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_RS06255 AZOBR_RS06255 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__azobra:AZOBR_RS06255 Length = 551 Score = 612 bits (1578), Expect = e-179 Identities = 298/551 (54%), Positives = 386/551 (70%), Gaps = 16/551 (2%) Query: 11 DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70 DL + AN L+PL FL R A V+P R +VIHG TW +TY+RC RLASALA R IG Sbjct: 12 DLDQNAANTVPLSPLSFLRRTAAVYPQRIAVIHGPVRRTWAETYERCVRLASALAKRGIG 71 Query: 71 PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130 G TVA++APN P +EAHFGVPM GAVLN +NIRL+A +AF+L H ++ V++ D+EF Sbjct: 72 LGDTVAVMAPNTPESFEAHFGVPMTGAVLNALNIRLDAEALAFILEHGEAKVLLTDREFS 131 Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190 + ++ ++E K +RP++I I D P++ L G YE FL TGDP Y W Sbjct: 132 GVISKAVHMLEPK-----RRPIVIDIDD----PQAKGGELI-GEQTYEQFLETGDPAYEW 181 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 PADEWQ+IAL YTSGTT +PKGVV HHRGAY+ A+ N L W M VYLWTLPMFHC Sbjct: 182 PMPADEWQAIALNYTSGTTGNPKGVVYHHRGAYLNAMGNVLTWAMPHHPVYLWTLPMFHC 241 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWCFPW++ ++GT++C+R +TAK +Y +A VTH C AP+++ IVNAP ED Sbjct: 242 NGWCFPWTVTAMAGTNVCVRTITAKGIYDALADLGVTHMCGAPIIMGLIVNAP-EDQKRE 300 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 +P V +MTAGAAPP +V+ + + GF V H YGL+E YGP T+CAW W+ LP E +A Sbjct: 301 IPRGVKMMTAGAAPPAAVIEKIERMGFDVTHVYGLTEVYGPVTICAWHEHWNDLPLEERA 360 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 L ARQGV Y +E L V D T +P DG T GEI RGN VMKGYLKNP A +E F+ Sbjct: 361 ALKARQGVNYATLEGLMVADPNTLQPTRKDGVTMGEIFMRGNTVMKGYLKNPRATQEAFS 420 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GGWFH+GD+ V H D YIE+KDRSKD+IISGGENIS++EVE+V+Y HP ++EA+VVARPD Sbjct: 421 GGWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVESVLYKHPDIVEAAVVARPD 480 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550 E+W E+PCAFVT+K + + +++ +CRE L + P++VVF LPKT+TGKIQ Sbjct: 481 EKWGETPCAFVTVKEGKQLTE-----AEVIAYCREHLAHFKCPRTVVFTALPKTSTGKIQ 535 Query: 551 KHILRTKAKEM 561 K++LR +A+ + Sbjct: 536 KYVLRDQARAL 546 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: 912 Number of extensions: 35 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: 551 Length adjustment: 36 Effective length of query: 533 Effective length of database: 515 Effective search space: 274495 Effective search space used: 274495 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