Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate HSERO_RS23535 HSERO_RS23535 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__HerbieS:HSERO_RS23535 Length = 546 Score = 389 bits (1000), Expect = e-112 Identities = 211/536 (39%), Positives = 312/536 (58%), Gaps = 6/536 (1%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G+ + Y+ LTP+ F+ RA + +TA+++ R + Y ASAL G Sbjct: 7 GLGRNAANYAALTPIDFIARAAAVYGKRTAIIHGALRQDWDQTYRRTRRLASALQGLGVG 66 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 + D +S + N P +E+ FGVP AG VL +N RL + + +++ H ++K +++D + Sbjct: 67 KNDTVSAMLPNTPAMVEAHFGVPMAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFA 126 Query: 131 NSLLEVKDQIKA-EIILLEDPDNPSASETARKEVRMTYRELVKGGSRD-PLPIPAKEEYS 188 +++ Q+ A +I+ + D P R + Y L+ GG +PA +E+ Sbjct: 127 ALAQQLRTQLPALKIVEVFDELGPPPVAGERFG-HLEYEALLAGGDEHFDWQMPA-DEWD 184 Query: 189 MITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWA 248 I L YTSGTTG PKGV++HHRGA LNA++ +LE + + VYLWTLPMFH W F W Sbjct: 185 AIALNYTSGTTGDPKGVVYHHRGAALNAVSNILEWDLPKHPVYLWTLPMFHCNGWCFPWT 244 Query: 249 TVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLV 308 A NVCL K + L++ L+ + +TH CAAP V+ LA+ + V +V Sbjct: 245 VAARAGVNVCLRKFEPKLVFDLIAEHGITHYCAAPIVHAALANAPEGWRAGIRGPVKAMV 304 Query: 309 AGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP 368 AGA P A L M+ + + HVYGLTE YGP ++C + EW++L ++++A K+RQG+ Sbjct: 305 AGAPPPAAVLAKMEAMQFELTHVYGLTEVYGPAAVCAEQDEWNTLSVDQRAVQKSRQGVR 364 Query: 369 Y-VSFEMDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDA 426 Y + + V + PV DG+ IGE++ RG+ GY KN T E+F GWFH+GD Sbjct: 365 YHLQSGVTVLSPDTMAPVAADGEEIGEIMFRGNICMKGYLKNDRATHEAFAGGWFHTGDL 424 Query: 427 AVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTA 486 V++ DGYI+I DR KD+I +GGE +SS+ VE L P V A AV PDEKWGE A Sbjct: 425 GVMNADGYIKIKDRSKDIIISGGENISSVEVEDVLYRHPAVLAAAVVAQPDEKWGETPCA 484 Query: 487 RIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542 +EL+EG ++ E+ +FC+ LA F+ PK + FGP+P T+TGK+QK+ LR K+ Sbjct: 485 FVELKEGAEVGAAELTEFCRSHLAGFKVPKAIYFGPLPKTSTGKIQKFELRKRMKS 540 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: 706 Number of extensions: 30 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: 546 Length adjustment: 36 Effective length of query: 513 Effective length of database: 510 Effective search space: 261630 Effective search space used: 261630 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