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_041098563.1 SUTH_RS08535 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000828635.1:WP_041098563.1 Length = 545 Score = 601 bits (1550), Expect = e-176 Identities = 291/548 (53%), Positives = 387/548 (70%), Gaps = 17/548 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L K PANY LTPL F++R+A ++P R + IHGSR YTW Q Y+R RRLASALA R +G Sbjct: 9 LDKNPANYVPLTPLSFIERSAYIYPERVASIHGSRRYTWGQEYERSRRLASALAMRGVGA 68 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA++ N P M+E HFGVPMCGAVLN +N RL+ ++AF+L+H ++ V++ D+E+ Sbjct: 69 GDTVAVMLNNTPEMFECHFGVPMCGAVLNTLNTRLDPESIAFMLNHGEARVLITDREYSG 128 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 M +KA + R +L+V D PE G+I++E LA+G P+Y W+ Sbjct: 129 --------MVKKALAELGREILVVDVDD---PEYTGPGERVGSIDFETLLASGRPDYAWK 177 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 PADEW +I+L YTSGTT +PKGVV HHRGAY+ ALSN + WGM +VYLWTLPMFHCN Sbjct: 178 TPADEWDAISLNYTSGTTGNPKGVVYHHRGAYLNALSNIVSWGMPPQSVYLWTLPMFHCN 237 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GWCFPW++A SGT++CLR+V K + I ++KVTH+C AP+V + +++AP E + Sbjct: 238 GWCFPWTVAANSGTNVCLRRVDPKLILDAIREHKVTHYCGAPIVHSMLISAPAEWR-KGI 296 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 H V + A A PP +V+ M + GF + H YGL+ETYGP+ VCA EW LP + Q + Sbjct: 297 EHKVSALVAAAPPPAAVIEGMGKIGFNITHVYGLTETYGPAAVCAKHDEWLELPLDEQVR 356 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 +N RQGVRY E + V+D +T +PVP D +T GEI+FRGN+VMKGYLKNP+A +E F G Sbjct: 357 MNGRQGVRYHCQEGVTVMDPETMQPVPWDDQTMGEIMFRGNIVMKGYLKNPKATEEAFHG 416 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 GW+H+GD+AV PD YI+IKDRSKDVIISGGENISS+EVE+ +Y HPAV+ A+VVA PD Sbjct: 417 GWYHTGDLAVMQPDGYIKIKDRSKDVIISGGENISSIEVEDTLYRHPAVMGAAVVATPDP 476 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 +W E PCAF+ L + + A+++ +FCRE++ + VPK +F LPKT+TGKIQK Sbjct: 477 KWGEVPCAFIEL-----REGSSVTAEELTEFCRERMARFKVPKHFIFEALPKTSTGKIQK 531 Query: 552 HILRTKAK 559 +LR KAK Sbjct: 532 FVLREKAK 539 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: 933 Number of extensions: 43 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: 545 Length adjustment: 36 Effective length of query: 533 Effective length of database: 509 Effective search space: 271297 Effective search space used: 271297 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 Apr 09 2024. 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