# 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/UPF0020.hmm.txt
# target sequence database: proteomes/Pseudomonas_aeruginosa.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: UPF0020 [M=197]
Accession: PF01170.17
Description: Putative RNA methylase family UPF0020
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-46 156.9 0.0 2.7e-43 146.3 0.0 2.4 2 sp|Q9HZG0|RLMKL_PSEAE Ribosomal RNA large subunit methyltra
2.5e-06 25.7 0.0 3.9e-06 25.0 0.0 1.2 1 tr|Q9I6D9|Q9I6D9_PSEAE Uncharacterized protein OS=Pseudomona
4.7e-06 24.8 0.0 8e-06 24.0 0.0 1.3 1 tr|Q9I1T6|Q9I1T6_PSEAE Uncharacterized protein OS=Pseudomona
9.1e-06 23.8 0.0 1.9e-05 22.8 0.0 1.5 1 tr|Q9HY94|Q9HY94_PSEAE Uncharacterized protein OS=Pseudomona
0.00049 18.2 0.0 0.0016 16.5 0.0 1.9 3 sp|Q9I347|PRMB_PSEAE 50S ribosomal protein L3 glutamine me
0.00088 17.3 0.0 0.0027 15.8 0.0 1.8 2 sp|Q9HUC0|UBIE_PSEAE Ubiquinone/menaquinone biosynthesis C
0.0011 17.0 0.0 0.0039 15.3 0.0 1.8 1 tr|Q9I0A7|Q9I0A7_PSEAE Probable restriction-modification sys
0.0035 15.4 0.1 0.011 13.7 0.1 1.7 1 sp|Q9HUW3|PRMA_PSEAE Ribosomal protein L11 methyltransfera
0.0053 14.8 0.0 0.015 13.3 0.0 1.7 2 tr|Q9I6C4|Q9I6C4_PSEAE Ribosomal RNA small subunit methyltra
------ inclusion threshold ------
0.015 13.3 0.0 0.027 12.5 0.0 1.3 1 sp|Q9HVC8|PRMC_PSEAE Release factor glutamine methyltransf
0.017 13.1 0.0 0.029 12.4 0.0 1.3 1 sp|Q9HVH4|RLMG_PSEAE Ribosomal RNA large subunit methyltra
0.02 12.9 0.0 0.39 8.7 0.0 2.5 2 tr|Q9I3U2|Q9I3U2_PSEAE Uncharacterized protein OS=Pseudomona
Domain annotation for each sequence (and alignments):
>> sp|Q9HZG0|RLMKL_PSEAE Ribosomal RNA large subunit methyltransferase K/L OS=Pseudomonas aeruginosa (strain ATCC 15692
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 146.3 0.0 5.9e-46 2.7e-43 1 194 [. 165 380 .. 165 383 .. 0.92
2 ! 8.2 0.0 0.0012 0.54 75 130 .. 586 642 .. 554 685 .. 0.81
Alignments for each domain:
== domain 1 score: 146.3 bits; conditional E-value: 5.9e-46
-SSS-SS---SS-HHHHHHHHHHTT-....-TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS.............HHHHHHH CS
UPF0020 1 RgyRefngpapLketLAaalvrlagw....kpgepllDPmCGsGtilIEaallganiapgllrefvle.............lkaeaee 71
RgyR +g apLke+LAaa + +agw +g l+DPmCG Gt+l+Eaal++a+iap l re++++ l++ea++
sp|Q9HZG0|RLMKL_PSEAE 165 RGYRLQQGAAPLKENLAAAVLIRAGWpkiaAEGGALADPMCGVGTFLVEAALMAADIAPNLKRERWGFsswlghvpalwrkLHEEAQQ 252
9*************************5554579********************************************99987777777 PP
HHH...HH--..EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE----------HHHHHHHHHHHHHHH CS
UPF0020 72 ear...aelk..lygsDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpPYGerlgskkalekLYseflrel 152
+a a+ + ++g + d+r++q a +N e+agv+d ++++q + a ++ ++g+ +++++npPYGerlg++ +l LY++++++l
sp|Q9HZG0|RLMKL_PSEAE 253 RAAaglARPPlwIRGYEADPRLIQPACNNIERAGVADWVKIYQGELATFEprPDKGQTGLVICNPPYGERLGDEASLLYLYQNLGERL 340
777554333367*************************************9966777******************************** PP
HHH-TT..-EEEEEESSHHHHHCC---ESEEEEEEETTEEEE CS
UPF0020 153 krvlrgggrlvlltsenkalekaleeralrkvkeknvklgll 194
+ + g +++ ++++ +l k ++ r+ +++ n+ l +
sp|Q9HZG0|RLMKL_PSEAE 341 RQSCIG--WSAGVFTGAPELGKRMGIRSHKQYAFWNGALACK 380
**9999..***********************99999999886 PP
== domain 2 score: 8.2 bits; conditional E-value: 0.0012
HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG.--STTS---EEEE--- CS
UPF0020 75 aelklygsDldrrvvqgareNaekagvgdliefsqadaak.LrlkegevdvivtnpP 130
+ +Dl + +++ ar+N++ g +d+ ++ d+ + Lr+++g++++i +pP
sp|Q9HZG0|RLMKL_PSEAE 586 GARSTTSVDLSKTYLDWARRNLSLNGFSDKQRLVHGDVMEwLREDDGQYELIFIDPP 642
45558899*****************************9874779999*********9 PP
>> tr|Q9I6D9|Q9I6D9_PSEAE Uncharacterized protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 25.0 0.0 8.4e-09 3.9e-06 77 168 .. 244 340 .. 234 358 .. 0.85
Alignments for each domain:
== domain 1 score: 25.0 bits; conditional E-value: 8.4e-09
--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--G.GG--...STTS---EEEE---.-------HHHHHHHHHHHHHHHHHH-TT CS
UPF0020 77 lklygsDldrrvvqgareNaekagvgdliefsqada.akLr...lkegevdvivtnpP.YGerlgskkalekLYseflrelkrvlrg 158
+++++D + +++g ++Na gv+++++ ++ d+ +Lr ++++ +dv++++pP + +r ++ k+ e+ Y+ + +++ r l++
tr|Q9I6D9|Q9I6D9_PSEAE 244 SEVMCVDASAFALDGVERNAALNGVAEKVACVEGDVfEALRelkAADERFDVVIADPPaFIKRKKDLKNGEAAYRRLNEQAMRLLSK 330
4599******************************974344444477889*********899999999999***************** PP
..-EEEEEES CS
UPF0020 159 ggrlvlltse 168
+g lv++ +
tr|Q9I6D9|Q9I6D9_PSEAE 331 DGILVSASCS 340
*999987655 PP
>> tr|Q9I1T6|Q9I1T6_PSEAE Uncharacterized protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 24.0 0.0 1.7e-08 8e-06 75 133 .. 159 214 .. 150 223 .. 0.85
Alignments for each domain:
== domain 1 score: 24.0 bits; conditional E-value: 1.7e-08
HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------ CS
UPF0020 75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe 133
+++++ g+D+++++++ ar Na agvg+l +++ + + g +d+iv+npPY
tr|Q9I1T6|Q9I1T6_PSEAE 159 PDAEVHGLDINPAALDLARVNAALAGVGNLTLARSDLLSQAP---GRFDLIVANPPYLL 214
567899*************************99996666555...78**********76 PP
>> tr|Q9HY94|Q9HY94_PSEAE Uncharacterized protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 22.8 0.0 4.1e-08 1.9e-05 70 125 .. 194 247 .. 166 266 .. 0.86
Alignments for each domain:
== domain 1 score: 22.8 bits; conditional E-value: 4.1e-08
HHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
UPF0020 70 eeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
++a +e+++yg D+ + +++ar Nae+agvgd++ f++ d +L + ++d +
tr|Q9HY94|Q9HY94_PSEAE 194 MAKAFPEAQVYGCDFHAPSIERARANAEAAGVGDRVRFEVSDSDALA-GK-KFDFV 247
34455899************************************999.54.57766 PP
>> sp|Q9I347|PRMB_PSEAE 50S ribosomal protein L3 glutamine methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 156
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 16.5 0.0 3.4e-06 0.0016 76 133 .. 149 205 .. 126 219 .. 0.86
2 ? -2.5 0.0 2.3 1.1e+03 81 100 .. 230 249 .. 229 271 .. 0.67
3 ? -3.4 0.0 4.4 2e+03 137 169 .. 258 289 .. 254 294 .. 0.68
Alignments for each domain:
== domain 1 score: 16.5 bits; conditional E-value: 3.4e-06
H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--.GGG--STTS---EEEE------ CS
UPF0020 76 elklygsDldrrvvqgareNaekagvgdliefsqad.aakLrlkegevdvivtnpPYGe 133
+++++ +Dl +++ a+ N e+ +g+++ +q d +a L+ + +d+iv+npPY +
sp|Q9I347|PRMB_PSEAE 149 QAEVVLADLSFDALEVANVNIERHDLGERVYTVQGDgFAGLP-GQ-RFDLIVSNPPYVD 205
4557778999999******************99999678999.55.7**********76 PP
== domain 2 score: -2.5 bits; conditional E-value: 2.3
