Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_012471443.1 GLOV_RS16915 fatty acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_000020385.1:WP_012471443.1 Length = 545 Score = 226 bits (575), Expect = 2e-63 Identities = 155/517 (29%), Positives = 252/517 (48%), Gaps = 26/517 (5%) Query: 41 VVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLV 100 +VYRD R++Y V A+AL G R D ++ + + +LE FF VP G VL Sbjct: 35 IVYRDHRFSYRDLRQRVARLANALTDLGVKRGDTVAVMDWDSNRYLECFFAVPMIGAVLH 94 Query: 101 PINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVK---DQIKAEIILLEDPDNPSASE 157 IN RLSP+++ Y I+H++ ++V+ +L L +++ D +K+ ++L ++P P + Sbjct: 95 TINVRLSPEQILYTIDHAEDDVLLVNSEFLPILEQIRGRMDTVKSFVLLNDEPTVPESHI 154 Query: 158 TARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAM 217 E Y L+ S D +E + T +YT+GTTG+PKGV HR L+ + Sbjct: 155 PFSGE----YEALLAAAS-DQFNFADFDENTRATTFYTTGTTGMPKGVYFSHRQLVLHTL 209 Query: 218 -------AEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYRL 270 + V + VY+ PMFH +WG + +G V + + L Sbjct: 210 GVLAVLGSSVSHGGFNRQDVYMPITPMFHVHAWGLPYVATMLGVKQVYPGRYLPDHLLEL 269 Query: 271 VEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYMCH 330 +++E+VT PT+ L + + S +++ GAA + A + G + Sbjct: 270 IDREKVTFSHCVPTILHMLLKHPHAGRMDLSGW-KVIIGGAAMSRALCLDALQRGIDLFT 328 Query: 331 VYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKT 390 YG++ET +I E L EEQA ++ + G ++ + D+ + P DGK+ Sbjct: 329 GYGMSETCPILTISHLTPEMLELSPEEQAVIRCKTGRSLPLVDLKIVDSARQEQPRDGKS 388 Query: 391 IGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGE 450 GE+V+R + GY K+ + + + G+ H+GD AV GY++I DR KD++ GE Sbjct: 389 TGEIVVRAPWLTQGYLKDHKASERLWEGGYLHTGDVAVRDEQGYVKITDRTKDVLKVSGE 448 Query: 451 KVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKE--- 507 VSS+ +E + PGV VAV G PDEKWGE A + + +TE+E+ +E Sbjct: 449 WVSSLELEDIIAHHPGVAEVAVIGQPDEKWGERPLALVVAKPDNPVTEKELTHLVREYAD 508 Query: 508 -----RLAHFECPKIVEFGPIPMTATGKMQKYVLRNE 539 + K+VE I T+ GK+ K LR + Sbjct: 509 KGVVTKQVVLLKVKLVE--AIDKTSVGKVNKVALREK 543 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: 754 Number of extensions: 33 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: 545 Length adjustment: 36 Effective length of query: 513 Effective length of database: 509 Effective search space: 261117 Effective search space used: 261117 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 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