Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Dsui_2808 Dsui_2808 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__PS:Dsui_2808 Length = 552 Score = 442 bits (1136), Expect = e-128 Identities = 231/537 (43%), Positives = 333/537 (62%), Gaps = 3/537 (0%) Query: 10 EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69 +G++ + Y L+PL F+ R+ + ++ +V++ RYT+ ++ ASAL RG Sbjct: 14 QGLEKNAANYVPLSPLTFIARSAYIYPERVSVIHGQRRYTWLETFNRARRLASALEARGI 73 Query: 70 SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129 D ++ + N PE E FGVP G VL +N RL P+ +A+++NH ++K ++ D+ Y Sbjct: 74 KEGDTVAVMLNNTPEMYECHFGVPVTGAVLNTLNTRLDPEAVAFMLNHGEAKILITDKEY 133 Query: 130 LNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189 + + +++ I++++ D+ + Y L+ G+ D ++E+ Sbjct: 134 SHIVGPALEKLGRSIVVIDVNDSEYTGPGDLLGEK-DYEALLAEGTPDYEWKGPQDEWDA 192 Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249 I+L YTSGTTG PKGV++HHRGA+LNAM+ ++ M +SVYLWTLPMFH W F W Sbjct: 193 ISLNYTSGTTGNPKGVVYHHRGAYLNAMSNIVSWGMPPHSVYLWTLPMFHCNGWCFPWTM 252 Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 A TNVCL +VD LI + + + +VTH C AP V+ LA+ ++ V L+A Sbjct: 253 AANAGTNVCLRRVDPKLILQSIRENKVTHYCGAPIVHSMLANAPAEWREGINHGVSGLIA 312 Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369 A P A ++ M +IG + HVYGLTETYGP S+C + EW LP+ EQ L RQG+ Y Sbjct: 313 AAPPPAAVIEGMAKIGFKITHVYGLTETYGPASVCAQQPEWFDLPVGEQVNLNGRQGVRY 372 Query: 370 VSFE-MDVFD-ANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427 + E + V D A + VPWD +T+GE++ RG+ V GY KNP+ T ESF G++H+GD A Sbjct: 373 HAQEAITVLDPATMEAVPWDNETMGEIMFRGNLVMKGYLKNPKATEESFAGGYYHTGDLA 432 Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487 V+ DGY++I DR KD+I +GGE +SSI VE TL P V A AV TPD KWGEV A Sbjct: 433 VMQADGYVKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMAAAVVATPDPKWGEVPAAF 492 Query: 488 IELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKAKA 544 IEL++GV +TE E+I+FC+E +A F+ PK V FGP+P T+TGK+QKYVLR AK+ A Sbjct: 493 IELKDGVSITEVEIIEFCREHMARFKVPKKVIFGPLPKTSTGKIQKYVLREMAKSTA 549 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: 820 Number of extensions: 28 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: 552 Length adjustment: 36 Effective length of query: 513 Effective length of database: 516 Effective search space: 264708 Effective search space used: 264708 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 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