Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_009764221.1 MICLODRAFT_RS22930 benzoate-CoA ligase family protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000262405.1:WP_009764221.1 Length = 557 Score = 234 bits (597), Expect = 7e-66 Identities = 163/503 (32%), Positives = 255/503 (50%), Gaps = 31/503 (6%) Query: 61 WRDINTGEEA-------KLSYHELSLMSNRVLSTL-RKHGLKKGDVVYLMTKVHPMHWAV 112 W D G+E L+Y L NR+ + L + G G+ V L + +PM A Sbjct: 47 WVDEGRGDEPCIISPTETLTYRTLQERVNRICNVLVHRLGFVPGNRVLLRSANNPMMVAA 106 Query: 113 FLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLID 172 +LAV+K G V+V + L E+ Y + + + + D A ME A + ++ Sbjct: 107 YLAVLKAGGVVVATMPLLRAKEIAYPLNKAQITIALCDHRLADEMERARAMAPGLQHVVY 166 Query: 173 GKRETWNSLEDESSNAEPE----DTRGEDVIINYFTSGTTGMPKRVIH-----TAVSYPV 223 +SLE + A PE DT +DV + FTSGTTG PK +H A+ Sbjct: 167 WGSGQPDSLEAMIAEASPEFAAVDTAADDVCLIGFTSGTTGEPKGTMHFHQDMLAICDGY 226 Query: 224 GSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGE 283 G +++ D + + P+ VGA+ V + G D L Sbjct: 227 GR----NVLRPEPDDRFIGSPPLAFTFGLGGIVLFPMRVGASTVLLEKAGPDDL---LPA 279 Query: 284 VENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRD 343 ++ T PTA+R ++ L+ + LR VSAGEPL + WK + + D Sbjct: 280 IQQYKATICFTAPTAYRAMLS-KLEGYDISSLRKCVSAGEPLPKGTFEAWKAATKIRLMD 338 Query: 344 FYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRP 403 G TE + +++PG+ GKP P Y+ +++DDEG+++ P +G + V+ P Sbjct: 339 GIGATEMLHIFIAATEDEIRPGATGKPVPGYEAKVVDDEGRDLP-PGSIGRLAVR---GP 394 Query: 404 IGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVES 463 G Y +++ + ++G+ TGD DE+GYF++ R DD+I ++ Y + EVE+ Sbjct: 395 TGC--RYLADERQRKYVQDGWNITGDTYLMDEDGYFWYQARSDDMIISAGYNIAGPEVEA 452 Query: 464 ALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPR 523 ALL HPAVAE VVG PD R +VKAY+VL+ G++P EL + +++ +K ++PYK PR Sbjct: 453 ALLTHPAVAECGVVGAPDDGRGTVVKAYVVLRSGHVPGPELTKVLQDHVKAEIAPYKYPR 512 Query: 524 IIEFVDELPKTISGKIRRVELRK 546 +IEFVD LP+T +GK++R ELR+ Sbjct: 513 LIEFVDALPRTQTGKLQRFELRR 535 Lambda K H 0.318 0.137 0.402 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: 669 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 564 Length of database: 557 Length adjustment: 36 Effective length of query: 528 Effective length of database: 521 Effective search space: 275088 Effective search space used: 275088 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