# 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/Ciona_intestinalis.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-52 178.1 0.0 2.6e-52 177.7 0.0 1.2 1 tr|F6ZA91|F6ZA91_CIOIN Uncharacterized protein OS=Ciona inte ------ inclusion threshold ------ 0.063 12.4 0.0 0.093 11.9 0.0 1.2 1 tr|F6RKZ8|F6RKZ8_CIOIN Uncharacterized protein OS=Ciona inte 0.08 12.1 0.0 0.11 11.7 0.0 1.2 1 tr|F6T569|F6T569_CIOIN Uncharacterized protein OS=Ciona inte Domain annotation for each sequence (and alignments): >> tr|F6ZA91|F6ZA91_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 177.7 0.0 4.7e-56 2.6e-52 3 274 .. 162 454 .. 160 455 .. 0.91 Alignments for each domain: == domain 1 score: 177.7 bits; conditional E-value: 4.7e-56 Rsm22 3 esiaYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselwe.eleevlvidaseelleiskelaadapelkea 88 +++a++lar ++ ya rvL +l++ v+df Pks+ldvg+g+gt +waa+ lw+ +l++++ +d s++++++s++++ + + tr|F6ZA91|F6ZA91_CIOIN 162 NTAAFLLARSAGCYASAFRVLSNLKNDVEDFNPKSILDVGSGTGTNMWAANSLWKdSLKQYVCVDVSDQMNKLSHYIVTAGDLNAPP 248 6789***************************************************99*********************998877766 PP Rsm22 89 alrrsvirealeleea...dLviisyvLleled.esreklvknlWakaskilvivEeGtpaGfrrvleaReal.............. 157 ++ir l + + d+vi sy+L el ++r +l+k lW+k+s++lv++E G +Gf+ ++eaR+ l tr|F6ZA91|F6ZA91_CIOIN 249 -PSGVFIRRFLPVSFKsvyDIVIASYTLSELPTsKERLTLLKLLWEKTSQYLVLIEYGNFNGFQIIMEARNLLlrgmegnnddkpwk 334 .788899777655544669************9989************************************************9998 PP Rsm22 158 .kaagfhivAPCPHeaaCPlvatedwChFsqrvaRlslhrlaksasvpvedekfsyvakerqprasaaaRvvrptkvrskkvlidlC 243 ++++ +v PCPH+ CP+ a++d C Fsq ++ + ++++ e+ f+ +k+++++ ++ +R++r + +++ v + +C tr|F6ZA91|F6ZA91_CIOIN 335 sWQKDASVVIPCPHSKPCPVWAKKDTCTFSQTYNVPGFAKALNKKQTIKEQFTFVVFEKNSNSNMNKLPRIIRGPFTQKTCVNCFVC 421 87899*****************************999888888766666666666688888899999******************** PP Rsm22 244 sedetlqrlvvtK.rkGeayka.ArkaeWGDrl 274 ++d+ l++ + K +G++ k+ +k + GD + tr|F6ZA91|F6ZA91_CIOIN 422 NKDGALENIQIHKnVHGAGLKTiVKKCKQGDYF 454 *************88**9998636888999987 PP >> tr|F6RKZ8|F6RKZ8_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.9 0.0 1.7e-05 0.093 147 173 .. 52 78 .. 45 87 .. 0.90 Alignments for each domain: == domain 1 score: 11.9 bits; conditional E-value: 1.7e-05 Rsm22 147 frrvleaRealkaagfhivAPCPHeaa 173 +++v+++R+ lk +++i+A C H a+ tr|F6RKZ8|F6RKZ8_CIOIN 52 YKMVIVVRQDLKMGKGKIAAQCSHAAV 78 99**********************986 PP >> tr|F6T569|F6T569_CIOIN Uncharacterized protein OS=Ciona intestinalis OX=7719 PE=4 SV=2 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 11.7 0.0 1.9e-05 0.11 32 117 .. 58 149 .. 50 180 .. 0.76 Alignments for each domain: == domain 1 score: 11.7 bits; conditional E-value: 1.9e-05 Rsm22 32 dflPkslldvgegpgtalwaaselweeleevlvidaseelleiskelaadapelkeaalrrsvireal.eleea......dLviisy 111 + Pk++l++g g + + +s l +e ++ +i+as++ +++e++ a k+++ r + e l ++ e+ d v i + tr|F6T569|F6T569_CIOIN 58 EASPKNVLEIGCYCGYSALRMSRLLKEDAKIFTIEASSQYADVAQEIISFAGMEKKVQILRGLSDEVLpTIAEKcgvrtfDFVFIDH 144 557********************************************9988777776655554444331333335555557777766 PP Rsm22 112 vLlele 117 +el+ tr|F6T569|F6T569_CIOIN 145 A-KELY 149 4.4555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 16678 (5370518 residues searched) Passed MSV filter: 461 (0.0276412); expected 333.6 (0.02) Passed bias filter: 328 (0.0196666); expected 333.6 (0.02) Passed Vit filter: 18 (0.00107927); expected 16.7 (0.001) Passed Fwd filter: 3 (0.000179878); expected 0.2 (1e-05) Initial search space (Z): 16678 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.11u 0.00s 00:00:00.11 Elapsed: 00:00:00.04 # Mc/sec: 36922.31 // [ok]