Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate BPHYT_RS33490 BPHYT_RS33490 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__BFirm:BPHYT_RS33490 Length = 543 Score = 405 bits (1041), Expect = e-117 Identities = 224/542 (41%), Positives = 321/542 (59%), Gaps = 18/542 (3%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G++ + Y LTP+ F+ RA + + ++ AVV+ + R + Y+ ASAL + G Sbjct: 8 GLERREANYVPLTPIDFIVRAAEVYGERPAVVHGEIRRNWRETYERARRLASALQQAGIQ 67 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY- 129 R D ++ + N P +E+ FGVP AG VL +N RL + +++ H ++K ++VD Y Sbjct: 68 RGDTVAALLPNIPPMIEAHFGVPMAGAVLNTLNTRLDVSSLLFMLRHGEAKALIVDTEYG 127 Query: 130 ---LNSLLEVKDQIKAEIILLED--PDNPSASETARKEVRMT-YRELVKGGSRDPLPIPA 183 + LE D +I + D P +PS + +R T Y ++ G + Sbjct: 128 EFAHRAALEFPD---LRVISVADAMPADPS------QFIRATDYEAFLQSGDPEFAWAMP 178 Query: 184 KEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASW 243 +E+ I L YTSGTTG PKGV++HHRGA+LNA++ +LE M +++YLWTLP+FH W Sbjct: 179 ADEWDAIALNYTSGTTGDPKGVVYHHRGAYLNALSNILEWDMPKHAIYLWTLPLFHCNGW 238 Query: 244 GFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNR 303 F W A NVCL K D ++ L+ +E +TH C AP V LA+ + +R Sbjct: 239 CFPWTVAARAGVNVCLRKFDAKTVFDLIRREGITHYCGAPIVQSALANAPAQWREGIEHR 298 Query: 304 VHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKA 363 V +VAGAAPAPA + M+EIG + HVYGLTETYGP ++C + EW++L +A++ A Sbjct: 299 VSTMVAGAAPAPAVIAKMKEIGFDLTHVYGLTETYGPAAVCAKQEEWEALDDGARAEMNA 358 Query: 364 RQGIPY-VSFEMDVFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWF 421 RQG+ Y + + V D + PVP DG+TIGE++ RG+ GY KN T +F+ GWF Sbjct: 359 RQGVRYHLQAAVTVLDPDTLTPVPDDGETIGEIMFRGNICMKGYLKNERATEATFQGGWF 418 Query: 422 HSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWG 481 H+GD V PDGYI I DR KD+I +GGE +SSI VE TL P V AV D KWG Sbjct: 419 HTGDLGVRMPDGYIRIRDRSKDIIISGGENISSIEVEDTLYRHPAVSVAAVVAMADPKWG 478 Query: 482 EVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 EV A +EL+EG +++ EE+I C+ LA ++ PK V FG +P T+TGK+QK+ LR K Sbjct: 479 EVPCAFVELKEGAQVSAEEIIAHCRLFLAGYKLPKAVRFGELPKTSTGKIQKFELRARIK 538 Query: 542 AK 543 A+ Sbjct: 539 AE 540 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: 777 Number of extensions: 29 Number of successful extensions: 3 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: 543 Length adjustment: 35 Effective length of query: 514 Effective length of database: 508 Effective search space: 261112 Effective search space used: 261112 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 17 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