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_009763961.1 MICLODRAFT_RS21665 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >NCBI__GCF_000262405.1:WP_009763961.1 Length = 546 Score = 615 bits (1586), Expect = e-180 Identities = 304/549 (55%), Positives = 384/549 (69%), Gaps = 17/549 (3%) Query: 11 DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70 +L K PANY LTPL FL+RAA VHP R +VIHG +R Y R RRLASALA R IG Sbjct: 9 NLDKNPANYQPLTPLSFLERAASVHPDRTAVIHGPLVRDYRDFYARARRLASALARRGIG 68 Query: 71 PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130 G TV+++ PN PAM E H+GVPM GAVLN +N RL+A +AF L HS++ V++ D+EF Sbjct: 69 RGDTVSVMLPNTPAMLECHYGVPMAGAVLNTLNTRLDAKIIAFSLDHSEAKVLITDREFS 128 Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190 + +L A SS K PL+I D PE GA+EYE+FLA GDP + W Sbjct: 129 ATVKAAL------ARSSVK-PLVIDYDD----PEFTGPGERLGAMEYEEFLAEGDPEFAW 177 Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250 PP DEW +I L YTSGTT PKGVV HHRGAY++A+ N L GM VYLWTLPMFHC Sbjct: 178 NPPRDEWDAITLNYTSGTTGDPKGVVYHHRGAYLLAMGNILTAGMGQHPVYLWTLPMFHC 237 Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310 NGWCFPWSL++++G +CLR V AK +Y +A +VTH C AP+V++ ++NAP + P Sbjct: 238 NGWCFPWSLSIVAGIHVCLRAVRAKPMYDALADQRVTHLCGAPIVMSTLLNAPASEK-RP 296 Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370 LPHTV +TA A PP +VL +M GF V H YGL+E YGP+ V W EWD+L A Sbjct: 297 LPHTVKFLTAAAPPPEAVLAAMKAAGFDVTHLYGLTEVYGPAVVNEWHDEWDALDQGGYA 356 Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430 ARQGVRY +E LDV+D +T +PVPADG+T GE++FRGN+VMKGYLKNP + F Sbjct: 357 AKKARQGVRYPVLEALDVLDPETMQPVPADGRTLGEVMFRGNVVMKGYLKNPSGTAKAFE 416 Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490 GGWFHSGD+ VK+PD Y+++KDRSKD+IISGGENISS+EVE+ +Y HPA+ A+VVA PD Sbjct: 417 GGWFHSGDLGVKYPDGYVQLKDRSKDIIISGGENISSIEVEDALYRHPAIQAAAVVAMPD 476 Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550 E+W E+PCAFV L+ DQ+ A+DI+ +CR+ L +Y P++V+F LPKT+TGKIQ Sbjct: 477 EKWGETPCAFVELRP-----DQSVPAEDIIAWCRQHLASYKCPRTVIFTELPKTSTGKIQ 531 Query: 551 KHILRTKAK 559 K LR A+ Sbjct: 532 KFQLREMAR 540 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: 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: 546 Length adjustment: 36 Effective length of query: 533 Effective length of database: 510 Effective search space: 271830 Effective search space used: 271830 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 24 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