Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AZOBR_RS06255 AZOBR_RS06255 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__azobra:AZOBR_RS06255 Length = 551 Score = 431 bits (1109), Expect = e-125 Identities = 229/529 (43%), Positives = 323/529 (61%), Gaps = 14/529 (2%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRN 81 L+PL FL R + + AV++ R T++ Y+ + ASAL +RG D ++ ++ N Sbjct: 23 LSPLSFLRRTAAVYPQRIAVIHGPVRRTWAETYERCVRLASALAKRGIGLGDTVAVMAPN 82 Query: 82 RPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY---LNSLLEVKD 138 PE E+ FGVP G VL +N RL + +A+I+ H ++K ++ D + ++ + + + Sbjct: 83 TPESFEAHFGVPMTGAVLNALNIRLDAEALAFILEHGEAKVLLTDREFSGVISKAVHMLE 142 Query: 139 QIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPL---PIPAKEEYSMITLYYT 195 + I++ D D+P A + TY + ++ G DP P+PA +E+ I L YT Sbjct: 143 PKRRPIVI--DIDDPQA-KGGELIGEQTYEQFLETG--DPAYEWPMPA-DEWQAIALNYT 196 Query: 196 SGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGAT 255 SGTTG PKGV++HHRGA+LNAM VL M + VYLWTLPMFH W F W A+ T Sbjct: 197 SGTTGNPKGVVYHHRGAYLNAMGNVLTWAMPHHPVYLWTLPMFHCNGWCFPWTVTAMAGT 256 Query: 256 NVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAP 315 NVC+ + IY + VTHMC AP + + + + + V M+ AGAAP Sbjct: 257 NVCVRTITAKGIYDALADLGVTHMCGAPIIMGLIVNAPEDQKREIPRGVKMMTAGAAPPA 316 Query: 316 ATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFE-M 374 A ++ ++ +G + HVYGLTE YGP +IC W W+ LPLEE+A LKARQG+ Y + E + Sbjct: 317 AVIEKIERMGFDVTHVYGLTEVYGPVTICAWHEHWNDLPLEERAALKARQGVNYATLEGL 376 Query: 375 DVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDG 433 V D N +P DG T+GE+ MRG+ V GY KNP T E+F GWFH+GD V H DG Sbjct: 377 MVADPNTLQPTRKDGVTMGEIFMRGNTVMKGYLKNPRATQEAFSGGWFHTGDLGVWHADG 436 Query: 434 YIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEG 493 YIE+ DR KD+I +GGE +S+I VE L + P + AV PDEKWGE A + ++EG Sbjct: 437 YIELKDRSKDIIISGGENISTIEVESVLYKHPDIVEAAVVARPDEKWGETPCAFVTVKEG 496 Query: 494 VKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542 +LTE EVI +C+E LAHF+CP+ V F +P T+TGK+QKYVLR++A+A Sbjct: 497 KQLTEAEVIAYCREHLAHFKCPRTVVFTALPKTSTGKIQKYVLRDQARA 545 Lambda K H 0.319 0.136 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 813 Number of extensions: 39 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 549 Length of database: 551 Length adjustment: 36 Effective length of query: 513 Effective length of database: 515 Effective search space: 264195 Effective search space used: 264195 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory