Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF1184 PGA1_c11990 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Phaeo:GFF1184 Length = 542 Score = 394 bits (1012), Expect = e-114 Identities = 215/535 (40%), Positives = 315/535 (58%), Gaps = 5/535 (0%) Query: 11 GVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFS 70 G++ T + Y LTPL L RA F D AVVY + R TY+ +YD ASAL G Sbjct: 9 GLEKTAANYVPLTPLSHLRRAAHVFADVPAVVYGNHRKTYAAYYDRCTRLASALAGMGVR 68 Query: 71 REDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYL 130 + ++ + N P E+ FGVP G VL IN RL +AYI +H ++K V+VD +L Sbjct: 69 PGEVVATLIPNLPAQAEAHFGVPACGAVLNTINTRLDVSTVAYIFDHGEAKVVLVDSQFL 128 Query: 131 NSLLEVKDQIKA-EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSM 189 E K +++E PD+ ++ + + Y +++ + D I ++E+ Sbjct: 129 TLAEEAKAACDGLGPLIIEVPDDQASYPASGRHP--IYEDILAAAAHDFDWIMPQDEWES 186 Query: 190 ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWAT 249 + L YTSGTTG PKGV++HHRGA+L M V+ +M + YL +P+FH W +W Sbjct: 187 LALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVMQPKYLAIVPLFHCNGWNHTWMM 246 Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 +G T +C + P IY + E TH AP V L + + + +F + V + A Sbjct: 247 PVLGGTLICCRDITAPAIYGAIADEGATHFGGAPIVLNMLVNAAEEDRRQFDHTVEVFTA 306 Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRRE-WDSLPLEEQAKLKARQGIP 368 GA PAPATL+ ++ +G ++ VYGLTETYG + C W+ + WD+L + +A +KARQG+ Sbjct: 307 GAPPAPATLEKIEALGFHVTQVYGLTETYGHVTECLWKGDSWDTLDQQGRAAIKARQGVA 366 Query: 369 YVSFE-MDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAA 427 + + + V + + + +G+ GE+VMRG++V GY KNP+ TAE+F+ G+FHSGD A Sbjct: 367 FPMMDHITVMRDDMQQIAMNGQDQGEIVMRGNSVMKGYLKNPDATAEAFQGGYFHSGDIA 426 Query: 428 VVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTAR 487 V HPDGYI+I DR KD+I +GGE +SS+ VE LM P V AV PD+KWGEV A Sbjct: 427 VQHPDGYIQIADRAKDIIISGGENISSVEVEGVLMGHPDVNLAAVVAKPDDKWGEVPCAF 486 Query: 488 IELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKA 542 +EL+ G + ++I+F +E LA F+ PK V F +P T+TGK+QK+ LR +AKA Sbjct: 487 VELKPGATVDPADLIRFARETLAGFKAPKQVVFQELPKTSTGKIQKFELRQQAKA 541 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: 740 Number of extensions: 25 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: 542 Length adjustment: 35 Effective length of query: 514 Effective length of database: 507 Effective search space: 260598 Effective search space used: 260598 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