Protein Info for Shew_2188 in Shewanella loihica PV-4
Annotation: long-chain-fatty-acid--CoA ligase (RefSeq)
These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.
Protein Families and Features
Best Hits
Swiss-Prot: 71% identical to LCFA_YERPE: Long-chain-fatty-acid--CoA ligase (fadD) from Yersinia pestis
KEGG orthology group: K01897, long-chain acyl-CoA synthetase [EC: 6.2.1.3] (inferred from 100% identity to slo:Shew_2188)MetaCyc: 68% identical to long-chain-fatty-acid--CoA ligase (Escherichia coli K-12 substr. MG1655)
Long-chain-fatty-acid--CoA ligase. [EC: 6.2.1.3]; 6.2.1.3 [EC: 6.2.1.3]; 6.2.1.3 [EC: 6.2.1.3]; 6.2.1.3 [EC: 6.2.1.3]; 6.2.1.3 [EC: 6.2.1.3]
Predicted SEED Role
"Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)" in subsystem Biotin biosynthesis or n-Phenylalkanoic acid degradation (EC 6.2.1.3)
MetaCyc Pathways
- superpathway of fatty acids biosynthesis (E. coli) (50/53 steps found)
- oleate β-oxidation (33/35 steps found)
- palmitate biosynthesis II (type II fatty acid synthase) (29/31 steps found)
- superpathway of fatty acid biosynthesis II (plant) (37/43 steps found)
- fatty acid salvage (5/6 steps found)
- stearate biosynthesis II (bacteria and plants) (5/6 steps found)
- long-chain fatty acid activation (1/1 steps found)
- palmitate biosynthesis III (21/29 steps found)
- phosphatidylcholine acyl editing (3/4 steps found)
- phytol degradation (3/4 steps found)
- stearate biosynthesis IV (4/6 steps found)
- γ-linolenate biosynthesis II (animals) (1/2 steps found)
- linoleate biosynthesis II (animals) (1/2 steps found)
- long chain fatty acid ester synthesis (engineered) (2/4 steps found)
- alkane biosynthesis II (1/3 steps found)
- oleate biosynthesis I (plants) (1/3 steps found)
- 3-methyl-branched fatty acid α-oxidation (3/6 steps found)
- octane oxidation (2/5 steps found)
- wax esters biosynthesis II (1/4 steps found)
- 6-gingerol analog biosynthesis (engineered) (2/6 steps found)
- 2-deoxy-D-ribose degradation II (3/8 steps found)
- ceramide degradation by α-oxidation (2/7 steps found)
- sphingosine and sphingosine-1-phosphate metabolism (4/10 steps found)
- stearate biosynthesis I (animals) (1/6 steps found)
- arachidonate biosynthesis III (6-desaturase, mammals) (1/7 steps found)
- capsaicin biosynthesis (1/7 steps found)
- icosapentaenoate biosynthesis II (6-desaturase, mammals) (1/7 steps found)
- icosapentaenoate biosynthesis III (8-desaturase, mammals) (1/7 steps found)
- ceramide and sphingolipid recycling and degradation (yeast) (4/16 steps found)
- sporopollenin precursors biosynthesis (5/18 steps found)
- cutin biosynthesis (2/16 steps found)
- suberin monomers biosynthesis (3/20 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 6.2.1.3
Use Curated BLAST to search for 6.2.1.3
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
See A3QF06 at UniProt or InterPro
Protein Sequence (557 amino acids)
>Shew_2188 long-chain-fatty-acid--CoA ligase (RefSeq) (Shewanella loihica PV-4) MEQLWTKNLPHDVPAIIDAKQYSSLIDLFESSVAKYADQPAFVNMGATLTYRKLEERSRA FAAYLQNELKLQKGDRVAIMMPNLLQYPIALFGILRAGMVVVNVNPLYTPRELKHQLNDS GAKAIVVVSNFANTLEQVVEQTPVKSVILTGLGDLLSAPKRTLVNFVVKYIKKMVPKYHL PHAISMRQSLSKGRRLQYVKPTIKGDDIAFLQYTGGTTGVSKGAMLTHGNIVSNLLQADA AYSPLLADGKEFVVTALPLYHIFALTVNCLLFLHKGANNLLITNPRDIPAFVSELKKHPF TALTGVNTLFNALVSSEEFKTLDFSNLKLSIGGGMAVQRAVADKWQGITKTRLLEGYGLT EASPLLTCCPYNLEGYNGSIGFPVANTDMQVRDEEGNVLPQGETGELFAKGPQVMKGYWQ RPEETAKVIDKDGYLATGDIGYMDEQGFFFIVDRKKDMILVSGFNVFPNEVEEVVALHPK VLEVAAVGVPHEVSGELVKVFVVPKDKSLTEEQVIKHCRHHLTGYKIPKLVEFRDELPKS NVGKILRRELRDEAKSA