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_043744440.1 AMB_RS12570 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000009985.1:WP_043744440.1 Length = 544 Score = 642 bits (1657), Expect = 0.0 Identities = 307/550 (55%), Positives = 393/550 (71%), Gaps = 18/550 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L K PANY LTPL FL+R+A V+P R SV+HG +TW+QTYDRCRRL SALA R +G Sbjct: 11 LDKNPANYVPLTPLGFLERSASVYPDRISVVHGDLRFTWKQTYDRCRRLGSALAARGVGV 70 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA++A N PA YEA FGVPM G VL +NIRL+A +AF+L H ++ V++ D+EF Sbjct: 71 GDTVAVMAANTPAAYEAAFGVPMTGGVLCALNIRLDAEAIAFMLQHGEAKVLLTDREFAP 130 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 + +L L+E K P++I I D + G +EYE F+A GDP Y W Sbjct: 131 TIKKALSLLEAK-------PIVIDIDDAAVTTGEM-----LGEMEYEAFIAGGDPEYAWV 178 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P+DEW +IAL YTSGTT +PKGVV HHRGAYI AL N + WGM VYLWTLPMFHCN Sbjct: 179 WPSDEWDAIALNYTSGTTGNPKGVVYHHRGAYINALGNVVNWGMTGHPVYLWTLPMFHCN 238 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GWCFPW+LA L+GT++CLR+V +++ I K+KVTH C AP+V+ ++NAP++D PL Sbjct: 239 GWCFPWTLAALAGTNVCLRRVDGGHMFAAIEKHKVTHMCGAPIVMGMLINAPEKDR-RPL 297 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 PH V MTA A PP +V+ + +GF++ H YGL+E YGP+TVCAWK EWD LP + +AK Sbjct: 298 PHPVEFMTAAAPPPAAVIGRLESQGFKITHVYGLTEVYGPATVCAWKEEWDELPLDERAK 357 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 + +RQGVRY E + V D + PVP DG T GE+ +RGN+VMKGYLKNP A E F+G Sbjct: 358 MKSRQGVRYVNEEAMMVADPVSLVPVPKDGATMGEVFYRGNVVMKGYLKNPSATNEAFSG 417 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 GWFH+GD+ V H D YIE+KDRSKD+IISGGENIS++EVE V+Y HP+V EA+VVARPDE Sbjct: 418 GWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVEGVLYQHPSVGEAAVVARPDE 477 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 +W E+PCAF+ LK A++IM FCRE+L Y P++VVF LPKT+TGK+QK Sbjct: 478 KWGETPCAFIGLKD-----GATATAEEIMAFCRERLAHYKCPRTVVFTNLPKTSTGKVQK 532 Query: 552 HILRTKAKEM 561 ++LR AK++ Sbjct: 533 YVLREMAKKL 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: 940 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: 544 Length adjustment: 36 Effective length of query: 533 Effective length of database: 508 Effective search space: 270764 Effective search space used: 270764 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