Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate WP_007153301.1 MDG893_RS08275 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000170835.1:WP_007153301.1 Length = 542 Score = 612 bits (1577), Expect = e-179 Identities = 292/545 (53%), Positives = 383/545 (70%), Gaps = 16/545 (2%) Query: 17 ANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVA 76 AN LTPL FL R A V+P +VIHG+ W+QTY+RCRRLASALADR +G G TVA Sbjct: 14 ANNATLTPLDFLARTASVYPEYPAVIHGATRRNWQQTYERCRRLASALADRGVGKGDTVA 73 Query: 77 IIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDS 136 + PNIP M E HFG+PM GAVLN +N RL+A +AF+L H ++ V++ D+EF + ++ Sbjct: 74 AMLPNIPPMLECHFGIPMLGAVLNALNTRLDAKAIAFMLEHGEAKVLIADREFGDVINEA 133 Query: 137 LRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADE 196 + +++ P +I + D PE ++Y+ F+A+GDP + WQ PADE Sbjct: 134 VGMLDNP-------PQVIDVND----PEFSGAGTQVSDLDYDAFVASGDPAFDWQMPADE 182 Query: 197 WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFP 256 W +I+L YTSGTT +PKGVV HHRGAY A+ N +W M VYLWTLPMFHCNGWCFP Sbjct: 183 WDAISLCYTSGTTGNPKGVVYHHRGAYENAMGNQAVWSMGMHPVYLWTLPMFHCNGWCFP 242 Query: 257 WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVH 316 W++ +GT +CLR+V +++ +I+++KV+H C AP+VLN ++ A E HTV Sbjct: 243 WTITAFAGTHVCLRKVEPEKILQLISEHKVSHMCGAPIVLNTLLGA-SEAAKSSFSHTVQ 301 Query: 317 VMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQ 376 MTAGAAPP V+ ++ GFRV H YGL+E YGP TVCAWK EWD LP E +A++ ARQ Sbjct: 302 AMTAGAAPPAKVIEAIENMGFRVTHVYGLTEVYGPVTVCAWKSEWDDLPVEDRARIKARQ 361 Query: 377 GVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHS 436 GVRY + + V D +T + VP DG T GEI RGN VMKGYLKNP+A +E F GGWFH+ Sbjct: 362 GVRYHTLAGMMVGDPETMEAVPKDGNTIGEIFLRGNTVMKGYLKNPKATEEAFRGGWFHT 421 Query: 437 GDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQES 496 GD+AV H D Y EIKDR KD+IISGGENIS++EVE+V+Y HP +LEA+VVARPDE+W E+ Sbjct: 422 GDLAVWHADGYAEIKDRLKDIIISGGENISTIEVEDVLYRHPDILEAAVVARPDEKWGET 481 Query: 497 PCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRT 556 PCAFVTLK + + ++ DI+ FCRE++ + VPK++VF LPKT+TGKIQK +LR Sbjct: 482 PCAFVTLKPEAGEVSED----DIIAFCRERMAKFKVPKTIVFSELPKTSTGKIQKFVLRD 537 Query: 557 KAKEM 561 AK++ Sbjct: 538 DAKKL 542 Lambda K H 0.319 0.134 0.422 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: 930 Number of extensions: 39 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: 569 Length of database: 542 Length adjustment: 36 Effective length of query: 533 Effective length of database: 506 Effective search space: 269698 Effective search space used: 269698 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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