Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate GFF894 PS417_04540 long-chain fatty acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__WCS417:GFF894 Length = 560 Score = 228 bits (581), Expect = 5e-64 Identities = 157/532 (29%), Positives = 254/532 (47%), Gaps = 23/532 (4%) Query: 24 PLLF--LERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISR 80 PLL L +G ++ +VYRD RYTY T + V A+ L G D ++ + Sbjct: 17 PLLIKRLLMSGARYEKTREIVYRDKLRYTYPTLIERVARLANVLTEAGVKAGDTVAVMDW 76 Query: 81 NRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQI 140 + +LE F +P G V+ IN RLSP+++ Y +NH++ +FV+V+ ++ + + Sbjct: 77 DSHRYLECMFAIPMIGAVIHTINVRLSPEQILYTMNHAEDRFVLVNSEFVGLYQAIAGHL 136 Query: 141 KA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGT 198 + +LL D D S+TA + E + + +E S+ T +YT+GT Sbjct: 137 TTVDKTLLLTDGD----SKTAELPNLVGEYESLLAAASPKYDFQDFDENSVATTFYTTGT 192 Query: 199 TGLPKGVMHHHRGAFLNAMAEVL-------EHQMDLNSVYLWTLPMFHAASWGFSWATVA 251 TG PKGV HR L+ + + N VY+ PMFH +WG + Sbjct: 193 TGNPKGVYFTHRQLVLHTIGVATIMGSVDSVRLLGTNDVYMPITPMFHVHAWGLPYVATM 252 Query: 252 VGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGA 311 +G V + D + L KE+VT PT+ + + + F +++ G+ Sbjct: 253 LGLKQVYPGRYDPEYLVELWRKEKVTFSHCVPTILQMVLNAKAAQGVDFGGW-KIVIGGS 311 Query: 312 APAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVS 371 A +A + G + YG++ET S E + +E+ + + G+P Sbjct: 312 ALNRTLYEAAKARGIQLTAAYGMSETGPLVSCAHLNEELMAGTEDERITYRIKAGVPGPL 371 Query: 372 FEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHP 431 E + DA G +P DG++ GE+V+R + GYY P+K AE + GW H+GD A + Sbjct: 372 VEAAIMDAEGNFLPADGESQGELVLRAPWLTEGYYNEPQKGAELWAGGWMHTGDVATLDA 431 Query: 432 DGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQ 491 G I+I DR KD+I TGGE +SS+ +E + P V+ VAV G D +WGE A + ++ Sbjct: 432 FGVIDIRDRIKDVIKTGGEWISSLALEDLVSRHPAVREVAVVGIADPQWGERPFALLVVR 491 Query: 492 EGVKLTEEEVIKFCKE-----RLAHFECP-KIVEFGPIPMTATGKMQKYVLR 537 +G + E+ + K L+ + P +I IP T+ GK+ K +R Sbjct: 492 DGHVIGARELKEHLKPFVELGHLSKWAIPSQIAVVTEIPKTSVGKLDKKRIR 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: 757 Number of extensions: 34 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: 560 Length adjustment: 36 Effective length of query: 513 Effective length of database: 524 Effective search space: 268812 Effective search space used: 268812 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 Apr 09 2024.
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