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) >FitnessBrowser__Cup4G11:RR42_RS27915 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:
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