Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AZOBR_RS09405 AZOBR_RS09405 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__azobra:AZOBR_RS09405 Length = 544 Score = 425 bits (1093), Expect = e-123 Identities = 230/530 (43%), Positives = 327/530 (61%), Gaps = 17/530 (3%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRN 81 LTPL FL R+ + DKTAVVY R ++ ASA+ R G + +S ++ N Sbjct: 20 LTPLDFLRRSAMVYPDKTAVVYGPLRRSWLEVEHRARALASAVSRAGVRPGEVVSVLAFN 79 Query: 82 RPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIK 141 P LE+ FGVP AG VL IN RL P +A+I+ H++S+ +VD +++ Sbjct: 80 TPAMLEAHFGVPGAGAVLNAINTRLDPPAVAFILEHAESRLFLVDRGLSAVARAALERMT 139 Query: 142 A--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTT 199 A ++ ++DP A++ A + Y + +K G + ++E+ I L YTSGTT Sbjct: 140 APPRVVWIDDP----AAQDADPVGDLEYEDFLKTGDPEAPWRRPEDEWESIALNYTSGTT 195 Query: 200 GLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCL 259 G PKGV++HHRGA LNA+ V+ + +SVYLWTLPMFH W + WA AVGAT+VCL Sbjct: 196 GNPKGVLYHHRGAHLNALGNVITFGLRPDSVYLWTLPMFHCNGWTYPWAVTAVGATHVCL 255 Query: 260 DKVDYPLIYRLVEKERVTHMCAAP---TVYVNLADYMKRNNLKFSN-RVHMLVAGAAPAP 315 VD I+RL+ +E+VTH+C AP T+ ++ D +KR F + V + GAAP Sbjct: 256 RAVDPAAIFRLIAEEKVTHLCGAPVVLTMLIHAPDAVKR---AFDHGPVQVATGGAAPPS 312 Query: 316 ATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSF-EM 374 A + M+ +G + H+YG+TE YGP + C W+ W LPLEE+A ARQG+P V+ E Sbjct: 313 AVIAGMERMGFRLTHLYGMTECYGPSTGCAWQEAWAELPLEERAVKMARQGVPNVTMSEQ 372 Query: 375 DVFDAN-GKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDG 433 V D + G+ VP DG+T+GE+ +RG+ V GY KNP T E+ RDGW H+GD AV+HPD Sbjct: 373 TVLDPDTGREVPADGETLGELALRGNTVMKGYLKNPAATDEALRDGWLHTGDLAVLHPDR 432 Query: 434 YIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEG 493 Y+EI DR KD+I +GGE ++S+ VE+ L + P V AV PD KWGE A + L+ G Sbjct: 433 YVEIKDRAKDIIISGGENIASLEVEEVLYKHPHVMEAAVVARPDAKWGETPCAFVTLKPG 492 Query: 494 V--KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 +++E EVI +C++ LAHF+ P+ V FG +P T+TGK+QK+VLR +A+ Sbjct: 493 SEGRVSEAEVIGWCRDHLAHFKTPRTVVFGALPKTSTGKIQKFVLREQAR 542 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: 804 Number of extensions: 37 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: 544 Length adjustment: 36 Effective length of query: 513 Effective length of database: 508 Effective search space: 260604 Effective search space used: 260604 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: 52 (24.6 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