# 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/RrnaAD.hmm.txt
# target sequence database: proteomes/Pseudomonas_aeruginosa.fasta
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: RrnaAD [M=265]
Accession: PF00398.19
Description: Ribosomal RNA adenine dimethylase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
9.7e-65 216.6 0.0 1.1e-64 216.5 0.0 1.0 1 sp|Q9I5U5|RSMA_PSEAE Ribosomal RNA small subunit methyltra
0.00033 18.2 0.0 0.00059 17.3 0.0 1.3 1 tr|Q9I5Y9|Q9I5Y9_PSEAE Probable transcriptional regulator OS
0.00051 17.5 0.0 0.00074 17.0 0.0 1.2 1 sp|P45683|PIMT_PSEAE Protein-L-isoaspartate O-methyltransf
0.00098 16.6 0.0 0.0015 15.9 0.0 1.3 1 sp|Q9HUC0|UBIE_PSEAE Ubiquinone/menaquinone biosynthesis C
0.0042 14.5 0.0 0.007 13.8 0.0 1.3 1 sp|Q9I525|RLMD_PSEAE 23S rRNA (uracil(1939)-C(5))-methyltr
------ inclusion threshold ------
0.012 13.1 0.0 0.016 12.6 0.0 1.1 1 tr|Q9HV18|Q9HV18_PSEAE tRNA 5-carboxymethoxyuridine methyltr
0.019 12.4 0.0 0.029 11.8 0.0 1.2 1 sp|Q9HV34|SPEE2_PSEAE Polyamine aminopropyltransferase 2 OS
0.02 12.3 0.0 0.03 11.7 0.0 1.2 1 sp|Q9HV78|TRMA_PSEAE tRNA/tmRNA (uracil-C(5))-methyltransf
0.029 11.8 0.0 0.043 11.2 0.0 1.2 1 tr|Q9I5X8|Q9I5X8_PSEAE Uncharacterized protein OS=Pseudomona
Domain annotation for each sequence (and alignments):
>> sp|Q9I5U5|RSMA_PSEAE Ribosomal RNA small subunit methyltransferase A OS=Pseudomonas aeruginosa (strain ATCC 15692 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 216.5 0.0 1.7e-67 1.1e-64 2 263 .. 7 261 .. 6 263 .. 0.95
Alignments for each domain:
== domain 1 score: 216.5 bits; conditional E-value: 1.7e-67
GCCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHH CS
RrnaAD 2 nklrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfet 90
+++rk++gqnfl++ vi +Il+++ +e + +leigpG+G+lTe L+ + v+Eld++L+ ll+ k+ ++++ + + D+lkf++
sp|Q9I5U5|RSMA_PSEAE 7 HRARKRFGQNFLHDAGVIHRILRAIHAREGQRLLEIGPGQGALTEGLLGSGARLDVIELDQDLIPLLKLKFGLESRFSLHQGDALKFDF 95
789************************************************************************************** PP
HHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCEC CS
RrnaAD 91 peevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifs 179
+ v + +++++vv+nlPy+ist+l+++lle + +++++m+++lqke+++rl+a pg +++rls+++++ + v+++ +v++ +f
sp|Q9I5U5|RSMA_PSEAE 96 ASLV----ESGEKLRVVGNLPYNISTPLIFHLLE-HAPVIEDMHFMLQKEVVERLAATPGGGDWGRLSIMVQYHCRVEHLFNVGPGAFN 179
**66....79***********************5.9999************************************************** PP
S--SSSEEEEEEEE-SS-S.--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHHHCTT.T--TTTCCCCSGHHHHHHHHHHH CS
RrnaAD 180 Pppkvdsalvelerkdedl.pqkdlkkyesvvrkllnrkrktlstslksllpggelqalsstgindnalvkklsaeqtldifkel 263
Pppkvdsa+v+l++ +e++ p d k +e+vvr+++n++rktl++ lk ll+ + +a+ +++ + ++l + ++++++ l
sp|Q9I5U5|RSMA_PSEAE 180 PPPKVDSAIVRLTPFAEPPhPARDPKLLERVVREAFNQRRKTLRNTLKPLLSVEDIEAA---EVDPTLRPEQLDLAAFVRLANQL 261
*****************************************************999998...57777777777777777766665 PP
>> tr|Q9I5Y9|Q9I5Y9_PSEAE Probable transcriptional regulator OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 17.3 0.0 9.5e-07 0.00059 23 87 .. 158 224 .. 152 273 .. 0.77
Alignments for each domain:
== domain 1 score: 17.3 bits; conditional E-value: 9.5e-07
HHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCG CS
RrnaAD 23 ldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflk 87
ld+l + t le+gpG G + eLa r++qv++l + ++++l +++ + +++ + +D+l+
tr|Q9I5Y9|Q9I5Y9_PSEAE 158 LDALAFAPGATALEVGPGDGGFLPELARRFRQVTALDNSAAMLELARQRCKeeGLGNVRLELADALQ 224
566677788999***********************************99885545566666666665 PP
>> sp|P45683|PIMT_PSEAE Protein-L-isoaspartate O-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 ! 17.0 0.0 1.2e-06 0.00074 30 73 .. 77 120 .. 53 128 .. 0.84
Alignments for each domain:
== domain 1 score: 17.0 bits; conditional E-value: 1.2e-06
TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
RrnaAD 30 ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
+ ++v+eig+G G +T+ La+ ++ v ++E ++L +++l
sp|P45683|PIMT_PSEAE 77 PLDKVMEIGTGSGYQTAVLAQLVERVFSVERIQALQDKAKERLA 120
