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_RS27915 RR42_RS27915 acyl-CoA synthetase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__Cup4G11:RR42_RS27915 Length = 545 Score = 541 bits (1395), Expect = e-158 Identities = 279/553 (50%), Positives = 361/553 (65%), Gaps = 18/553 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L KN AN+ LTP+ FL RAA+V+ R +++HG W TY R R+ AS L + +G Sbjct: 9 LGKNPANHVPLTPIDFLARAASVYGDRLAIVHGPVRQNWRDTYARARRLASGLASLGVGK 68 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G TVA + PN PA+ EAHF VPMAGAV+N +NIRL+AS + F+L H A ++ D EF Sbjct: 69 GDTVAALLPNTPAMVEAHFGVPMAGAVLNALNIRLDASNLIFMLRHGEARVLLADTEFAD 128 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 +A + +A E P L VV ++ P+ A G +YE+ L GDPEF W+ Sbjct: 129 VARQ----IANEI-----PGLKVVAVLDALGPQD---APAFGETDYERLLASGDPEFAWQ 176 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEW +I+L YTSGTT PKGVV HRGA + ++S + W + + A+YLWTLPMFHCN Sbjct: 177 MPADEWDAIALNYTSGTTGDPKGVVYHHRGAAINAISNILEWDLPKHAVYLWTLPMFHCN 236 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC+ W +AA G N+CLR+ K V+ + GVTH+CAAP+V +VNAP + Sbjct: 237 GWCFPWTIAARAGVNVCLRKFEPKLVFDLMRDEGVTHYCAAPIVHTALVNAPLAWRD-GV 295 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 V M AGA PP +VL M GF + H YGL+ETYGP+ +CA + +W SL +A Sbjct: 296 RGPVRGMVAGAPPPAAVLAQMEAMGFALTHVYGLTETYGPAAVCAEQDDWASLSQEDRAT 355 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 ARQGVRY + V+D TM+PV +DG +GEI+ RGN MKGYLKN KA E+FA Sbjct: 356 KKARQGVRYHLQTEVAVLDPDTMQPVASDGEEIGEIMFRGNICMKGYLKNEKATREAFAG 415 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWFH+GDL V PDGY++IKDRSKDIIISGGENISS+EVE+ +Y HPAVL V+VVA+PD Sbjct: 416 GWFHTGDLGVCTPDGYVKIKDRSKDIIISGGENISSVEVEDAIYRHPAVLAVAVVAQPDV 475 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 +WGE+PCAFV L K A+++I C++ + + VPK+V FGPLPKT+TGKIQK Sbjct: 476 KWGETPCAFVEL-----KDGASATADELIAHCRTLLAGFKVPKAVYFGPLPKTSTGKIQK 530 Query: 551 HVLRAKAKEMGAL 563 LR K K A+ Sbjct: 531 FELRKKVKSDAAI 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: 890 Number of extensions: 31 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: 545 Length adjustment: 36 Effective length of query: 532 Effective length of database: 509 Effective search space: 270788 Effective search space used: 270788 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