Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate AO356_29235 AO356_29235 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29235 Length = 550 Score = 545 bits (1404), Expect = e-159 Identities = 269/553 (48%), Positives = 357/553 (64%), Gaps = 19/553 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L ++ ANY LTPL FL+RAA VHP R +V+HG TW QT RC + ASAL+N +G Sbjct: 10 LEQSKANYLPLTPLGFLDRAALVHPDRVAVVHGDLRRTWRQTRERCYRLASALSNEGMGA 69 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TV++++PN PA+ EAHF VP+ GAV+N VN RL+A +AF+L H ++VD+EF + Sbjct: 70 GDTVSILSPNTPAMLEAHFGVPLCGAVLNTVNYRLDAEGVAFILRHGECKLLLVDREFAA 129 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 LA AL+ L PP+++ I D G ++YE F+ G P+F Sbjct: 130 LAVAALERLEH-------PPVVIDINDHLAP-----LGSSIGDVDYETFIGRGSPDFQGV 177 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEWQ I+L YTSGTT PKGVV SHRG YLMS+ W ++ YLWTLPMFH N Sbjct: 178 WPSDEWQPIALNYTSGTTGDPKGVVASHRGTYLMSMLQMTNWPLSRAPRYLWTLPMFHAN 237 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC+TW + A GT++CLR+V+A+ V+ AI GV HFCAAP+V+ I N+ PL Sbjct: 238 GWCFTWAITAAAGTHVCLRKVSAEAVFDAIDTQGVDHFCAAPIVMAMIANSADRP---PL 294 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 V V+TAG+ PP +VL A+ GF V H YG++E G C W+ W++L Q Sbjct: 295 ETPVRVLTAGSPPPATVLDAVVSLGFDVDHVYGITEVSGTPISCVWQDGWNALAQSDQGA 354 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 L RQG R EGL V D T++PVP DG T GE++++GN VM GYLKN A ++F Sbjct: 355 LRVRQGARAAGFEGLMVADADTLQPVPKDGHTTGELLLKGNTVMMGYLKNENATRKAFEG 414 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWFH+GD+AV HP+GYI+I DR KD+IISGGENISS+E+E ++ HPAVL +VVA+PD+ Sbjct: 415 GWFHTGDVAVVHPNGYIQITDRCKDVIISGGENISSVEIEEAIHCHPAVLHAAVVAQPDD 474 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 WGE PCAF+ LK ++ E D+I FC++++ + P+ V+F LPKTATGKIQK Sbjct: 475 IWGEVPCAFIELKGGAERPTE----ADMIAFCQARLARFKCPRRVIFMELPKTATGKIQK 530 Query: 551 HVLRAKAKEMGAL 563 +LR +A A+ Sbjct: 531 FLLREQAGSRDAI 543 Lambda K H 0.318 0.134 0.415 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: 878 Number of extensions: 36 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: 568 Length of database: 550 Length adjustment: 36 Effective length of query: 532 Effective length of database: 514 Effective search space: 273448 Effective search space used: 273448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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