# 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/Rsm22.hmm.txt # target sequence database: proteomes/Dictyostelium_discoideum.fasta # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: Rsm22 [M=275] Accession: PF09243.9 Description: Mitochondrial small ribosomal subunit Rsm22 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-69 232.8 0.0 6e-69 231.9 0.0 1.5 1 tr|Q54DG6|Q54DG6_DICDI Uncharacterized protein OS=Dictyostel ------ inclusion threshold ------ 0.11 11.3 0.0 0.11 11.3 0.0 1.2 1 tr|Q54LN7|Q54LN7_DICDI Uncharacterized protein OS=Dictyostel Domain annotation for each sequence (and alignments): >> tr|Q54DG6|Q54DG6_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB0184302 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.9 0.0 9.4e-73 6e-69 3 274 .. 624 939 .. 622 940 .. 0.91 Alignments for each domain: == domain 1 score: 231.9 bits; conditional E-value: 9.4e-73 Rsm22 3 esiaYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselwe.eleevlvidaseelleiskelaadapelkea 88 +++aY+ +r+p+ ya +rv e+++r p+f+P+slld g+gpgt+lw a +w +++++ ++ s + ++k+l++ +++ + tr|Q54DG6|Q54DG6_DICDI 624 QVLAYISHRMPGVYACTHRVFSEINSRLPNFKPTSLLDYGSGPGTVLWSADTIWGdSIKRIRAVEPSTYMSDVAKKLLEGNTNRVKW 710 689****************************************************99********************9876554333 PP Rsm22 89 alrrsvirealeleea..........dLviisyvLleled.esreklvknlWakask..ilvivEeGtpaGfrrvleaReal..... 157 s + ++++l+ + ++v+ syvL el e r++lv++lW +++ ilv++E+Gtp Gf+ ++eaR+ + tr|Q54DG6|Q54DG6_DICDI 711 ----SPYLNTANLKRQdgtipstelnEMVTASYVLSELPSqEARNDLVRELWSHVKPsgILVLIEPGTPIGFNIIKEARQLIldeep 793 ....33334445544445666679999***********9989**********9987666*********************999**** PP Rsm22 158 ......kaagfhivAPCPHeaaCPlvatedwChFsqrvaRlslhrlak..sasvpvedekfsyvakerqprasa............. 223 k ++++vAPCPH+ +CP+ wChFsqrv+R + lak + +p+edek+sy+ ++ ++s tr|Q54DG6|Q54DG6_DICDI 794 eilsiyKSTKAQVVAPCPHSGKCPMGSL-SWCHFSQRVERPVFQKLAKgpHSTMPYEDEKYSYIVLSKVVHSSIqnqlekqlqiypt 879 ****99999***************9887.9******************988899*********77666666666678999******* PP Rsm22 224 ........aaRvvrptkvrskkvlidlCsedetlqrlvvtKrkG.eaykaArkaeWGDrl 274 ++R++ + +r ++v++d+Cs +++l+r++v +++G ++y+ Ark+ W D + tr|Q54DG6|Q54DG6_DICDI 880 eeleptknWSRLIEAPLKRGGHVIMDVCSPNGSLNRVTVARSHGkQMYREARKSFWSDSF 939 ********************************************999***********87 PP >> tr|Q54LN7|Q54LN7_DICDI Uncharacterized protein OS=Dictyostelium discoideum OX=44689 GN=DDB_G0286529 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.3 0.0 1.7e-05 0.11 31 61 .. 52 82 .. 9 85 .] 0.83 Alignments for each domain: == domain 1 score: 11.3 bits; conditional E-value: 1.7e-05 Rsm22 31 pdflPkslldvgegpgtalwaaselweelee 61 ++ +P ++ld++ g+g +++a+e++++l+ tr|Q54LN7|Q54LN7_DICDI 52 NQEKPMKILDIACGTGPLTIVANEIFKKLQI 82 4568***********************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 12739 (6856946 residues searched) Passed MSV filter: 421 (0.0330481); expected 254.8 (0.02) Passed bias filter: 320 (0.0251197); expected 254.8 (0.02) Passed Vit filter: 28 (0.00219797); expected 12.7 (0.001) Passed Fwd filter: 2 (0.000156998); expected 0.1 (1e-05) Initial search space (Z): 12739 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.15u 0.00s 00:00:00.15 Elapsed: 00:00:00.05 # Mc/sec: 37713.20 // [ok]