Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Dino:3607419 Length = 541 Score = 413 bits (1062), Expect = e-120 Identities = 234/541 (43%), Positives = 316/541 (58%), Gaps = 8/541 (1%) Query: 6 IPNYEGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALM 65 + N G+D + Y LTPL L RA + D+ AVVY R+TY+ ++ V ASAL Sbjct: 4 LANETGLDKCAANYVPLTPLSHLARAALVYPDREAVVYGARRFTYAEYHARVSRLASALA 63 Query: 66 RRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVV 125 G + D ++ + N P +E+ FGVP G VL IN RL +AYI++H +K V+V Sbjct: 64 GAGIAPGDVVATLLPNIPAMVEAHFGVPACGAVLNTINIRLDVDTVAYILSHGGAKAVLV 123 Query: 126 DEPYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKE 185 D +L E +++ LL + + +A A Y + + GG D I ++ Sbjct: 124 DSQFLPLAAEACERLDGPAPLLIEVADDAAGVHALGGYT-EYEDFLAGGDPDFPWIMPRD 182 Query: 186 EYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF 245 E+ + L YTSGTTG PKGV++HHRGA+L M V+ +M L +L +P+FH W Sbjct: 183 EWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYPRWLAIVPLFHCNGWNH 242 Query: 246 SWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVY---VNLADYMKRNNLKFSN 302 SW +G T VC V IY + + VTH AP V VN D +R FS+ Sbjct: 243 SWMMPMLGGTVVCCRDVSAQAIYTAIAENGVTHFGGAPIVLNMIVNAPDAARR---PFSH 299 Query: 303 RVHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLK 362 V + AGA PA ATL A++E+G + VYGLTETYG + C W +WD+LP E+A +K Sbjct: 300 TVEVFTAGAPPAAATLAAIEELGFNVTQVYGLTETYGHVTECVWNPDWDTLPQAERAAIK 359 Query: 363 ARQGIPYVSFE-MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWF 421 ARQG+ E + V D + VP DG T GEV+MRG++V GYY+NP+ TAE+F G+F Sbjct: 360 ARQGVALPQMEHITVMDPEMRQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAFAGGYF 419 Query: 422 HSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWG 481 HSGD A+ HPDGYI+I DR KD+I +GGE +SS+ VE LM P V AV PD WG Sbjct: 420 HSGDIALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDPTWG 479 Query: 482 EVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 EV A +EL++G E E+I F +ERLA F+ PK V F +P T+TGK+QK+ LRN AK Sbjct: 480 EVPCAFVELKDGKTAEEAEIIAFARERLAGFKTPKKVVFTELPKTSTGKIQKFELRNRAK 539 Query: 542 A 542 A Sbjct: 540 A 540 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: 811 Number of extensions: 35 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: 541 Length adjustment: 35 Effective length of query: 514 Effective length of database: 506 Effective search space: 260084 Effective search space used: 260084 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