779***************************99999988888765 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 ! 15.9 0.0 2.5e-06 0.0015 30 96 .. 68 140 .. 59 166 .. 0.86
Alignments for each domain:
== domain 1 score: 15.9 bits; conditional E-value: 2.5e-06
TTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHHCT CS
RrnaAD 30 ekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeevte 96
vl+i+ G+G lT+++ + +vv+ + +++k+ ++kl ++++ v++D+ k +p + +
sp|Q9HUC0|UBIE_PSEAE 68 SGNRVLDIAGGTGDLTRQFSRLVgptGEVVLADINASMLKVGRDKLLdkgVSGNVSFVQADAEKLPFPDNHFD 140
6678***************99999999*******************999999************999997655 PP
>> sp|Q9I525|RLMD_PSEAE 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Pseudomonas aeruginosa (strain ATCC 1569
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 13.8 0.0 1.1e-05 0.007 14 68 .. 288 342 .. 282 363 .. 0.91
Alignments for each domain:
== domain 1 score: 13.8 bits; conditional E-value: 1.1e-05
--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHH CS
RrnaAD 14 knkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakll 68
+n+++i ++ld l ++ + vl++ G G+++ +La r+ vv +E +++++
sp|Q9I525|RLMD_PSEAE 288 VNESMIRQALDWLAPTADERVLDLFCGLGNFSLPLARRVARVVGVEGVAAMVERA 342
6999******************************************988888765 PP
>> tr|Q9HV18|Q9HV18_PSEAE tRNA 5-carboxymethoxyuridine methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 12.6 0.0 2.5e-05 0.016 28 73 .. 39 84 .. 22 95 .. 0.79
Alignments for each domain:
== domain 1 score: 12.6 bits; conditional E-value: 2.5e-05
GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT CS
RrnaAD 28 leekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls 73
+e l vl+ig+G G+++ La r v++ E + ++ ++++
tr|Q9HV18|Q9HV18_PSEAE 39 PERPLRVLDIGAGLGHMSLWLAARGHRVTLAEPAQPMLDGARQRFA 84
346789**************************98888877777665 PP
>> sp|Q9HV34|SPEE2_PSEAE Polyamine aminopropyltransferase 2 OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 /
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 11.8 0.0 4.7e-05 0.029 15 74 .. 86 157 .. 80 171 .. 0.77
Alignments for each domain:
== domain 1 score: 11.8 bits; conditional E-value: 4.7e-05
-HHHHHHHHHHH-GG...TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.......T CS
RrnaAD 15 nkkvineIldklnle...ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.......k 74
+++++ e l++ + e vl ig G+G++ +e++ a + v++ ld++L++l +++l+ +
sp|Q9HV34|SPEE2_PSEAE 86 DESLYHELLVQPAMLahdEPRDVLIIGGGEGATLREVLSHAsvRRAVMVDLDRELVELCREHLFqwhqgafD 157
6666666666655555778889***************998889*******************9855555555 PP
>> sp|Q9HV78|TRMA_PSEAE tRNA/tmRNA (uracil-C(5))-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 ? 11.7 0.0 4.8e-05 0.03 30 63 .. 207 240 .. 190 259 .. 0.86
Alignments for each domain:
== domain 1 score: 11.7 bits; conditional E-value: 4.8e-05
TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HH CS
RrnaAD 30 ekltvleigpGkGilTeeLakrakqvvvlElder 63
++ +le++ G G++T +La r+++v + E+ ++
sp|Q9HV78|TRMA_PSEAE 207 RDDDLLELYCGNGNFTLPLATRVRKVLATEISKS 240
57899*************************9765 PP
>> tr|Q9I5X8|Q9I5X8_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 ? 11.2 0.0 7e-05 0.043 24 70 .. 36 82 .. 30 92 .. 0.85
Alignments for each domain:
== domain 1 score: 11.2 bits; conditional E-value: 7e-05
HHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHC CS
RrnaAD 24 dklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqk 70
d+l l++++ +++g+G+G +T+ La vv++E ++ + l +
tr|Q9I5X8|Q9I5X8_PSEAE 36 DALGLRPQTVAVDLGAGTGKFTRLLARTGARVVAVEPVDAMRAQLAE 82
567899********************999*******76666666655 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (265 nodes)
Target sequences: 5563 (1857172 residues searched)
Passed MSV filter: 101 (0.0181557); expected 111.3 (0.02)
Passed bias filter: 97 (0.0174366); expected 111.3 (0.02)
Passed Vit filter: 20 (0.00359518); expected 5.6 (0.001)
Passed Fwd filter: 9 (0.00161783); expected 0.1 (1e-05)
Initial search space (Z): 5563 [actual number of targets]
Domain search space (domZ): 9 [number of targets reported over threshold]
# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.02
# Mc/sec: 24607.53
//
[ok]