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_011385011.1 AMB_RS13240 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000009985.1:WP_011385011.1 Length = 541 Score = 583 bits (1504), Expect = e-171 Identities = 291/553 (52%), Positives = 376/553 (67%), Gaps = 24/553 (4%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L + AN+ ALTPL FL+RAA V P R +VIHG TW +T+ RCR+LA+AL R IG Sbjct: 10 LDRNAANFVALTPLTFLERAAAVWPDRLAVIHGPVRRTWAETFVRCRKLAAALTARGIGL 69 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TVA++ N P +EAHFGVP+ GAVLN +N RL+A + F+L+H+++ +++ D+EF Sbjct: 70 GDTVALMGANTPETFEAHFGVPLTGAVLNAINTRLDADAITFILNHAEAKILITDREFSP 129 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 + + +L + P++ + E L G YE L PW Sbjct: 130 VVKKALAALGRTI------PVIDIDDPQFKGGELL------GEKNYEQLLDEAASEAPWT 177 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P DEWQ+IAL YTSGTT +PKGVV HHRGA++ A+SN L W M D VYLWTLPMFHCN Sbjct: 178 LPTDEWQAIALNYTSGTTGNPKGVVYHHRGAHLNAVSNALSWQMGDNTVYLWTLPMFHCN 237 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAP---KEDTI 308 GWCFPW++AV++GTS+CLR V + I KVT+FC AP+VLN I NAP KE Sbjct: 238 GWCFPWTMAVVAGTSVCLRHVRVDAIMGAIRDEKVTNFCGAPIVLNMINNAPAALKEG-- 295 Query: 309 LPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPET 368 + H V VMTAGAAPP V+ M + G+ V H YGL+E YGP+ C W +W+ L + Sbjct: 296 --ISHAVKVMTAGAAPPAPVIAGMERMGWEVTHVYGLTECYGPTVQCVWHDKWNGLSIDE 353 Query: 369 QAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKET 428 +A++ ARQGVR +E L + D + +P P DGKT GEI RGN VMKGYLKN +A +E Sbjct: 354 KAQIKARQGVRGPMLEGLMIADPISLEPAPKDGKTVGEIFMRGNNVMKGYLKNEKATEEA 413 Query: 429 FAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVAR 488 FAGGWFH+GD+AV HPD YIEIKDRSKD+IISGGENISS+EVE+++Y H AVLEA+VVAR Sbjct: 414 FAGGWFHTGDLAVCHPDGYIEIKDRSKDIIISGGENISSIEVEDILYAHLAVLEAAVVAR 473 Query: 489 PDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGK 548 PDE+W E+PCAF+ LK E + DI+ FCRE++ + VP+++VFG LPKT+TGK Sbjct: 474 PDEKWGETPCAFIALKDGAEATE-----ADIITFCRERMAHFKVPRTIVFGGLPKTSTGK 528 Query: 549 IQKHILRTKAKEM 561 +QK +LR KAKE+ Sbjct: 529 VQKFMLRQKAKEL 541 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: 872 Number of extensions: 31 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: 541 Length adjustment: 36 Effective length of query: 533 Effective length of database: 505 Effective search space: 269165 Effective search space used: 269165 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