# hmmscan :: search sequence(s) against a profile 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 sequence file: AA/23726_FusoPortal_Gene_257.faa # target HMM database: Pfam-A.hmm # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 23726_FusoPortal_Gene_257 [L=377] Description: # 275654 # 276784 # -1 # ID=1_257;partial=00;start_type=ATG;rbs_motif=GGxGG;rbs_spacer=3-4bp;gc_cont=0.280 Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-20 73.4 0.0 2.4e-20 72.4 0.0 1.6 1 BATS Biotin and Thiamin Synthesis associated domain 3e-10 40.6 0.1 7.2e-10 39.4 0.1 1.6 1 Radical_SAM Radical SAM superfamily ------ inclusion threshold ------ 0.22 11.7 5.6 0.32 11.2 0.4 2.8 3 Fer4_12 4Fe-4S single cluster domain Domain annotation for each model (and alignments): >> BATS Biotin and Thiamin Synthesis associated domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 72.4 0.0 4.2e-24 2.4e-20 1 85 [. 260 364 .. 260 365 .. 0.97 Alignments for each domain: == domain 1 score: 72.4 bits; conditional E-value: 4.2e-24 E--B----...........TCCCCHHHHHHHHHHSTTSECCCTCHH-HHHHHHHHHCCT--EEE-C---TTTGGG......... CS BATS 1 siprlrpi...........kdtpllkiiaalRlllPkagillsgResaefrdqlllklGansisagsktevggya......... 64 s+prlrp+ +++l++ii+a+Rl+lP a+i++s+Re+ frd+++ k++a++isag+ t++g ++ 23726_FusoPortal_Gene_257 260 SCPRLRPVinnlkvekeivTERELFQIICAYRLFLPFANITISTRENSIFRDNII-KIAATKISAGVDTGIGAHTecstkkgde 342 78*****************************************************.**************************** PP .SESSTT-TCCCCHHHHHHTT- CS BATS 65 .flttdgrsleedvkmleelGl 85 f++ d+r++ ++ + +++ +l 23726_FusoPortal_Gene_257 343 qFEIADKRTAAQIFEKVKSEDL 364 *************999998877 PP >> Radical_SAM Radical SAM superfamily # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 39.4 0.1 1.3e-13 7.2e-10 3 121 .. 84 197 .. 82 214 .. 0.88 Alignments for each domain: == domain 1 score: 39.4 bits; conditional E-value: 1.3e-13 EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECS CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF Radical_SAM 3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetng 86 +++ C + C++C ++++ + + + l+ e+i++e+ke+ a+ g e++++ ge y++++ + e++ kla + ++++ + + 23726_FusoPortal_Gene_257 84 ISNYCDNYCVYCGFNSH--NKIKRAKLDFEQIEQELKEI-AKSGLQEILILTGESERYSNIEYIGEAC-KLARKYFSNVGIEIY 163 6789***********98..********************.899************9999775555555.554588888888888 PP SCH.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHH CS xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF Radical_SAM 87 tlpdeeklerllelgvdrvslgleaaddekvlklm 121 ++ e + l g d+v++ e++++ek++kl+ 23726_FusoPortal_Gene_257 164 PVN-VEDYKYLNSCGADYVTIFQETYNNEKYKKLH 197 887.9************************888876 PP >> Fer4_12 4Fe-4S single cluster domain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 2.3 0.1 0.031 1.8e+02 78 110 .. 5 37 .. 3 66 .. 0.82 2 ? 11.2 0.4 5.7e-05 0.32 13 85 .. 86 157 .. 71 187 .. 0.79 3 ? -2.0 0.1 0.66 3.7e+03 25 52 .. 335 363 .. 333 368 .. 0.70 Alignments for each domain: == domain 1 score: 2.3 bits; conditional E-value: 0.031 Fer4_12 78 evkeekpekdiwlytgytleelskkekeellke 110 ++ ++ ++k+i +++ y ++ +s++++ee l++ 23726_FusoPortal_Gene_257 5 NINSNIMDKVISEMNTYDYNSFSNEDVEEALNK 37 566667799999**********99988887765 PP == domain 2 score: 11.2 bits; conditional E-value: 5.7e-05 Fer4_12 13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 + C+ C +C ++ + k+ k ++e +e+ +++++k+ +++ +l GE ++n e + e +k ++ +++ 23726_FusoPortal_Gene_257 86 NYCDNYCVYCGFNSHNKIKRAK-LDFEQIEQELKEIAKSGLQEILILTGESERYSNIEYIGEACKLARKYFSN 157 57********988888888765.56666777778899**************9999999998888877776664 PP == domain 3 score: -2.0 bits; conditional E-value: 0.66 Fer4_12 25 ketwsfksgkef.tkelleeiiedlkkes 52 ++t++ +++ e+ +k ++++i+e++k e 23726_FusoPortal_Gene_257 335 CSTKKGDEQFEIaDKRTAAQIFEKVKSED 363 67777777777734888888888886654 PP Internal pipeline statistics summary: ------------------------------------- Query sequence(s): 1 (377 residues searched) Target model(s): 16712 (2907032 nodes) Passed MSV filter: 980 (0.0586405); expected 334.2 (0.02) Passed bias filter: 511 (0.0305768); expected 334.2 (0.02) Passed Vit filter: 50 (0.00299186); expected 16.7 (0.001) Passed Fwd filter: 3 (0.000179512); expected 0.2 (1e-05) Initial search space (Z): 16712 [actual number of targets] Domain search space (domZ): 3 [number of targets reported over threshold] # CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.34 # Mc/sec: 3223.39 // [ok]