Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate Dsui_0644 Dsui_0644 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__PS:Dsui_0644 Length = 558 Score = 233 bits (594), Expect = 1e-65 Identities = 161/526 (30%), Positives = 256/526 (48%), Gaps = 32/526 (6%) Query: 41 VVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVL 99 +VYRDS RYTY T + A+AL G ++ + + +LE FF VP G VL Sbjct: 35 IVYRDSVRYTYRTLQQRIGRLANALAALGVEPGHTVAMMDWDSHRYLECFFAVPMMGAVL 94 Query: 100 VPINFRLSPKEMAYIINHSDSKFVVVDE---PYLNSLLEVKDQIKAEIILLEDPDNPSAS 156 +N RL+ ++M Y +NH+ + V+V+ P L ++ E + +K +++ D +NP Sbjct: 95 QTVNVRLTAEQMLYTLNHARADVVLVNSEFFPLLQAMAERLESVKTFVLIHGDHENPEKM 154 Query: 157 ETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNA 216 + A Y EL+ + D P +E + T +YT+GTTGLPKGV HR ++ Sbjct: 155 Q-APVSFAGEYEELLAAAATD-YDFPDFDENAKATTFYTTGTTGLPKGVYFSHRQLVMHT 212 Query: 217 MAEV-------LEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYR 269 M ++ ++ + VY+ PMFH +WG + +G V + ++ R Sbjct: 213 MGAATGLGTAPVQGRLHRDDVYMPITPMFHVHAWGLPYVATMLGLKQVYPGRYQPEVLLR 272 Query: 270 LVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYMC 329 L +ERVT PT+ L ++ S M+ A P + A+++ G + Sbjct: 273 LKARERVTFSHCVPTILHMLLNHALARETDLSGWKVMIGGSALPQAMAVAALEK-GIDVF 331 Query: 330 HVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGK 389 YG++ET S+ PL EQA L+AR G+P ++ + D +P P DG+ Sbjct: 332 TGYGMSETCPILSVAHLPTAKLQAPLAEQAALRARTGLPLPLVDLRIVDPEMRPQPHDGQ 391 Query: 390 TIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGG 449 +GE+V+R + GY K+P E + G+ H+ D + +G I+I DR KD+I TGG Sbjct: 392 AVGELVVRSPWLTQGYLKDPAAAEELWGGGYLHTADIGNIDANGSIQITDRIKDVIKTGG 451 Query: 450 EKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQ---EGVKLTEEEVIKFCK 506 E SS+ +E + + P V VAV G DEKWGE A + L+ EG ++TE + + Sbjct: 452 EWTSSLQLEDIIGQHPAVHEVAVIGVKDEKWGERPLALVVLKPEMEG-QVTEHAI----R 506 Query: 507 ERLAHF-ECPKIVEFG---------PIPMTATGKMQKYVLRNEAKA 542 AH E + +G + T+ GK+ K +R +A Sbjct: 507 NHAAHLAETLGVSRYGVLMQVSFVKTLARTSIGKINKRFMRENLEA 552 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: 703 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 549 Length of database: 558 Length adjustment: 36 Effective length of query: 513 Effective length of database: 522 Effective search space: 267786 Effective search space used: 267786 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 09 2024. The underlying query database was built on Apr 09 2024.
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