# 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/Branchiostoma_floridae.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-60 203.6 1.0 2.6e-32 112.9 0.0 2.8 3 tr|C3XZS8|C3XZS8_BRAFL Uncharacterized protein OS=Branchiost 9e-06 25.8 0.0 0.0024 17.9 0.0 2.2 2 tr|C3YC49|C3YC49_BRAFL Uncharacterized protein OS=Branchiost ------ inclusion threshold ------ 0.18 11.7 0.0 0.31 10.9 0.0 1.3 1 tr|C3ZE13|C3ZE13_BRAFL Uncharacterized protein OS=Branchiost 0.35 10.8 0.0 0.52 10.2 0.0 1.2 1 tr|C3YCR0|C3YCR0_BRAFL Uncharacterized protein OS=Branchiost Domain annotation for each sequence (and alignments): >> tr|C3XZS8|C3XZS8_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_85605 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -1.9 0.1 0.36 2.5e+03 48 90 .. 97 139 .. 92 160 .. 0.75 2 ! 112.9 0.0 3.6e-36 2.6e-32 4 162 .. 176 339 .. 173 346 .. 0.91 3 ! 88.0 0.2 1.4e-28 9.7e-25 161 275 .] 413 535 .. 407 535 .. 0.84 Alignments for each domain: == domain 1 score: -1.9 bits; conditional E-value: 0.36 Rsm22 48 alwaaselweeleevlvidaseelleiskelaadapelkeaal 90 a++ ++ lw++ ++v + ++++ei++e +++ +e++l tr|C3XZS8|C3XZS8_BRAFL 97 ATYLTNYLWSRKRPVEDAEVRRKAQEIAEEYTQQGLLQEEENL 139 6677888999999999999999999999998887766555543 PP == domain 2 score: 112.9 bits; conditional E-value: 3.6e-36 Rsm22 4 siaYalarlpatyavlrrvLdelaervpdflPkslldvgegpgtalwaaselwe.eleevlvidaseelleiskelaadapelkeaa 89 +aY++ + p+ ya+ +rvL el +r p+f+P +l+d g+g g+++waa+ +w l+e+ d+s++++ +++ l++ +e+ + tr|C3XZS8|C3XZS8_BRAFL 176 GLAYLVGKAPGVYAATYRVLAELSKREPKFRPMTLMDYGSGAGMTVWAAHTIWGhWLREYSCFDTSSSMNDLAELLLRGGEENGKLL 262 589***************************************************7799***********************999996 PP Rsm22 90 lrrsvirealeleea....dLviisyvLleled.esreklvknlWakaskilvivEeGtpaGfrrvleaRealkaagf 162 + + + + el + dLv+++y L e +r +v++lW+k+s+ lvivE+Gt +G+++v+eaR+ + ++ tr|C3XZS8|C3XZS8_BRAFL 263 HPNIFF-RQYELPNPnikhDLVVCAYSLSEQPSaVQRMRVVRRLWRKTSQFLVIVENGTNEGHKMVMEARDLVLSGKA 339 666666.666776656888***********99989***********************************98755554 PP == domain 3 score: 88.0 bits; conditional E-value: 1.4e-28 Rsm22 161 gfhivAPCPHeaaCPlvate..dwChFsqrvaRls.lhrlaksasvpvedekfsy..vakerqprasa.aaRvvrptkvrskkvlid 241 +h+ PCPH++ CP++a++ ++C+F q+++ + + + ks + e fsy ++k++ +++s ++R+vrp r ++v ++ tr|C3XZS8|C3XZS8_BRAFL 413 SAHVFSPCPHDTSCPRLADNsrTPCNFQQSYQPPNfMPVPPKSDGNSSLFETFSYvvLRKGQRSEESIrWPRIVRPVLRRPRHVHCR 499 68****************9999**********5441444455444444445666655899998888877****************** PP Rsm22 242 lCsedetlqrlvvtK.rkG.eaykaArkaeWGDrlp 275 +C +++lq v+t ++G +y++Ar +eWGD lp tr|C3XZS8|C3XZS8_BRAFL 500 MCLGNGQLQDAVLTGrKHGkPLYRCARMSEWGDMLP 535 **************989**88************985 PP >> tr|C3YC49|C3YC49_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_126511 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 17.9 0.0 3.4e-07 0.0024 33 141 .. 