Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate Ac3H11_4302 Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4302 Length = 546 Score = 219 bits (559), Expect = 2e-61 Identities = 161/530 (30%), Positives = 263/530 (49%), Gaps = 22/530 (4%) Query: 24 PLL---FLERAGKYFKDKTAVVYRDS-----RYTYSTFYDNVMVQASALMRRGFSREDKL 75 PLL LE + D+ +V RD+ RY ++ ASAL G + Sbjct: 13 PLLVSAILEHGENQYGDRQ-IVSRDTDGRLHRYRFADMAQRARQLASALQALGLRPGSVV 71 Query: 76 SFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE---PYLNS 132 ++ N LE+++ V +G V+ N RL P+++AYI+NH+D + V+ D P + + Sbjct: 72 GSLAWNNHRHLEAYYAVSGSGMVMHTCNPRLHPEQLAYIVNHADDEVVLFDTTFAPLVRA 131 Query: 133 LLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITL 192 + +++ + L D D + Y LV D P +E + L Sbjct: 132 IAASCPRVRHWVALC-DADTLGTMDMQGVSGVEAYETLV-ASQNDRFTWPLCDEKAGAAL 189 Query: 193 YYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNS--VYLWTLPMFHAASWGFSWATV 250 YTSGTTG PKGV++ HR L+A++ + + +++ L +PMFH +W +A + Sbjct: 190 CYTSGTTGNPKGVLYSHRALVLSALSACMPGVLSISARETILPVVPMFHINAWCLPYAAL 249 Query: 251 AVGATNVCLD-KVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 GA V ++D +Y L+E ERVT PT+++ L +++++ L+F+ V Sbjct: 250 IGGAKLVLPGPRLDAASLYELMETERVTVSAGVPTIWMGLIQHVEQHGLRFTTMRRTGVG 309 Query: 310 GAAPAPATLKAMQEIGGY-MCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIP 368 G+A A + ++ + H +G+TET ++ LP E++ L A+QG Sbjct: 310 GSAMPKALIAKFNDLYDVEVRHGWGMTETTAIATMSVLGAGDAELPPEDRHALVAKQGKS 369 Query: 369 YVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAV 428 E+ + D NG +P DG GE+++RG + Y+K E++A DGWF +GD A Sbjct: 370 VFGIELKLVDENGASLPRDGVAQGELMVRGQWIVDRYHK-AERSA--LVDGWFPTGDIAT 426 Query: 429 VHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARI 488 ++P G ++I DR KD+I +GGE +SSI +E + P V AV G KW E I Sbjct: 427 INPQGVVQIRDRTKDVIKSGGEWISSIDLENAAVAHPAVAMAAVIGVKHPKWDERPLLFI 486 Query: 489 ELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 + G L + +++ F +R+A + P V F +P+ TGK+QK LR Sbjct: 487 VRKPGQSLDKAQILDFLAQRVAKWWLPDDVLFVDSLPLGGTGKVQKNELR 536 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: 609 Number of extensions: 28 Number of successful extensions: 7 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: 546 Length adjustment: 36 Effective length of query: 513 Effective length of database: 510 Effective search space: 261630 Effective search space used: 261630 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