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 GFF1060 HP15_1039 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__Marino:GFF1060 Length = 542 Score = 617 bits (1591), Expect = 0.0 Identities = 303/547 (55%), Positives = 381/547 (69%), Gaps = 21/547 (3%) Query: 16 ANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGLGSTVA 75 ANY +P+ F+ER ATV+P +VIHG+ Y W QTY RCR+ ASAL IG G TVA Sbjct: 14 ANYAVQSPVDFIERTATVYPEYPAVIHGAIRYNWAQTYERCRRLASALKGRGIGRGDTVA 73 Query: 76 VIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFSLAEEA 135 V+ PN+PA+ EAHF VPM GAV+N +N+RL+A IAF+L H A V+ D+EF + +A Sbjct: 74 VMLPNIPAMVEAHFGVPMIGAVLNTLNVRLDAEAIAFMLDHGEAKVVIADREFGEVIRDA 133 Query: 136 LKILAQESKSHYKPPLLVVIGDESCDPKTLEYA--LKTGAIEYEKFLEGGDPEFDWKPPE 193 + L + PL++ + D EY ++ ++YE FL+ GDP F W PE Sbjct: 134 VSRLDTK-------PLVIDVDDP-------EYGEGVQVSDLDYEAFLQEGDPTFQWSFPE 179 Query: 194 DEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCNGWC 253 +EW +ISL YTSGTT +PKGVV HRGAY+ ++ VW ++ +YLWTLPMFHCNGWC Sbjct: 180 NEWDAISLNYTSGTTGNPKGVVYHHRGAYINAIGNQTVWSMDMHPVYLWTLPMFHCNGWC 239 Query: 254 YTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHL 313 + W + A GT++CLR+V + + I + VTH C AP+VLN ++N P E A + H Sbjct: 240 FPWTITAMAGTHVCLRRVDPEKILQLIRDHQVTHMCGAPIVLNALLNVP-ESAKAGIDHD 298 Query: 314 VHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNA 373 V MTAGAAPP V+ A+ E G +V H YGL+E YGP T+CAWK EWD+LP +AR A Sbjct: 299 VKSMTAGAAPPAQVIGAIEEMGIQVTHVYGLTEVYGPVTVCAWKSEWDALPLHDRARKKA 358 Query: 374 RQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFADGWF 433 RQGVRY L G V D TM+PVP DG T+GEI +RGN VMKGYLKNPKA EE+F GWF Sbjct: 359 RQGVRYHTLAGTMVGDPNTMEPVPKDGKTIGEIFLRGNTVMKGYLKNPKATEEAFRGGWF 418 Query: 434 HSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWG 493 H+GDLAV H DGY+EIKDR KDIIISGGENIS++EVE+TLY HPAVLE +VVARPDE+WG Sbjct: 419 HTGDLAVWHEDGYMEIKDRLKDIIISGGENISTIEVEDTLYRHPAVLEAAVVARPDEKWG 478 Query: 494 ESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQKHVL 553 E+PCAFVTLKP +E EDII FC+ + + VPK++VF LPKT+TGKIQK VL Sbjct: 479 ETPCAFVTLKPEAGDVSE----EDIINFCREHLARFKVPKTIVFSELPKTSTGKIQKFVL 534 Query: 554 RAKAKEM 560 R +AKE+ Sbjct: 535 RDQAKEL 541 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: 918 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: 568 Length of database: 542 Length adjustment: 36 Effective length of query: 532 Effective length of database: 506 Effective search space: 269192 Effective search space used: 269192 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