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 AO356_29235 AO356_29235 acyl-CoA synthetase
Query= SwissProt::Q8VZF1 (569 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29235 Length = 550 Score = 546 bits (1407), Expect = e-160 Identities = 275/555 (49%), Positives = 358/555 (64%), Gaps = 19/555 (3%) Query: 12 LPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGP 71 L + ANY LTPL FLDRAA+VHP R +V+HG TWRQT +RC RLASAL++ +G Sbjct: 10 LEQSKANYLPLTPLGFLDRAALVHPDRVAVVHGDLRRTWRQTRERCYRLASALSNEGMGA 69 Query: 72 GSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFT 131 G TV+I++PN PAM EAHFGVP+CGAVLN VN RL+A VAF+L H + +++VD+EF Sbjct: 70 GDTVSILSPNTPAMLEAHFGVPLCGAVLNTVNYRLDAEGVAFILRHGECKLLLVDREFAA 129 Query: 132 LAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQ 191 LA +L +E P++I I DH S S G ++YE F+ G P++ Sbjct: 130 LAVAALERLEHP-------PVVIDINDHLAPLGS-----SIGDVDYETFIGRGSPDFQGV 177 Query: 192 PPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCN 251 P+DEWQ IAL YTSGTT PKGVV HRG Y+M++ W + YLWTLPMFH N Sbjct: 178 WPSDEWQPIALNYTSGTTGDPKGVVASHRGTYLMSMLQMTNWPLSRAPRYLWTLPMFHAN 237 Query: 252 GWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPL 311 GWCF W++ +GT +CLR+V+A+ V+ I V HFCAAP+V+ I N+ PL Sbjct: 238 GWCFTWAITAAAGTHVCLRKVSAEAVFDAIDTQGVDHFCAAPIVMAMIANSADRP---PL 294 Query: 312 PHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAK 371 V V+TAG+ PP +VL ++ GF V H YG++E G C W+ W++L Q Sbjct: 295 ETPVRVLTAGSPPPATVLDAVVSLGFDVDHVYGITEVSGTPISCVWQDGWNALAQSDQGA 354 Query: 372 LNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAG 431 L RQG R G E L V D T +PVP DG T GE++ +GN VM GYLKN A ++ F G Sbjct: 355 LRVRQGARAAGFEGLMVADADTLQPVPKDGHTTGELLLKGNTVMMGYLKNENATRKAFEG 414 Query: 432 GWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDE 491 GWFH+GD+AV HP+ YI+I DR KDVIISGGENISSVE+E ++ HPAVL A+VVA+PD+ Sbjct: 415 GWFHTGDVAVVHPNGYIQITDRCKDVIISGGENISSVEIEEAIHCHPAVLHAAVVAQPDD 474 Query: 492 RWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQK 551 W E PCAF+ LK E+ + D++ FC+ +L + P+ V+F LPKTATGKIQK Sbjct: 475 IWGEVPCAFIELKGGAERPTE----ADMIAFCQARLARFKCPRRVIFMELPKTATGKIQK 530 Query: 552 HILRTKAKEMGPVPR 566 +LR +A + R Sbjct: 531 FLLREQAGSRDAIVR 545 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: 879 Number of extensions: 48 Number of successful extensions: 5 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: 550 Length adjustment: 36 Effective length of query: 533 Effective length of database: 514 Effective search space: 273962 Effective search space used: 273962 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