# 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/WD40.hmm.txt # target sequence database: proteomes/Pseudomonas_aeruginosa.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: WD40 [M=38] Accession: PF00400.32 Description: WD domain, G-beta repeat 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0.0068 15.6 0.4 27 4.2 0.0 4.6 5 tr|Q9I609|Q9I609_PSEAE Probable c-type cytochrome OS=Pseudom 0.0073 15.5 0.1 0.37 10.1 0.1 3.5 4 tr|Q9HWH7|Q9HWH7_PSEAE Periplasmic gluconolactonase, PpgL OS Domain annotation for each sequence (and alignments): >> tr|Q9I609|Q9I609_PSEAE Probable c-type cytochrome OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 4.2 0.0 0.0098 27 18 38 .] 170 190 .. 137 190 .. 0.78 2 ? 1.7 0.0 0.062 1.7e+02 16 28 .. 209 221 .. 204 224 .. 0.86 3 ? 2.6 0.0 0.031 86 15 29 .. 300 313 .. 280 318 .. 0.84 4 ? -2.0 0.0 0.9 2.5e+03 16 26 .. 346 356 .. 341 359 .. 0.79 5 ? -0.4 0.0 0.28 7.9e+02 15 38 .] 435 460 .. 420 460 .. 0.68 Alignments for each domain: == domain 1 score: 4.2 bits; conditional E-value: 0.0098 EETTSSEEEEEETTSEEEEEE CS WD40 18 fspdgawlasGsdDgtvriWd 38 fspdg+++ +s+Dg v ++d tr|Q9I609|Q9I609_PSEAE 170 FSPDGRLVYFASRDGWVTLYD 190 9******976788*9998887 PP == domain 2 score: 1.7 bits; conditional E-value: 0.062 EEEETTSSEEEEE CS WD40 16 lafspdgawlasG 28 la+s+dg+w++ G tr|Q9I609|Q9I609_PSEAE 209 LAVSDDGRWVLVG 221 789******9877 PP == domain 3 score: 2.6 bits; conditional E-value: 0.031 EEEEETTSSEEEEEE CS WD40 15 slafspdgawlasGs 29 +++fspd ++l+ Gs tr|Q9I609|Q9I609_PSEAE 300 DFSFSPDYRYLL-GS 313 467********9.76 PP == domain 4 score: -2.0 bits; conditional E-value: 0.9 EEEETTSSEEE CS WD40 16 lafspdgawla 26 + + +dg+w++ tr|Q9I609|Q9I609_PSEAE 346 IYWKRDGRWVF 356 66899****86 PP == domain 5 score: -0.4 bits; conditional E-value: 0.28 EEEEETTSSE.EEEE.ETTSEEEEEE CS WD40 15 slafspdgaw.lasG.sdDgtvriWd 38 ++ f +dg++ l+s ++Dg + ++d tr|Q9I609|Q9I609_PSEAE 435 HVEFTRDGRYaLLSVwDRDGALVVYD 460 56677888885455566677777766 PP >> tr|Q9HWH7|Q9HWH7_PSEAE Periplasmic gluconolactonase, PpgL 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 ? -2.4 0.0 1.2 3.3e+03 15 26 .. 126 135 .. 112 142 .. 0.62 2 ! 10.1 0.1 0.00013 0.37 6 27 .. 176 195 .. 171 204 .. 0.79 3 ? -3.6 0.0 2 5.6e+03 15 24 .. 235 244 .. 233 252 .. 0.79 4 ? -0.0 0.0 0.21 6e+02 16 28 .. 336 348 .. 325 356 .. 0.81 Alignments for each domain: == domain 1 score: -2.4 bits; conditional E-value: 1.2 EEEEETTSSEEE CS WD40 15 slafspdgawla 26 sl s+dg++l+ tr|Q9HWH7|Q9HWH7_PSEAE 126 SL--SHDGRYLF 135 34..77888775 PP == domain 2 score: 10.1 bits; conditional E-value: 0.00013 EEESSSSEEEEEEETTSSEEEE CS WD40 6 tltGHssvtslafspdgawlas 27 +GH v+s+ spdg++l++ tr|Q9HWH7|Q9HWH7_PSEAE 176 QVSGH--VHSVVSSPDGQYLFA 195 568**..************986 PP == domain 3 score: -3.6 bits; conditional E-value: 2 EEEEETTSSE CS WD40 15 slafspdgaw 24 +l fs dg++ tr|Q9HWH7|Q9HWH7_PSEAE 235 HLIFSADGRF 244 5678999987 PP == domain 4 score: -0.0 bits; conditional E-value: 0.21 EEEETTSSEEEEE CS WD40 16 lafspdgawlasG 28 +afsp g++++ + tr|Q9HWH7|Q9HWH7_PSEAE 336 FAFSPGGRFVLVA 348 68*******8755 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (38 nodes) Target sequences: 5563 (1857172 residues searched) Passed MSV filter: 126 (0.0226496); expected 111.3 (0.02) Passed bias filter: 112 (0.020133); expected 111.3 (0.02) Passed Vit filter: 9 (0.00161783); expected 5.6 (0.001) Passed Fwd filter: 2 (0.000359518); expected 0.1 (1e-05) Initial search space (Z): 5563 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 3528.63 // [ok]