# 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/Pseudomonas_aeruginosa.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.6e-63 212.3 0.0 2.4e-63 211.8 0.0 1.2 1 sp|Q9I7A9|RSMB_PSEAE Ribosomal RNA small subunit methyltra
0.00046 18.2 0.1 0.0031 15.5 0.0 2.2 2 tr|Q9I6D9|Q9I6D9_PSEAE Uncharacterized protein OS=Pseudomona
------ inclusion threshold ------
0.061 11.3 0.0 0.076 11.0 0.0 1.1 1 tr|Q9I6C4|Q9I6C4_PSEAE Ribosomal RNA small subunit methyltra
0.066 11.2 0.0 0.18 9.8 0.0 1.6 2 sp|P95454|RLME_PSEAE Ribosomal RNA large subunit methyltra
0.067 11.2 0.0 0.26 9.2 0.0 1.9 3 sp|Q9HUC0|UBIE_PSEAE Ubiquinone/menaquinone biosynthesis C
Domain annotation for each sequence (and alignments):
>> sp|Q9I7A9|RSMB_PSEAE Ribosomal RNA small subunit methyltransferase B OS=Pseudomonas aeruginosa (strain ATCC 15692 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 211.8 0.0 2.1e-66 2.4e-63 4 199 .. 239 428 .. 236 429 .. 0.94
Alignments for each domain:
== domain 1 score: 211.8 bits; conditional E-value: 2.1e-66
H---TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE--CCG CS
Methyltr_RsmB-F 4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaPCsgt 92
L+ +++++lD+c+aPGgKT h++e + ++vvAvd +++Rl rv enl+rLg++ + ++ aDar + ++ g+ f riLlDaPCs+t
sp|Q9I7A9|RSMB_PSEAE 239 LESAPGQRVLDACCAPGGKTCHLLETQPELAEVVAVDLEESRLVRVRENLQRLGLQ-ASLVAADARATGEWWDGKPFQRILLDAPCSAT 326
788899**************************************************.99****************************** PP
GGTTT-TTHHHH.-CCHHCCHHHHHHHHHHHHHHHEEEEEEEEEEES---CTCTHHHHHHHHHH-TTEEEESSBSTTSTTSSECEECT- CS
Methyltr_RsmB-F 93 gvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepkglklgeeagt 181
gvirr+pd+kl rk++dia+la+lq ell+a++++l gGvl+Y+TCsv ++En+ i+++L +++ ++ ++ +p g+k ++
sp|Q9I7A9|RSMB_PSEAE 327 GVIRRHPDIKLARKPEDIAALAHLQGELLDALWPTLEVGGVLLYATCSVMPAENSDSIAAFLARTPGARELDL--PGPWGMKQPHG--- 410
******************************************************************9998888..55545544444... PP
EEE-TTTTS.-SEEEEEE CS
Methyltr_RsmB-F 182 lrllPhtenkdgffiakl 199
++llP+ e +dgf++akl
sp|Q9I7A9|RSMB_PSEAE 411 RQLLPQVEGHDGFYYAKL 428
488**************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 ? -3.3 0.0 1.6 1.8e+03 114 134 .. 135 155 .. 131 168 .. 0.74
2 ! 15.5 0.0 2.8e-06 0.0031 32 148 .. 242 348 .. 214 375 .. 0.72
Alignments for each domain:
== domain 1 score: -3.3 bits; conditional E-value: 1.6
HHHHHHHHHHHHHHEEEEEEE CS
Methyltr_RsmB-F 114 aklqkellsaaidllkkgGvl 134
++ e+l a++++lk+ vl
tr|Q9I6D9|Q9I6D9_PSEAE 135 ELRKDEVLAALLQVLKPAAVL 155
567778888888888887665 PP
== domain 2 score: 15.5 bits; conditional E-value: 2.8e-06
TTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CCCCHHHHCC..--EEEEEEEE--CCGGGTTT-TTHHHH.-CCHHCCHHH CS
Methyltr_RsmB-F 32 nkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlgg..elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlak 115
+++v+ vda++ l+ v++n gv ++ ++e+D+ + + l e fD ++ D P i+r++d+ ++
tr|Q9I6D9|Q9I6D9_PSEAE 242 GASEVMCVDASAFALDGVERNAALNGVAeKVACVEGDVFEALRELKAadERFDVVIADPPA----FIKRKKDL---------KNGEA 315
5677899999999999999998888876468888889877654443334899999999884....67777777.........33344 PP
HHHHHHHHHHHHEEEEEEEEEEES---CTCTHH CS
Methyltr_RsmB-F 116 lqkellsaaidllkkgGvlvYsTCsvlveEnee 148
