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 AZOBR_RS19480 AZOBR_RS19480 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__azobra:AZOBR_RS19480 Length = 556 Score = 575 bits (1481), Expect = e-168 Identities = 286/547 (52%), Positives = 373/547 (68%), Gaps = 18/547 (3%) Query: 16 PANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTV 75 PAN+ L+PL FL RAA V+P + ++ HG R T+ Q +DR RR A AL + G TV Sbjct: 20 PANHVPLSPLSFLKRAAKVYPDKPAIRHGRRTITYAQFHDRVRRFAGALLRAGVRRGDTV 79 Query: 76 AIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAED 135 +++APN+PA+ EAH+ VP+ GAVLN +N RL+A +AF+L HS++ +++VD+E +A+ Sbjct: 80 SVLAPNVPALLEAHYAVPLAGAVLNALNTRLDAAAIAFILDHSETKLLIVDRELSPVAKA 139 Query: 136 SLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPAD 195 +L E RP+ +V A E A S GA+EYEDFLA DP PW P D Sbjct: 140 ALARTE--------RPITLV----EIADEQAPDAPSLGAVEYEDFLAAADPA-PWHGPDD 186 Query: 196 EWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCF 255 EWQ+IAL YTSGTT +PKGVV HHRGAY+ AL N ++ +V+LWTLPMFHCNGW + Sbjct: 187 EWQAIALNYTSGTTGNPKGVVYHHRGAYLNALGNAFTLNVRPESVFLWTLPMFHCNGWTY 246 Query: 256 PWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTV 315 W++ GT +CLR+V ++ IA+ VTH C AP+VLN +++AP P P V Sbjct: 247 SWAVTAAGGTHVCLRRVEPAAIFDAIAELGVTHLCGAPIVLNMLIHAPAA-VRRPAPRRV 305 Query: 316 HVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNAR 375 V T GAAPP +VL M GF V H YGL+E YGP+TVCA + W+ L + A AR Sbjct: 306 IVGTGGAAPPSAVLAGMATLGFEVVHMYGLTECYGPATVCAPQDGWEDLDADGLALQFAR 365 Query: 376 QGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFH 435 QGV + +E V+D +TG+PVPAD +T GEI RGN VMKGYLKNP A KE GWF Sbjct: 366 QGVNHVAVEDATVLDRETGRPVPADAQTIGEIALRGNTVMKGYLKNPAATKEALKDGWFR 425 Query: 436 SGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQE 495 +GD+ V HPD YIE+KDRSKD+IISGGENISS+EVE +Y HPAVLEA+VVARPD+RW E Sbjct: 426 TGDLGVLHPDGYIEVKDRSKDIIISGGENISSLEVEEALYRHPAVLEAAVVARPDDRWGE 485 Query: 496 SPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILR 555 SPCAFVT+K E+ ++ DI+++CR+++ Y VP++VVF LPKT+TGKIQK +LR Sbjct: 486 SPCAFVTVKPGAERPSES----DIIQWCRDRIAHYKVPRTVVFSDLPKTSTGKIQKTVLR 541 Query: 556 TKAKEMG 562 A+E+G Sbjct: 542 DAARELG 548 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: 911 Number of extensions: 32 Number of successful extensions: 5 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: 556 Length adjustment: 36 Effective length of query: 533 Effective length of database: 520 Effective search space: 277160 Effective search space used: 277160 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 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