEEEEEEEEE-...STTHHHHHHHHG CS
FtsJ 98 .........dvsgvhdldeylq.......sqLllaalelalkllkpggtfvlkifr...geeteallkqlk 149
+ + ++ +a + a+k l++ggt+v +++ +e+ +++ + l+
tr|Q5JEW7|Q5JEW7_THEKO 279 algirpklwETR---------TpkdieatARYQRAFIWAAIKSLRKGGTLVYSTCTisyEENEANVKYMLQ 340
333333333333.........23333332334455555556999999999988887664333334444455 PP
>> tr|Q5JDB4|Q5JDB4_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family, fused to N-terminal NusB regulator dom
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.7 0.0 1.6e-06 0.00037 20 96 .. 260 338 .. 245 408 .. 0.65
Alignments for each domain:
== domain 1 score: 17.7 bits; conditional E-value: 1.6e-06
-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--........---...TT-EEEE--TTSSSHHHHHHHHHHHSSEEEEEE-- CS
FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........apl...pgvttiqgditdpetiekikealserkvdlvvsDg 95
+pg++ +Dl+aaPG+ + ++ +++kg +vavD a++ ++v+++++d ++ + +e k+d ++ D
tr|Q5JDB4|Q5JDB4_THEKO 260 EPGERLLDLAAAPGSKTFHAAALMENKGEIVAVDYSYDrlmrmkekAKVlgvKNVRFVHADGQSFRDKE---------KFDKIILDA 337
38999******************9999********9995555444322234456666655555555444.........444444444 PP
- CS
FtsJ 96 a 96
tr|Q5JDB4|Q5JDB4_THEKO 338 P 338
4 PP
>> tr|Q5JHQ2|Q5JHQ2_THEKO SAM-dependent methyltransferase, UbiE/COQ5 family OS=Thermococcus kodakarensis (strain ATCC B
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 14.3 0.0 1.9e-05 0.0044 18 74 .. 35 98 .. 21 115 .. 0.79
2 ? 1.2 0.0 0.2 45 118 137 .. 125 144 .. 109 154 .. 0.79
Alignments for each domain:
== domain 1 score: 14.3 bits; conditional E-value: 1.9e-05
-S-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEES.S--.........---.TT-EEEE--TTSSS CS
FtsJ 18 lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.........apl.pgvttiqgditdpe 74
++k ++v+Dl+++ Gg+s l + lg vv++D + m + ++v++i+gd ++
tr|Q5JHQ2|Q5JHQ2_THEKO 35 FMKTRGRVLDLACGVGGFSFLL-EDLG--FEVVGLDNsRFMlekarefakE-KeSRVEFIEGDARELP 98
3466789***********9655.6666..79******55559988877633.359********98765 PP
== domain 2 score: 1.2 bits; conditional E-value: 0.2
HHHHHHHEEEEEEEEEEEE- CS
FtsJ 118 lelalkllkpggtfvlkifr 137
++ + ++lkpgg f+l++ +
tr|Q5JHQ2|Q5JHQ2_THEKO 125 FKETARVLKPGGKFILQFTD 144
5556789********98765 PP
>> tr|Q5JCY9|Q5JCY9_THEKO tRNA/rRNA cytosine-C5-methylase, NOL1/NOP2/Sun family OS=Thermococcus kodakarensis (strain AT
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 16.3 0.0 4.4e-06 0.001 20 138 .. 106 243 .. 87 265 .. 0.69
Alignments for each domain:
== domain 1 score: 16.3 bits; conditional E-value: 4.4e-06
-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--......---TT-EEEE--TTSSSHHHHHHHHHHHSSEEEEEE----... CS
FtsJ 20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpetiekikealserkvdlvvsDgap... 97
kpg+ v+D +aaPG+ + ++q ++++g ++a D + a+l+++ ++ + +t+ + + + e+ +d v+ D
tr|Q5JCY9|Q5JCY9_THEKO 106 KPGELVLDMAAAPGSKTGQIAQYMQNEGCIIANDPNRDranvliANLNRMGVLIARVTTRDGASFAR---FENTFDRVLLDAPCssv 189
47888*******************999********99876555444455555555554444444332...23467777777542223 PP
........---S-HHHHHHHH......HHHHHHHHHHHHHHEEEEEEEEEEEE-.....S CS
FtsJ 98 ........dvsgvhdldeylq......sqLllaalelalkllkpggtfvlkifr.....g 138
+ + + ++ ++ + + + lkpgg++v +++ +