++l + a+ ll k+G+lv + Cs+++ E+
tr|Q9I6D9|Q9I6D9_PSEAE 316 AYRRLNEQAMRLLSKDGILVSASCSMHLPEDDL 348
445566677888899************999865 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 ? 11.0 0.0 6.9e-05 0.076 8 88 .. 58 136 .. 50 144 .. 0.85
Alignments for each domain:
== domain 1 score: 11.0 bits; conditional E-value: 6.9e-05
TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CCCCHHHHCC--EEEEEEEE- CS
Methyltr_RsmB-F 8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDaP 88
e+ ++lD a+ G ++ +l + + + +A+d+n e + ++ + l L + ++++ +Da ++ + + fD + lD P
tr|Q9I6C4|Q9I6C4_PSEAE 58 EGARVLDPFAGSG--ALFLEALSRGAREGLALDTNGEAVAALRNHLDALKCGTAQLVLGDAVRYLGNQAPSAFDLVFLDPP 136
6667888888666..46888999999999*******************************999977777799*******99 PP
>> sp|P95454|RLME_PSEAE Ribosomal RNA large subunit methyltransferase E OS=Pseudomonas aeruginosa (strain ATCC 15692 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 9.8 0.0 0.00016 0.18 9 41 .. 49 81 .. 35 86 .. 0.86
2 ? -2.3 0.0 0.81 9e+02 71 90 .. 170 189 .. 159 193 .. 0.62
Alignments for each domain:
== domain 1 score: 9.8 bits; conditional E-value: 0.00016
T-EEEECS-TT-HHHHHHHHHTTTTSEEEEEES CS
Methyltr_RsmB-F 9 eetilDlcaaPGgKTthiaelmknkgtvvAvda 41
+ t++Dl aaPGg + ++ ++g+++A d+
sp|P95454|RLME_PSEAE 49 GMTVVDLGAAPGGWSQVTSRVIGDRGRLIASDI 81
55789*************************997 PP
== domain 2 score: -2.3 bits; conditional E-value: 0.81
CHHHHCC--EEEEEEEE--C CS
Methyltr_RsmB-F 71 idkvlggelfDriLlDaPCs 90
+ + e+fD++ + P s
sp|P95454|RLME_PSEAE 170 QYHKQAREMFDKVQMRKPLS 189
22333448999998877766 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 ? 9.2 0.0 0.00023 0.26 8 72 .. 68 133 .. 63 145 .. 0.86
2 ? -2.2 0.0 0.74 8.2e+02 116 135 .. 153 172 .. 148 174 .. 0.81
3 ? -3.5 0.0 1.8 2e+03 64 83 .. 219 238 .. 212 243 .. 0.72
Alignments for each domain:
== domain 1 score: 9.2 bits; conditional E-value: 0.00023
TT-EEEECS-TT-HHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CCCCH CS
Methyltr_RsmB-F 8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkid 72
++++lD++ + G T + l+ ++g+vv d+n++ lk + l gv n+ ++aDa k +
sp|Q9HUC0|UBIE_PSEAE 68 SGNRVLDIAGGTGDLTRQFSRLVGPTGEVVLADINASMLKVGRDKLLDKGVSgNVSFVQADAEKLP 133
6789**********************************9999999888888878888999988764 PP
== domain 2 score: -2.2 bits; conditional E-value: 0.74
HHHHHHHHHHHHEEEEEEEE CS
Methyltr_RsmB-F 116 lqkellsaaidllkkgGvlv 135
+ e + +++ +lk+gG l+
sp|Q9HUC0|UBIE_PSEAE 153 HKDEAIRSMLRVLKPGGRLL 172
5677889999999**99986 PP
== domain 3 score: -3.5 bits; conditional E-value: 1.8
EES-CCCCHHHHCC--EEEE CS
Methyltr_RsmB-F 64 leaDarkidkvlggelfDri 83
++ D + ++ ++ fDr+
sp|Q9HUC0|UBIE_PSEAE 219 MHPDQETLKAMMVEAGFDRV 238
55677777777777778887 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (200 nodes)
Target sequences: 5563 (1857172 residues searched)
Passed MSV filter: 176 (0.0316376); expected 111.3 (0.02)
Passed bias filter: 164 (0.0294805); expected 111.3 (0.02)
Passed Vit filter: 21 (0.00377494); expected 5.6 (0.001)
Passed Fwd filter: 5 (0.000898796); expected 0.1 (1e-05)
Initial search space (Z): 5563 [actual number of targets]
Domain search space (domZ): 5 [number of targets reported over threshold]
# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12381.15
//
[ok]