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 3607419 Dshi_0833 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__Dino:3607419 Length = 541 Score = 541 bits (1395), Expect = e-158 Identities = 280/550 (50%), Positives = 365/550 (66%), Gaps = 18/550 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L K AANY LTPL L RAA V+P R +V++G+R +T+ + + R + ASAL I Sbjct: 10 LDKCAANYVPLTPLSHLARAALVYPDREAVVYGARRFTYAEYHARVSRLASALAGAGIAP 69 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G VA + PN+PA+ EAHF VP GAV+N +NIRL+ T+A++L H A AV+VD +F Sbjct: 70 GDVVATLLPNIPAMVEAHFGVPACGAVLNTINIRLDVDTVAYILSHGGAKAVLVDSQFLP 129 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 LA EA + L + PLL+ + D++ L G EYE FL GGDP+F W Sbjct: 130 LAAEACERLDGPA------PLLIEVADDAAGVHALG-----GYTEYEDFLAGGDPDFPWI 178 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 P DEW+S++L YTSGTT PKGVV HRGAYLM++ + W + +L +P+FHCN Sbjct: 179 MPRDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVLYPRWLAIVPLFHCN 238 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GW ++W M GT +C R V+A+ +Y+AIA+ GVTHF AP+VLN IVNAP + A P Sbjct: 239 GWNHSWMMPMLGGTVVCCRDVSAQAIYTAIAENGVTHFGGAPIVLNMIVNAP-DAARRPF 297 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 H V V TAGA P + L A+ E GF V YGL+ETYG T C W P+WD+LP ++A Sbjct: 298 SHTVEVFTAGAPPAAATLAAIEELGFNVTQVYGLTETYGHVTECVWNPDWDTLPQAERAA 357 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 + ARQGV +E + V+D + M+ VP DG T GE++MRGN+VMKGY +NP A E+FA Sbjct: 358 IKARQGVALPQMEHITVMDPE-MRQVPMDGATTGEVMMRGNSVMKGYYRNPDATAEAFAG 416 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 G+FHSGD+A++HPDGYI+I DR+KDIIISGGENISS+EVE L HPAVL +VVA+PD Sbjct: 417 GYFHSGDIALQHPDGYIQIADRAKDIIISGGENISSVEVEGALMHHPAVLLCAVVAKPDP 476 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 WGE PCAFV LK K+ E+ +II F + ++ + PK VVF LPKT+TGKIQK Sbjct: 477 TWGEVPCAFVELKDG--KTAEEA---EIIAFARERLAGFKTPKKVVFTELPKTSTGKIQK 531 Query: 551 HVLRAKAKEM 560 LR +AK + Sbjct: 532 FELRNRAKAL 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: 888 Number of extensions: 32 Number of successful extensions: 5 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: 541 Length adjustment: 36 Effective length of query: 532 Effective length of database: 505 Effective search space: 268660 Effective search space used: 268660 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