Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate PP_3553 PP_3553 AMP-binding domain protein
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Putida:PP_3553 Length = 540 Score = 416 bits (1068), Expect = e-120 Identities = 223/536 (41%), Positives = 318/536 (59%), Gaps = 5/536 (0%) Query: 10 EGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGF 69 +G+ P + LTPL F+ER + + AV++ R + Y ASAL RG Sbjct: 6 QGLMPAAVNHVALTPLSFIERTAAVYGNYPAVIHGAIRRNWQETYQRCRRLASALAGRGI 65 Query: 70 SREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPY 129 R D ++ + N P LE+ FGVP G VL +N RL + +A+++ H ++K ++ D + Sbjct: 66 GRGDTVAVMLPNTPTMLEAHFGVPMTGAVLNTLNVRLDAEAIAFMLQHGEAKVLITDREF 125 Query: 130 LNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189 ++++E + L+ D D+P E R ++ Y L+ G + +E+ Sbjct: 126 -HAVIEGALALLEHPPLVVDVDDPEYGE-GRAVSQLDYEALLNEGDPEFAWEWPDDEWQA 183 Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249 I+L YTSGTTG PKGV++HHRGA+LNA+ + M VYLWTLPMFH W + W Sbjct: 184 ISLNYTSGTTGNPKGVVYHHRGAYLNALGNQMTWAMGHRPVYLWTLPMFHCNGWCYPWTI 243 Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 A+ T+V L +VD I L+ + +V+H+C AP V L + + + V +VA Sbjct: 244 TALAGTHVFLRRVDPQKILTLIREHKVSHLCGAPIVLNALVNMPEAAKAAIEHPVQAMVA 303 Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369 GAAP + A++++G + H YGLTE YGP ++C W EWD+L LEE+A++K+RQG+ Y Sbjct: 304 GAAPPAKVIGAVEQMGIKVTHTYGLTEVYGPVTVCAWHDEWDALSLEERARIKSRQGVRY 363 Query: 370 VSFE--MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427 + + M +PVP DG T+GE+ MRG+ V GY KNPE TAE+FR GWFH+GD A Sbjct: 364 PTLDGLMVADPQTLQPVPRDGDTLGEIFMRGNTVMKGYLKNPEATAEAFRGGWFHTGDLA 423 Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487 V H DGYIEI DR KD+I +GGE +S+I VE L + V AV PDEKWGE A Sbjct: 424 VWHADGYIEIKDRLKDIIISGGENISTIEVEDALYKHSAVLEAAVVARPDEKWGETPCAF 483 Query: 488 IELQEGVKLTEE-EVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542 + L+ G + T E ++ +C+E LA F+ PK V FG +P T+TGK+QKYVLR+ AKA Sbjct: 484 VALKPGREDTREADITSWCREHLAGFKVPKTVVFGELPKTSTGKIQKYVLRDRAKA 539 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: 778 Number of extensions: 40 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: 540 Length adjustment: 35 Effective length of query: 514 Effective length of database: 505 Effective search space: 259570 Effective search space used: 259570 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 Aug 03 2021. The underlying query database was built on Aug 03 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