Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_010529673.1 ON01_RS03745 acyl--CoA ligase
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000224785.1:WP_010529673.1 Length = 526 Score = 339 bits (870), Expect = 1e-97 Identities = 198/504 (39%), Positives = 295/504 (58%), Gaps = 14/504 (2%) Query: 56 KTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWAVFLA 115 + A++W GE +++Y +L N++ + ++ GL+KGD V +M + +LA Sbjct: 28 RNAVVWCS-EKGESKEITYEQLMKNVNKIGNAFKEKGLEKGDRVLIMIPRLIEAYETYLA 86 Query: 116 VIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLIDGKR 175 +K G +++P + L +++YR S + SAI+S + ++ F + Sbjct: 87 ALKSGIIVIPGSEMLKTKDLQYRISHGEVSAIVSYYPYVGQFTDVKEFEQLTLFSVGNSV 146 Query: 176 ETWNSLEDESSNAEPE----DTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSITTA-- 229 + W++++ NA + DT +DV +TSGTTG PK V+HT + + TA Sbjct: 147 DGWHNMDKLKENASDKLDMADTTKDDVAFFSYTSGTTGNPKAVVHTH-GWGYAHLNTAPE 205 Query: 230 SIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVENLGV 289 + + + E D + GW K+ WS F S L GAT G Y GK D + YLG +++ + Sbjct: 206 NWLCINEGDKVWATAGPGWQKWIWSPFLSVLGSGAT--GFVYLGKFDPKTYLGLLQDEDI 263 Query: 290 TSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQT 348 C PT +R +D LD ++ L S VSAGEPLN EVI ++ FN+T+RD YGQT Sbjct: 264 NVLCCTPTEYRLMAKVDNLDDYQLPALHSAVSAGEPLNREVIDTFRKYFNVTVRDGYGQT 323 Query: 349 ETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPIGLFL 408 E T ++G KVKPGSMGKP P ++ +++++G+ + ++G I VKL+ P Sbjct: 324 ENTLLLGFMKDTKVKPGSMGKPTPGNEVEIINEDGQPVPAN-KIGDIAVKLDS-PALFRE 381 Query: 409 GYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLEH 468 Y D ++ S R YY TGD+A DE+GYF+F GR DD+I +S Y +GPFEVE AL++H Sbjct: 382 YYKDAERTRMSQRGEYYVTGDQASKDEDGYFWFEGRSDDIIISSGYTIGPFEVEDALVKH 441 Query: 469 PAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMP-SKELAEEIREKMKTLLSPYKVPRIIEF 527 P V E AVV PD VR +VKA+IVL++G P +L ++++ +K L +PYK PR IEF Sbjct: 442 PFVQECAVVASPDEVRGNVVKAFIVLQQGVNPDDPDLVRDLQKHVKELTAPYKYPRKIEF 501 Query: 528 VDELPKTISGKIRRVELRKREEEK 551 +DELPKT SGKIRRVELR+ E+ K Sbjct: 502 IDELPKTTSGKIRRVELRQNEKVK 525 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: 785 Number of extensions: 50 Number of successful extensions: 7 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: 564 Length of database: 526 Length adjustment: 35 Effective length of query: 529 Effective length of database: 491 Effective search space: 259739 Effective search space used: 259739 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