Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_011840694.1 RSPH17029_RS04730 acyl-CoA synthetase
Query= BRENDA::A4YDT1 (564 letters) >NCBI__GCF_000015985.1:WP_011840694.1 Length = 629 Score = 110 bits (276), Expect = 1e-28 Identities = 112/368 (30%), Positives = 159/368 (43%), Gaps = 23/368 (6%) Query: 192 DTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKF 251 D + V + T GTTGMPK H VS + + + + +D + Sbjct: 212 DPETDRVAAYFHTGGTTGMPKVAQHK-VSGMIYNGWCGQRLLFQPTDTVMCPLPLFHVFA 270 Query: 252 AWSSFFSPLLVGATVV-----GINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLD 306 A+ S + GA VV G EG D L +E T PTA + Sbjct: 271 AYPILMSMIASGAHVVFPTPAGYRGEGVFDNLWKL--IERWRCTYLVTVPTALAALMQRP 328 Query: 307 LDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVG-NFPFLKVKPG 365 +D LR S PL E+ ++ + I + YG TE T +V N P K G Sbjct: 329 IDA-DVSSLRGAFSGSAPLPVELFNRFEKATGVQIVEGYGLTECTCLVSVNPPEGAKKIG 387 Query: 366 SMGKPHPLYDIRLLDDEGK-EITKPY---EVGHITVKLNPRPIGLFLG--YSDEKKNMES 419 S+G P P +R+L G + K EVG I V NP G++ G Y++ KN Sbjct: 388 SVGLPFPHTHVRILHSNGSGHVLKECGVDEVGEICVA-NP---GVYEGSTYTELDKNHGL 443 Query: 420 FREGYYY-TGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVG 478 F E + TGD D EGY + GR D+I + + P +E+AL+ HPAV+ +G Sbjct: 444 FAEDRFLRTGDLGRLDAEGYLFITGRAKDLIIRGGHNIDPAGIEAALMSHPAVSFVGAIG 503 Query: 479 VPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGK 538 PD +L AY+ L +G E A + VP+ IE + ELPKT GK Sbjct: 504 QPDAFAGELPCAYVELVQG--AEVETAALFDHARAHIHERAAVPKHIEILPELPKTAVGK 561 Query: 539 IRRVELRK 546 + + +LR+ Sbjct: 562 VFKPDLRR 569 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: 687 Number of extensions: 31 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: 564 Length of database: 629 Length adjustment: 37 Effective length of query: 527 Effective length of database: 592 Effective search space: 311984 Effective search space used: 311984 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 10 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