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 RR42_RS25360 RR42_RS25360 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__Cup4G11:RR42_RS25360 Length = 554 Score = 561 bits (1445), Expect = e-164 Identities = 284/553 (51%), Positives = 367/553 (66%), Gaps = 17/553 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L + AAN+ LTPL FL+R A +P RT++IHG +W T RCRQ ASAL +G Sbjct: 10 LDRRAANHMPLTPLHFLDRCAEQYPDRTAIIHGPVRQSWKVTRERCRQLASALVKRGVGR 69 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TV+++APN PA+ EAH +P++GAV+N +N RL+A + F++ H + VD+EF + Sbjct: 70 GDTVSILAPNTPAMVEAHHGIPLSGAVLNAINCRLDADGVRFIVAHGECKVLFVDREFSA 129 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 LA EAL+ L PL++ I D GA+EYE+FL GD +F Sbjct: 130 LAAEALQGLPNA-------PLVIDIADALAPAGE-----PIGAMEYEQFLREGDIDFPGV 177 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P+DEW +I+L YTSGTT+ PKGVV SHRGAYLMS+ WG+ YLWTLPMFH N Sbjct: 178 WPDDEWNAIALNYTSGTTSDPKGVVPSHRGAYLMSMLQLTDWGMPRAPKYLWTLPMFHAN 237 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC++W + A GT++CLR+VTA ++SAI YG HFCAAP+VL+++ A EE P Sbjct: 238 GWCFSWAVTAAAGTHVCLRKVTAANIFSAIEAYGADHFCAAPIVLSSLATATQEERR-PF 296 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 H+V + TAG+ PP SVL A+ E+GF V H YG++E G P W+ ++AR Sbjct: 297 SHVVRIRTAGSPPPASVLKAVIEQGFDVEHVYGITEASGTPVSSYANPAWNEKSGDEKAR 356 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 L ARQG R LEGL V D TM+ VP DGTT GE+++RGN VMKGYLKNP+A E +FA Sbjct: 357 LMARQGNRAAGLEGLRVADPDTMESVPWDGTTQGELLLRGNIVMKGYLKNPEATEAAFAG 416 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWFH+GDLAV HPDGY++I DRSKD+IISGGENISS+EVE+ L+ HPAVL +VVA+P Sbjct: 417 GWFHTGDLAVVHPDGYVQITDRSKDVIISGGENISSVEVEDVLHQHPAVLIAAVVAQPHP 476 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 +WGESPCAF+ LK + E +II FC+S++ Y P VV+G LPKT TGKIQK Sbjct: 477 KWGESPCAFIELKNGVAAPTE----AEIIAFCRSRLAHYKCPTRVVYGALPKTGTGKIQK 532 Query: 551 HVLRAKAKEMGAL 563 + LRA A A+ Sbjct: 533 YRLRALAGSREAI 545 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: 894 Number of extensions: 40 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: 554 Length adjustment: 36 Effective length of query: 532 Effective length of database: 518 Effective search space: 275576 Effective search space used: 275576 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