Protein Info for Shew_2256 in Shewanella loihica PV-4
Name: trpA
Annotation: tryptophan synthase subunit alpha (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: 79% identical to TRPA_SHEON: Tryptophan synthase alpha chain (trpA) from Shewanella oneidensis (strain MR-1)
KEGG orthology group: K01695, tryptophan synthase alpha chain [EC: 4.2.1.20] (inferred from 100% identity to slo:Shew_2256)MetaCyc: 64% identical to tryptophan synthase subunit alpha (Escherichia coli K-12 substr. MG1655)
Tryptophan synthase. [EC: 4.2.1.20]; Indole-3-glycerol-phosphate lyase. [EC: 4.2.1.20, 4.1.2.8]
Predicted SEED Role
"Tryptophan synthase alpha chain (EC 4.2.1.20)" in subsystem Auxin biosynthesis or Tryptophan synthesis (EC 4.2.1.20)
MetaCyc Pathways
- superpathway of chorismate metabolism (51/59 steps found)
- superpathway of aromatic amino acid biosynthesis (18/18 steps found)
- superpathway of L-tryptophan biosynthesis (13/13 steps found)
- L-tryptophan biosynthesis (6/6 steps found)
- DIBOA-glucoside biosynthesis (1/6 steps found)
- superpathway of benzoxazinoid glucosides biosynthesis (1/13 steps found)
KEGG Metabolic Maps
- Benzoxazinone biosynthesis
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of phenylpropanoids
- Biosynthesis of plant hormones
- Glycine, serine and threonine metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 4.2.1.20
Use Curated BLAST to search for 4.1.2.8 or 4.2.1.20
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 A3QF74 at UniProt or InterPro
Protein Sequence (267 amino acids)
>Shew_2256 tryptophan synthase subunit alpha (RefSeq) (Shewanella loihica PV-4) MSNRYQAAFAALNASGRGAFVPFVTIGDPNRELSLKIIETLVENGADALELGFPFSDPLA DGPVIQGANLRALAAGTTPGGCFEIITAVRAKYPELPIGLLLYANLVYANGVEAFYAKAK AAGVDSVLIADVPVEEAAPFIAAAKAHEVAPIFIAPPNGDAETLRQVAEQGQGYTYLLSR AGVTGTESKAGMPLDDILAQLKAFDAPPPLLGFGIAEPDQVKAAIDSGAAGAISGSAVVK IIETHQDDEQALLSALGQFTREMKAAT