Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate RR42_RS27915 RR42_RS27915 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS27915 RR42_RS27915 acyl-CoA synthetase Length = 545 Score = 390 bits (1003), Expect = e-113 Identities = 215/530 (40%), Positives = 306/530 (57%), Gaps = 14/530 (2%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRN 81 LTP+ FL RA + D+ A+V+ R + Y AS L G + D ++ + N Sbjct: 19 LTPIDFLARAASVYGDRLAIVHGPVRQNWRDTYARARRLASGLASLGVGKGDTVAALLPN 78 Query: 82 RPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIK 141 P +E+ FGVP AG VL +N RL + +++ H +++ ++ D + + ++ ++I Sbjct: 79 TPAMVEAHFGVPMAGAVLNALNIRLDASNLIFMLRHGEARVLLADTEFADVARQIANEIP 138 Query: 142 -----AEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTS 196 A + L D P+ ET + R L G +PA +E+ I L YTS Sbjct: 139 GLKVVAVLDALGPQDAPAFGETDYE------RLLASGDPEFAWQMPA-DEWDAIALNYTS 191 Query: 197 GTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATN 256 GTTG PKGV++HHRGA +NA++ +LE + ++VYLWTLPMFH W F W A N Sbjct: 192 GTTGDPKGVVYHHRGAAINAISNILEWDLPKHAVYLWTLPMFHCNGWCFPWTIAARAGVN 251 Query: 257 VCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPA 316 VCL K + L++ L+ E VTH CAAP V+ L + V +VAGA P A Sbjct: 252 VCLRKFEPKLVFDLMRDEGVTHYCAAPIVHTALVNAPLAWRDGVRGPVRGMVAGAPPPAA 311 Query: 317 TLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY-VSFEMD 375 L M+ +G + HVYGLTETYGP ++C + +W SL E++A KARQG+ Y + E+ Sbjct: 312 VLAQMEAMGFALTHVYGLTETYGPAAVCAEQDDWASLSQEDRATKKARQGVRYHLQTEVA 371 Query: 376 VFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGY 434 V D + +PV DG+ IGE++ RG+ GY KN + T E+F GWFH+GD V PDGY Sbjct: 372 VLDPDTMQPVASDGEEIGEIMFRGNICMKGYLKNEKATREAFAGGWFHTGDLGVCTPDGY 431 Query: 435 IEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGV 494 ++I DR KD+I +GGE +SS+ VE + P V AVAV PD KWGE A +EL++G Sbjct: 432 VKIKDRSKDIIISGGENISSVEVEDAIYRHPAVLAVAVVAQPDVKWGETPCAFVELKDGA 491 Query: 495 KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKAKA 544 T +E+I C+ LA F+ PK V FGP+P T+TGK+QK+ LR + K+ A Sbjct: 492 SATADELIAHCRTLLAGFKVPKAVYFGPLPKTSTGKIQKFELRKKVKSDA 541 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: 764 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: 549 Length of database: 545 Length adjustment: 36 Effective length of query: 513 Effective length of database: 509 Effective search space: 261117 Effective search space used: 261117 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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