# 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]