EEES-HHHHHHHHHHHHHTT CS
UPF0020 81 gsDldrrvvqgareNaekag 100
g+Dl rr+++ a + +++ g
sp|Q9I347|PRMB_PSEAE 230 GLDLVRRMLAEAADHLSEKG 249
56777777777766666554 PP
== domain 3 score: -3.4 bits; conditional E-value: 4.4
-HHHHHHHHHHHHHHHHHH-TT..-EEEEEESS CS
UPF0020 137 skkalekLYseflrelkrvlrgggrlvlltsen 169
s+ +++LY+e+ + + +++gg v+++s+
sp|Q9I347|PRMB_PSEAE 258 SEVHVQALYPEVDFTWLE-FEHGGHGVFMLSAA 289
566788999988666655.55557777777665 PP
>> sp|Q9HUC0|UBIE_PSEAE Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE OS=Pseudomonas aeruginosa (strain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? -2.7 0.0 2.7 1.2e+03 22 41 .. 62 81 .. 58 84 .. 0.86
2 ! 15.8 0.0 5.8e-06 0.0027 79 125 .. 96 142 .. 80 186 .. 0.87
Alignments for each domain:
== domain 1 score: -2.7 bits; conditional E-value: 2.7
HHTT--TTS-EEETT-TTSH CS
UPF0020 22 rlagwkpgepllDPmCGsGt 41
+l+g++ g++ lD G+G
sp|Q9HUC0|UBIE_PSEAE 62 ELSGVRSGNRVLDIAGGTGD 81
799*********99999985 PP
== domain 2 score: 15.8 bits; conditional E-value: 5.8e-06
EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EE CS
UPF0020 79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvi 125
++ +D+++++++ +r+++ gv++ ++f+qada kL+ +++ +d +
sp|Q9HUC0|UBIE_PSEAE 96 VVLADINASMLKVGRDKLLDKGVSGNVSFVQADAEKLPFPDNHFDCV 142
6668**********************************888899987 PP
>> tr|Q9I0A7|Q9I0A7_PSEAE Probable restriction-modification system protein OS=Pseudomonas aeruginosa (strain ATCC 15692
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 15.3 0.0 8.3e-06 0.0039 75 137 .. 259 326 .. 224 331 .. 0.51
Alignments for each domain:
== domain 1 score: 15.3 bits; conditional E-value: 8.3e-06
HH--EEEEES-HHHHHHHHHHHHHTT-GGGEE..EEE--GGG--...STTS---EEEE---------- CS
UPF0020 75 aelklygsDldrrvvqgareNaekagvgdlie..fsqadaakLr...lkegevdvivtnpPYGerlgs 137
+ ++l+g ++ + + ++ + g g + e + ad L ++ e+d +++npPYG++ ++
tr|Q9I0A7|Q9I0A7_PSEAE 259 VSIHLFGQEISDETYAICKADLLLKGEGAEAEniVGGADKSTLSadqFRSREFDFMISNPPYGKSWKT 326
4444555555555555555443322222222200222333333333323559************9876 PP
>> sp|Q9HUW3|PRMA_PSEAE Ribosomal protein L11 methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 2264
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.7 0.1 2.4e-05 0.011 29 128 .. 158 229 .. 138 231 .. 0.83
Alignments for each domain:
== domain 1 score: 13.7 bits; conditional E-value: 2.4e-05
TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--S CS
UPF0020 29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrl 117
g++ lD CGsG ++I a llga++a +g D+d+++++++r+Na++ g++ f + a+L+
sp|Q9HUW3|PRMA_PSEAE 158 GRQVLDFGCGSGILAIAALLLGAERA-------------------------VGTDIDPQALEASRDNASRNGIEP-ARFPVYLPADLP- 219
66778888*****************9.........................8********************975.567777778888. PP
TTS---EEEE- CS
UPF0020 118 kegevdvivtn 128
++ + dv+v+n
sp|Q9HUW3|PRMA_PSEAE 220 QR-QADVLVAN 229
44.57888887 PP
>> tr|Q9I6C4|Q9I6C4_PSEAE Ribosomal RNA small subunit methyltransferase D OS=Pseudomonas aeruginosa (strain ATCC 15692
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.3 0.0 3.3e-05 0.015 24 47 .. 54 77 .. 48 114 .. 0.86
2 ? -1.9 0.0 1.5 6.8e+02 115 133 .. 120 139 .. 81 148 .. 0.60
Alignments for each domain:
== domain 1 score: 13.3 bits; conditional E-value: 3.3e-05
TT--TTS-EEETT-TTSHHHHHHH CS