tr|Q5JCY9|Q5JCY9_THEKO 190 gmirkswrFLREWR------EkavvkyMNVQKRLILAGYRALKPGGVMVYSTCTidpleN 243
33444443334444......1555555999999999999********9998888654432 PP
>> tr|Q5JGN8|Q5JGN8_THEKO SAM-dependent methyltransferase, UbiE/COQ5 family OS=Thermococcus kodakarensis (strain ATCC B
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 14.0 0.0 2.2e-05 0.0052 17 80 .. 32 107 .. 16 147 .. 0.75
Alignments for each domain:
== domain 1 score: 14.0 bits; conditional E-value: 2.2e-05
--S-.....TT-EEEEES-TT-HHHHHHTTT...-SEEEEEES.S--........---.TT-EEEE--TTSSSHHHHHH CS
FtsJ 17 klfk.....pgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm........apl.pgvttiqgditdpetiekik 80
++f+ ++k+v+Dl++++G + l++r g v+++Dl +m + + +v++i+g+ +d + +e++
tr|Q5JGN8|Q5JGN8_THEKO 32 EIFRedakrEVKRVLDLACGTGIPTLELAER-G--YEVLGLDLhEEMlrvarrkaEARgLNVKFIRGNALDISFEEEFD 107
4553111125588******************.5..68******66779997766433367*****99999988877554 PP
>> sp|Q5JFN1|FLPA_THEKO Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.2 0.0 4e-05 0.0091 13 102 .. 65 157 .. 54 210 .. 0.84
Alignments for each domain:
== domain 1 score: 13.2 bits; conditional E-value: 4e-05
HHHH--S-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--.........---TT-EEEE--TTSSSHHHHHHHHHHHSSEEEEE CS
FtsJ 13 dekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgditdpetiekikealserkvdlvv 92
++ f +kpg tv+ lg a G + ++ +g +gkv++v p + + ++ i gd t+pe +++ + kvd++
sp|Q5JFN1|FLPA_THEKO 65 LKNFP-IKPGSTVLYLGVASGTTASHVSDIVGWEGKVFGVEFSPRvlrelvplvEERRNIVPILGDATKPEGYRALVP-----KVDVIF 147
56677.89***********************999********999898776555555778888***********9997.....8***** PP
E-------S- CS
FtsJ 93 sDgapdvsgv 102
D+a ++ +
sp|Q5JFN1|FLPA_THEKO 148 EDVAQPTQAK 157
***9765544 PP
>> tr|Q5JGS7|Q5JGS7_THEKO tRNA (1-methyladenosine) methyltransferase OS=Thermococcus kodakarensis (strain ATCC BAA-918
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 7.9 0.0 0.0017 0.4 18 65 .. 90 140 .. 80 173 .. 0.73
2 ? 3.4 0.0 0.041 9.5 119 151 .. 178 210 .. 159 221 .. 0.84
Alignments for each domain:
== domain 1 score: 7.9 bits; conditional E-value: 0.0017
-S-TT-EEEEES-TT-HHHHHHTTT...-SEEEEEESS--..---..TT-EE CS
FtsJ 18 lfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..apl..pgvtt 65
++pg+tv++ ga+ G+ + +l++ +g++gkv+++ +++ + + ++v++
tr|Q5JGS7|Q5JGS7_THEKO 90 GISPGDTVIEAGAGSGALTIFLANAVGPTGKVISYEVRKDfyE-IakKNVEL 140
4779********************************9887541.22355544 PP
== domain 2 score: 3.4 bits; conditional E-value: 0.041
HHHHHHEEEEEEEEEEEE-STTHHHHHHHHGGG CS
FtsJ 119 elalkllkpggtfvlkifrgeeteallkqlkkf 151
a+++l+pgg fv+ + + ++ +++++l++f
tr|Q5JGS7|Q5JGS7_THEKO 178 PHAVDVLRPGGYFVAYTPCMNQVHRFFRALEEF 210
55889*********9999999999998888765 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (177 nodes)
Target sequences: 2301 (637680 residues searched)
Passed MSV filter: 78 (0.0338983); expected 46.0 (0.02)
Passed bias filter: 78 (0.0338983); expected 46.0 (0.02)
Passed Vit filter: 16 (0.0069535); expected 2.3 (0.001)
Passed Fwd filter: 10 (0.00434594); expected 0.0 (1e-05)
Initial search space (Z): 2301 [actual number of targets]
Domain search space (domZ): 10 [number of targets reported over threshold]
# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11286.94
//
[ok]