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 H281DRAFT_05558 H281DRAFT_05558 fatty-acyl-CoA synthase
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__Burk376:H281DRAFT_05558 Length = 550 Score = 489 bits (1260), Expect = e-143 Identities = 253/544 (46%), Positives = 335/544 (61%), Gaps = 18/544 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L AAN+ ALTP+ FL+RA V P RT+V++GS TW + CR+FASAL I Sbjct: 11 LRPRAANFDALTPVTFLQRAEKVFPDRTAVVYGSHRETWREHAATCRRFASALARAGIEY 70 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G VA++ N P + AHFAVPMAGAV+N +N RL+A ++++LGHS A ++VD EF Sbjct: 71 GDVVALLMTNTPPMLAAHFAVPMAGAVLNTINTRLDAENVSYILGHSEARLIIVDAEFLE 130 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 LA A+ L PP LV DE +A + +Y FL GD + Sbjct: 131 LARTAVARLQH-------PPRLVCFADEQA-----AFAASSDVEDYVSFLASGDENASFC 178 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 E+EW I++ YTSGTT PKGVV SHRGAYL ++S+ + WG+ + A YLWTLP+FHCN Sbjct: 179 KVEEEWTPIAVNYTSGTTGRPKGVVYSHRGAYLSAVSSIISWGVPKAASYLWTLPLFHCN 238 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC W +A G ++CLR+V + I VTH+C AP+V I + ++ ++ Sbjct: 239 GWCMPWVLALQGGKSVCLRRVDGDKIVQLINDERVTHYCGAPIVHALIRDRAQQQDLVFN 298 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 P V + GA PP S++ AM G ++ H YGL+ETYGP+ IC +P W L ++A Sbjct: 299 P-AVSALIGGAPPPASLIAAMDAIGVQLTHIYGLTETYGPAAICEQQPAWAELGEAERAD 357 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 ARQGV Y G+ V++ + V ADG MGEIV RGN M GYLK+ ++ + +F Sbjct: 358 RKARQGVNYALQAGMTVMNCNSSDEVSADGAMMGEIVFRGNMTMMGYLKDSESTDRAFDG 417 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWF SGDLAV PDGY+ IKDRSKDIIISGGENISS+EVE+ LY H V +VVA PDE Sbjct: 418 GWFRSGDLAVLEPDGYVRIKDRSKDIIISGGENISSVEVEDVLYRHETVAAAAVVAMPDE 477 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 +WGE P A V L+ S + ++A C+ ++ + PK V+F P+PKTATGKIQK Sbjct: 478 KWGEVPVAIVELREGSHASEDALIAH-----CREQLAHFKCPKRVIFHPIPKTATGKIQK 532 Query: 551 HVLR 554 +VLR Sbjct: 533 NVLR 536 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: 851 Number of extensions: 37 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