Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_086509504.1 BZY95_RS08440 fatty acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_002151265.1:WP_086509504.1 Length = 550 Score = 243 bits (620), Expect = 1e-68 Identities = 163/518 (31%), Positives = 255/518 (49%), Gaps = 25/518 (4%) Query: 41 VVYRD-SRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVL 99 +VYRD SR+ Y F + V A L +G D ++ + + +LE+FF +P G VL Sbjct: 38 IVYRDLSRHDYRRFRERVHQLAHTLSSQGIKAGDVVAVLDWDSHRYLEAFFAIPMLGAVL 97 Query: 100 VPINFRLSPKEMAYIINHSDSKFVVVDE---PYLNSLLEVKDQIKAEIILLEDPDNPSAS 156 +N RLSP+++ Y + H++ FV+V E P L L +I+ ++ + P +S Sbjct: 98 HTVNVRLSPEQILYTMEHAEDDFVLVHEDFVPLLEPLATRLPRIRGYLLCQDAPAEVQSS 157 Query: 157 ETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNA 216 E E + P +E ++ TL+YT+GTTG PKGV HR L+ Sbjct: 158 LNLVGEY-----EALLATQPSHYDFPTFDENAVATLFYTTGTTGNPKGVFFTHRQLVLHT 212 Query: 217 MAEVLEHQ------MDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYRL 270 + E Q ++ + VY+ PMFH +WG + +GAT V + + ++ +L Sbjct: 213 LGEANAFQTPGFELLNRDKVYMPITPMFHVHAWGVPYTATLMGATQVYPGRYEPEMLVKL 272 Query: 271 VEKERVTHMCAAPTVY--VNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYM 328 + E+V PT+ V A+ + + S +LV G+A + E+G Sbjct: 273 LVGEKVDFSHCVPTLLNMVVGAEAIASGKVDLSGW-KVLVGGSALTQPLAQKAWELGIDT 331 Query: 329 CHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDG 388 YG++ET + R+ + Q + + G+P + V D +G P+P DG Sbjct: 332 RSAYGMSETCPLLTADILPRDINEADFATQLPWRCKAGVPVPLVHLQVVDESGTPLPHDG 391 Query: 389 KTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTG 448 +++GEV +R + GYYK ++ E +RDGW H+GD AV+ G+++I DR KD+I TG Sbjct: 392 ESVGEVRVRAPWLTQGYYKEETRSEELWRDGWLHTGDVAVLDERGFLQIRDRIKDVIKTG 451 Query: 449 GEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTA-RIELQEGVKLTEEEVIKFCKE 507 GE +SS+ +E + + PG+ VAV G PDEKWGE A + EEV F + Sbjct: 452 GEWISSLELENLIGQCPGITEVAVIGVPDEKWGERPAALAVPSDPNSPPQAEEVQAFLQR 511 Query: 508 -----RLAHFECPKIVEF-GPIPMTATGKMQKYVLRNE 539 RL + P V F IP T+ GK+ K +R E Sbjct: 512 FVDEGRLNRWAIPSFVRFVDEIPKTSVGKLDKKRIRQE 549 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: 753 Number of extensions: 30 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: 550 Length adjustment: 36 Effective length of query: 513 Effective length of database: 514 Effective search space: 263682 Effective search space used: 263682 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 Apr 09 2024. 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