Protein Info for GFF3355 in Hydrogenophaga sp. GW460-11-11-14-LB1
Annotation: Tryptophan synthase beta chain (EC 4.2.1.20)
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: 91% identical to TRPB_RHOFT: Tryptophan synthase beta chain (trpB) from Rhodoferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)
KEGG orthology group: K01696, tryptophan synthase beta chain [EC: 4.2.1.20] (inferred from 91% identity to rfr:Rfer_1788)MetaCyc: 62% identical to tryptophan synthase beta subunit (Thermococcus kodakarensis)
Tryptophan synthase. [EC: 4.2.1.122, 4.2.1.20]
Predicted SEED Role
"Tryptophan synthase beta chain (EC 4.2.1.20)" in subsystem Auxin biosynthesis or Tryptophan synthesis (EC 4.2.1.20)
MetaCyc Pathways
- 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)
- superpathway of chorismate metabolism (43/59 steps found)
- DIBOA-glucoside biosynthesis (1/6 steps found)
- superpathway of benzoxazinoid glucosides biosynthesis (1/13 steps found)
KEGG Metabolic Maps
- 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 4.2.1.122 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)
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
Find the best match in UniProt
Protein Sequence (423 amino acids)
>GFF3355 Tryptophan synthase beta chain (EC 4.2.1.20) (Hydrogenophaga sp. GW460-11-11-14-LB1) MQTTYQQPDARGHFGIYGGSFVSETLTHAINELKAAYAKYQHDPEFLAEFESELAHFVGR PSPVYHAARMSREAGGAQIFLKREDLNHTGAHKVNNTIGQAMLARRMGKPRVIAETGAGQ HGVATATICARYGLECVVYMGSEDVKRQSPNVYRMKLLGATVVPVESGSKTLKDALNEAM RDWVANVDNTFYIIGTVAGPHPYPMMVRDFQSVIGKECLVQVPEMLAAAGCRGEQPDAVI ACVGGGSNAMGIFHPYIPYEGTRLIGVEAAGEGLESGKHSASLQMGSPGVLHGNRTYVLQ DDNGQVTETHSISAGLDYPGVGPEHAFLKDIGRAEYVGITDTEALEAFHHLCRTEGIIPA LESSHAVAYALKLAKTMKPDQSILVNLSGRGDKDIGTVADLSGVDFYDRPSMRGLTVKGG NAK