Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_072787138.1 BUA36_RS20265 AMP-binding protein
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_900143065.1:WP_072787138.1 Length = 538 Score = 204 bits (518), Expect = 9e-57 Identities = 158/498 (31%), Positives = 238/498 (47%), Gaps = 22/498 (4%) Query: 54 GSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKH-GLKKGDVVYLMTKVHPMHWAV 112 G +TAL G + +Y +L +R+ LR L+ G+ V L PM A Sbjct: 55 GGRTALC------GAQGDWTYAQLRERVDRIAHVLRGPLQLEAGNRVLLRGANTPMMAAC 108 Query: 113 FLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAII-SDSLRASVMEEALGSLKVEKFLI 171 LAV+K G + VP+ L E+ + +A++ +DSLRA + L + L Sbjct: 109 ILAVMKAGLIAVPTMPLLRARELGKIADKAQINAVLCADSLRAELEAATLPEAARARTLF 168 Query: 172 ---DGKRETWNSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPV-GSIT 227 DG+ + + E DT +DV + FTSGTTG+PK +H V Sbjct: 169 FGTDGEDALEALMATQPPAFEAVDTAADDVCLISFTSGTTGIPKGTMHFHRDVMVICDCF 228 Query: 228 TASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVENL 287 SI+ R D+ + + PL VG T V + KL L +E Sbjct: 229 PRSILQSRPGDIFIGTPPLAFTFGLGGLLLFPLRVGGTAVLLE---KLTPETLLKAIETY 285 Query: 288 GVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQ 347 T PT +RQ L QF L+ VSAGE L + W+ L + D G Sbjct: 286 RATVCFTAPTFYRQMAVL-APQFDLASLQKSVSAGEALPLATRESWRQATGLRMIDGIGA 344 Query: 348 TETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPIGLF 407 TE + + +++PG+ GKP P Y +LD +G + P +G + VK P G Sbjct: 345 TELLHIFISASGEQIRPGATGKPVPGYQACILDFDGNPVG-PGVIGRLAVK---GPTGC- 399 Query: 408 LGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLE 467 Y + + + G+ TGD D +GYFY+ R DD+I ++ Y + EVE LL Sbjct: 400 -RYLADDRQRDYVLNGWNLTGDAYEMDADGYFYYRSRTDDMIISAGYNIAGPEVEDVLLR 458 Query: 468 HPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRIIEF 527 HPAVAE V+G PD R Q+V+A++VL+ G+ S EL ++++ +K ++PYK PR ++F Sbjct: 459 HPAVAECGVIGRPDEERGQIVEAHVVLRAGFAASPELVVQLQDFVKEQIAPYKYPRAVKF 518 Query: 528 VDELPKTISGKIRRVELR 545 + LP+T +GK++R +LR Sbjct: 519 LKALPRTETGKLQRFKLR 536 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: 548 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: 564 Length of database: 538 Length adjustment: 36 Effective length of query: 528 Effective length of database: 502 Effective search space: 265056 Effective search space used: 265056 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