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 WP_009564552.1 RSPH17029_RS01295 acyl--CoA ligase family protein
Query= SwissProt::M4IS88 (568 letters) >NCBI__GCF_000015985.1:WP_009564552.1 Length = 549 Score = 522 bits (1344), Expect = e-152 Identities = 270/548 (49%), Positives = 351/548 (64%), Gaps = 18/548 (3%) Query: 11 LPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGL 70 L K AANY ALTPL L+RAA VH RT++++GS T+ + + R + ASAL I Sbjct: 10 LEKCAANYAALTPLSHLKRAAEVHTDRTALVNGSIRLTYGEYHARVSRLASALAGMGIQP 69 Query: 71 GSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFS 130 G VA + PN+ A EAHF VP GA++N +N RL+ T++++L H A ++ D F Sbjct: 70 GDVVATLLPNIAAHAEAHFGVPACGAILNAINTRLDLDTVSYILEHGGAKLLLCDTAFLK 129 Query: 131 LAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWK 190 LA++A ++ K P+LV E CD + ++ +EYE ++ G+P W Sbjct: 130 LAKDAC------ARLEGKAPILV----EVCD-REAGFSPSGEVLEYEDLMDRGNPWAPWV 178 Query: 191 PPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCN 250 PEDEW+SI+L YTSGTT PKGVV HRGAYL + ++ W + +YL +P+FHCN Sbjct: 179 MPEDEWESIALNYTSGTTGRPKGVVYHHRGAYLSTYGNAIAWRMQLYPVYLTIVPLFHCN 238 Query: 251 GWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPL 310 GWC+TW + GT +C R +TAK +Y+AIA GVTHF AP+VLNT++NA PE+ Sbjct: 239 GWCHTWMVPMLGGTVVCCRDITAKAIYAAIADEGVTHFGGAPIVLNTLINAAPEDRR-SF 297 Query: 311 PHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQAR 370 +V V TAGA PP + L A+ GF V YGL+E YGP+T C WKPEWD ++A Sbjct: 298 DQVVEVFTAGAPPPAATLAAIEPLGFNVTQVYGLTEVYGPATECIWKPEWDETAGEERAA 357 Query: 371 LNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFAD 430 L AR GV LEG +V DT +P+P D +GEI MRGN VMKGY KNP+A E+F D Sbjct: 358 LKARTGVAMATLEGAEVHDTHG-QPIPRDTVHLGEIAMRGNMVMKGYYKNPEATAEAFRD 416 Query: 431 GWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDE 490 GWF SGD+A +HPDGYI+I DR+KDIIISGGEN+SS+EVE + HPAV +VVA+PDE Sbjct: 417 GWFRSGDIAFQHPDGYIKITDRAKDIIISGGENVSSVEVEGVIAHHPAVSLCAVVAKPDE 476 Query: 491 RWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQK 550 RWGE PCAFV L K Q E+II F + ++ + PK V+F LPKT+TGKIQK Sbjct: 477 RWGEVPCAFVEL-----KRGRQATEEEIIAFARERLAGFKTPKQVIFCELPKTSTGKIQK 531 Query: 551 HVLRAKAK 558 LRA AK Sbjct: 532 FELRAVAK 539 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: 880 Number of extensions: 38 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: 549 Length adjustment: 36 Effective length of query: 532 Effective length of database: 513 Effective search space: 272916 Effective search space used: 272916 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 16 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