Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_100845302.1 C0J26_RS20655 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_003031005.1:WP_100845302.1 Length = 562 Score = 133 bits (334), Expect = 2e-35 Identities = 117/367 (31%), Positives = 174/367 (47%), Gaps = 34/367 (9%) Query: 192 LYYTSGTTGLPKGVMHHHRGAFLN------AMAEVLEHQMDL----NSVYLWTLPMFHAA 241 L YT GTTGL KG M H N +A++ L V + LP++H Sbjct: 212 LQYTGGTTGLAKGAMLTHGNLVANMQQVRACLAQLGPDGQPLLREGQEVMIAPLPLYHIY 271 Query: 242 SWGFSWATVAV-GATNVCLDKV-DYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLK 299 ++ + + V G NV + D + ++ + + + T++V L D+ L Sbjct: 272 AFTANCMCMMVSGNHNVLITNPRDIAGFIKELKNWKFSELLGLNTLFVALMDHPDFKTLD 331 Query: 300 FSNRVHMLVAGAAPAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLE 356 FS G A AT + ++I G C + YGLTET P + P Sbjct: 332 FSTLKLTNSGGTALVKATAERWEQITG--CRITEGYGLTET-SPVACTN--------PYG 380 Query: 357 EQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESF 416 +Q++L G+P + V + +G P + GE+ ++G + GY++ PE TAE Sbjct: 381 DQSRL-GTVGLPVPGTLLKVINDDGVEQPLGER--GELCIKGPQIMKGYWQKPEATAEVL 437 Query: 417 -RDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGT 475 +GWF SGD AV+ PDG++ IVDR KD+I G V +E +M P V AV G Sbjct: 438 DAEGWFKSGDIAVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGV 497 Query: 476 PDEKWGEVVTARIELQE-GVKLTEEEVIKFCKERLAHFECPK-IVEFGPIPMTATGKMQK 533 PDE+ GE V + +E GV L EE+ +CKE ++ PK IV +PMT GK+ + Sbjct: 498 PDERSGEAVKLFVVARESGVSL--EELKAYCKENFTAYKVPKHIVLRESLPMTPVGKILR 555 Query: 534 YVLRNEA 540 LR+ A Sbjct: 556 RELRDIA 562 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: 689 Number of extensions: 29 Number of successful extensions: 4 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: 562 Length adjustment: 36 Effective length of query: 513 Effective length of database: 526 Effective search space: 269838 Effective search space used: 269838 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 24 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