Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AZOBR_RS19480 AZOBR_RS19480 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__azobra:AZOBR_RS19480 Length = 556 Score = 393 bits (1010), Expect = e-114 Identities = 214/542 (39%), Positives = 314/542 (57%), Gaps = 6/542 (1%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G+ P + + L+PL FL+RA K + DK A+ + TY+ F+D V A AL+R G Sbjct: 15 GLAPDPANHVPLSPLSFLKRAAKVYPDKPAIRHGRRTITYAQFHDRVRRFAGALLRAGVR 74 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 R D +S ++ N P LE+ + VP AG VL +N RL +A+I++HS++K ++VD Sbjct: 75 RGDTVSVLAPNVPALLEAHYAVPLAGAVLNALNTRLDAAAIAFILDHSETKLLIVDRELS 134 Query: 131 NSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMI 190 + + I L+E D + + V Y + + P P +E+ I Sbjct: 135 PVAKAALARTERPITLVEIADEQAPDAPSLGAVE--YEDFLAAADPAPWHGP-DDEWQAI 191 Query: 191 TLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATV 250 L YTSGTTG PKGV++HHRGA+LNA+ + SV+LWTLPMFH W +SWA Sbjct: 192 ALNYTSGTTGNPKGVVYHHRGAYLNALGNAFTLNVRPESVFLWTLPMFHCNGWTYSWAVT 251 Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310 A G T+VCL +V+ I+ + + VTH+C AP V L RV + G Sbjct: 252 AAGGTHVCLRRVEPAAIFDAIAELGVTHLCGAPIVLNMLIHAPAAVRRPAPRRVIVGTGG 311 Query: 311 AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYV 370 AAP A L M +G + H+YGLTE YGP ++C + W+ L + A ARQG+ +V Sbjct: 312 AAPPSAVLAGMATLGFEVVHMYGLTECYGPATVCAPQDGWEDLDADGLALQFARQGVNHV 371 Query: 371 SFE-MDVFDAN-GKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428 + E V D G+PVP D +TIGE+ +RG+ V GY KNP T E+ +DGWF +GD V Sbjct: 372 AVEDATVLDRETGRPVPADAQTIGEIALRGNTVMKGYLKNPAATKEALKDGWFRTGDLGV 431 Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488 +HPDGYIE+ DR KD+I +GGE +SS+ VE+ L P V AV PD++WGE A + Sbjct: 432 LHPDGYIEVKDRSKDIIISGGENISSLEVEEALYRHPAVLEAAVVARPDDRWGESPCAFV 491 Query: 489 ELQEGV-KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKAKANKE 547 ++ G + +E ++I++C++R+AH++ P+ V F +P T+TGK+QK VLR+ A+ + Sbjct: 492 TVKPGAERPSESDIIQWCRDRIAHYKVPRTVVFSDLPKTSTGKIQKTVLRDAARELGERR 551 Query: 548 KS 549 ++ Sbjct: 552 EA 553 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: 765 Number of extensions: 34 Number of successful extensions: 5 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: 556 Length adjustment: 36 Effective length of query: 513 Effective length of database: 520 Effective search space: 266760 Effective search space used: 266760 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