Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Ga0059261_0337 Ga0059261_0337 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Korea:Ga0059261_0337 Length = 539 Score = 224 bits (571), Expect = 7e-63 Identities = 150/493 (30%), Positives = 247/493 (50%), Gaps = 25/493 (5%) Query: 61 ASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDS 120 A AL R G + D+++ ++ N L ++ G GGV+ IN RL ++A+I NH++ Sbjct: 53 AQALERMGIKKGDRVATMAMNHSRHLVAWHGTIGMGGVIHTINPRLFEDQLAFIGNHAED 112 Query: 121 KFVVVDEPYLNSLLEVKDQIKA-EIILLEDP--------DNPSASETARKEVRMTYRELV 171 + ++ D + + ++K Q K E ++ DP D P + E Y V Sbjct: 113 RVLMYDRMFQPIVDKMKPQWKTIEHYIVFDPGSEAGAGADGPDSFEAVIGAEDGNYA-WV 171 Query: 172 KGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLN--S 229 +G R+P L YTSGTTG PKGV++ HR + ++AMAE+ DL+ S Sbjct: 172 EGDEREPC-----------MLCYTSGTTGNPKGVLYTHRSSVIHAMAEIQPAVFDLSTQS 220 Query: 230 VYLWTLPMFHAASWGFSWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNL 289 V L +PMFHA WG +A VG V + ++ L+ +E+VTH PTV+ + Sbjct: 221 VVLPVVPMFHAVGWGMPFAAPMVGVKLVMSAINEGKVLCELMNREKVTHTAGVPTVWFAM 280 Query: 290 ADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRRE 349 +M + + + G+A A ++ + ++G + H +G+TET ++ + Sbjct: 281 FQHMDETGDVPAYLKVVTIGGSAAPRAMIERIMKMGARVNHAWGMTETSPIGTMGSPSAD 340 Query: 350 WDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNP 409 WD L E + QG E+ D G +P DG++ G + +RG + Y+K+ Sbjct: 341 WDDLSFEAKVDKMVCQGRAPFGVELRTVDDAGNLLPRDGESSGRLQVRGPWIIKQYFKDE 400 Query: 410 EKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKA 469 + DGWF +GD AV+HPDG ++I DR KD+I +GGE +SS+ +E + PGV Sbjct: 401 SGPCLT-ADGWFDTGDVAVLHPDGIMQITDRAKDVIKSGGEWISSVELENAAVGCPGVAE 459 Query: 470 VAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTAT 528 A G KW E + + G ++T +++ + + +A + P + F +P TAT Sbjct: 460 AAAIGIHHPKWDERPLLLVIRKPGSEVTADQIQQHLAKHVAKWWLPDEIHFVEALPHTAT 519 Query: 529 GKMQKYVLRNEAK 541 GK+ K +R++ K Sbjct: 520 GKLLKTAIRDQYK 532 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: 698 Number of extensions: 49 Number of successful extensions: 6 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: 539 Length adjustment: 35 Effective length of query: 514 Effective length of database: 504 Effective search space: 259056 Effective search space used: 259056 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