UPF0020 24 agwkpgepllDPmCGsGtilIEaa 47
a + +g + lDP+ GsG++ +Ea
tr|Q9I6C4|Q9I6C4_PSEAE 54 APYVEGARVLDPFAGSGALFLEAL 77
66678999**************95 PP
== domain 2 score: -1.9 bits; conditional E-value: 1.5
--.STTS---EEEE------ CS
UPF0020 115 Lr.lkegevdvivtnpPYGe 133
L ++ + +d++ +pP+ +
tr|Q9I6C4|Q9I6C4_PSEAE 120 LGnQAPSAFDLVFLDPPFHQ 139
33333346888888888865 PP
>> sp|Q9HVC8|PRMC_PSEAE Release factor glutamine methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.5 0.0 5.7e-05 0.027 71 131 .. 127 185 .. 96 191 .. 0.81
Alignments for each domain:
== domain 1 score: 12.5 bits; conditional E-value: 5.7e-05
HHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
UPF0020 71 eearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
+++r+ + ++D +++v+ a++N ++ +++ ++ + +L + +++iv+npPY
sp|Q9HVC8|PRMC_PSEAE 127 ASERPLWTVTAVDRVEEAVALAERNRQRLLLENVEVRRSHWFSALD-GR-RFRMIVGNPPY 185
4556777799*********************999999999999999.55.7********** PP
>> sp|Q9HVH4|RLMG_PSEAE Ribosomal RNA large subunit methyltransferase G OS=Pseudomonas aeruginosa (strain ATCC 15692 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.4 0.0 6.3e-05 0.029 74 131 .. 253 309 .. 230 324 .. 0.88
Alignments for each domain:
== domain 1 score: 12.4 bits; conditional E-value: 6.3e-05
HHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
UPF0020 74 raelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
+++++l+ +D +vq areN ++a + +f++ d + + + g+ d++++npP+
sp|Q9HVH4|RLMG_PSEAE 253 NPQAELALVDESYMAVQSARENWRAALGERPATFRADDGLAGQ-AAGSLDLVLCNPPF 309
56677888999999**********************8887777.999**********9 PP
>> tr|Q9I3U2|Q9I3U2_PSEAE Uncharacterized protein OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 0.1 0.0 0.37 1.7e+02 135 174 .. 43 82 .. 40 89 .. 0.86
2 ? 8.7 0.0 0.00084 0.39 78 165 .. 108 185 .. 81 203 .. 0.73
Alignments for each domain:
== domain 1 score: 0.1 bits; conditional E-value: 0.37
---HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHH CS
UPF0020 135 lgskkalekLYseflrelkrvlrgggrlvlltsenkalek 174
+gsk + +++Y + + + v r+ g l+++++ +++ +
tr|Q9I3U2|Q9I3U2_PSEAE 43 MGSKTEYREFYGRLKDLALPVSRETGCLLYMLARSSSARS 82
7899999*****************9**9999998877655 PP
== domain 2 score: 8.7 bits; conditional E-value: 0.00084
-EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEE CS
UPF0020 78 klygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvl 164
+l+gs+++++ ++ar+N+ + g+ dl+e+++ da + ++ ++P + l ++LY+e+l l+++lr g lv+
tr|Q9I3U2|Q9I3U2_PSEAE 108 RLIGSEFEPSKAERARRNLAAGGLLDLVELREGDALQT---------LAKDLPDSIDLVLLDGAKALYPEVLALLESRLRP-GALVI 184
4899****************************999743.........3445555555555556666666666666666666.55555 PP
E CS
UPF0020 165 l 165
+
tr|Q9I3U2|Q9I3U2_PSEAE 185 A 185
5 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (197 nodes)
Target sequences: 5563 (1857172 residues searched)
Passed MSV filter: 195 (0.035053); expected 111.3 (0.02)
Passed bias filter: 163 (0.0293007); expected 111.3 (0.02)
Passed Vit filter: 30 (0.00539277); expected 5.6 (0.001)
Passed Fwd filter: 12 (0.00215711); expected 0.1 (1e-05)
Initial search space (Z): 5563 [actual number of targets]
Domain search space (domZ): 12 [number of targets reported over threshold]
# CPU time: 0.07u 0.00s 00:00:00.07 Elapsed: 00:00:00.02
# Mc/sec: 18293.14
//
[ok]