294 405 .. 272 407 .. 0.89 2 ! 5.7 0.0 0.0017 12 97 141 .. 521 569 .. 475 571 .. 0.81 Alignments for each domain: == domain 1 score: 17.9 bits; conditional E-value: 3.4e-07 Rsm22 33 flPkslldvgegpgtalwaaselweeleevlvidaseelleiskelaadapelkeaalrrsvirealeleea..dLviisyvLlele 117 +Pk++ldvg g + ++ e++++ +v+ +d +++ + + + p + + + +e+l++ ++ d+v +yvL+e+ tr|C3YC49|C3YC49_BRAFL 294 LKPKTILDVGTGNCFSAFVFGEMFPQ-SDVIGVDLAAPFVRFCRLWKSHRPGGAPNVKFYQDNGEKLHFPDStfDVVNFAYVLHEMP 379 57**********************97.57999******************9988887777888899***99899************* PP Rsm22 118 desreklvknlWakask..ilvivEe 141 ++ + + ++W+ ++ +l i+E+ tr|C3YC49|C3YC49_BRAFL 380 SDNAQRALAEAWRVLKPggTLNIIEP 405 *999*********9886668888876 PP == domain 2 score: 5.7 bits; conditional E-value: 0.0017 Rsm22 97 ealeleea..dLviisyvLleledesreklvknlWakask..ilvivEe 141 e+l++ ++ d+v +yvL+e+ ++ + + ++W+ ++ +l i+E+ tr|C3YC49|C3YC49_BRAFL 521 EKLHFPDStfDVVNFAYVLHEMPSDNAQRALAEAWRVLKPggTLNIIEP 569 5666666678**************999*********9886668888876 PP >> tr|C3ZE13|C3ZE13_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_65542 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.9 0.0 4.3e-05 0.31 36 124 .. 8 104 .. 4 112 .. 0.82 Alignments for each domain: == domain 1 score: 10.9 bits; conditional E-value: 4.3e-05 Rsm22 36 kslldvgegpgtalwaaselweeleevlvidaseelleisk.elaadapelkeaalrrsvireale.leea.......dLviisyvL 113 +++ld+g+g g +a +l e +v+ +d++ee le ++ ++ + ++ + +++++++ +e l ea d viis + tr|C3ZE13|C3ZE13_BRAFL 8 THVLDLGSGAGHDCFALAKLVGEKGHVTGVDMTEEQLEFARsYIDYHRETFGYSEPNTDFVMAYIEkLGEAglkddtfD-VIISNCV 93 589*******************************999998625677888888899999999998762555578875533.8999999 PP Rsm22 114 leledesrekl 124 +l +++r++l tr|C3ZE13|C3ZE13_BRAFL 94 VNLSPDKRAVL 104 99999998765 PP >> tr|C3YCR0|C3YCR0_BRAFL Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_115286 PE=4 SV=1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 10.2 0.0 7.3e-05 0.52 147 173 .. 51 77 .. 45 83 .. 0.90 Alignments for each domain: == domain 1 score: 10.2 bits; conditional E-value: 7.3e-05 Rsm22 147 frrvleaRealkaagfhivAPCPHeaa 173 +++v ++R+ lk +++++A C H a+ tr|C3YCR0|C3YCR0_BRAFL 51 YKMVFVVRQDLKMGKGKVAAQCSHAAV 77 99**********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (275 nodes) Target sequences: 28542 (13248087 residues searched) Passed MSV filter: 850 (0.0297807); expected 570.8 (0.02) Passed bias filter: 539 (0.0188845); expected 570.8 (0.02) Passed Vit filter: 38 (0.00133137); expected 28.5 (0.001) Passed Fwd filter: 4 (0.000140144); expected 0.3 (1e-05) Initial search space (Z): 28542 [actual number of targets] Domain search space (domZ): 4 [number of targets reported over threshold] # CPU time: 0.27u 0.01s 00:00:00.28 Elapsed: 00:00:00.09 # Mc/sec: 40480.27 // [ok]