Protein Info for GFF3403 in Variovorax sp. SCN45

Annotation: Benzoate catabolism regulator with shikimate kinase domain

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

• PF01381: HTH_3
  • amino acids 40 to 94 (55 residues), 35.2 bits, E=2e-12
• PF13671: AAA_33
  • amino acids 144 to 273 (130 residues), 27.6 bits, E=6.7e-10
• PF13238: AAA_18
  • amino acids 144 to 271 (128 residues), 30.2 bits, E=1.1e-10
• PF01202: SKI
  • amino acids 150 to 302 (153 residues), 118.1 bits, E=8.2e-38

Best Hits

KEGG orthology group: K00891, shikimate kinase [EC: 2.7.1.71] (inferred from 91% identity to vap:Vapar_0092)

Predicted SEED Role

"Regulatory protein of benzoate catabolism" in subsystem Benzoate transport and degradation cluster

MetaCyc Pathways

• superpathway of aromatic amino acid biosynthesis (18/18 steps found)
• superpathway of L-tryptophan biosynthesis (13/13 steps found)
• superpathway of L-phenylalanine biosynthesis (10/10 steps found)
• superpathway of L-tyrosine biosynthesis (10/10 steps found)
• chorismate biosynthesis I (7/7 steps found)
• chorismate biosynthesis from 3-dehydroquinate (5/5 steps found)
• superpathway of chorismate metabolism (42/59 steps found)
• chorismate biosynthesis II (archaea) (8/12 steps found)

KEGG Metabolic Maps

• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Phenylalanine, tyrosine and tryptophan biosynthesis

Isozymes

Compare fitness of predicted isozymes for: 2.7.1.71

Use Curated BLAST to search for 2.7.1.71

Protein Sequence (314 amino acids)

>GFF3403 Benzoate catabolism regulator with shikimate kinase domain (Variovorax sp. SCN45)
MNEHVDAVLATAPESAAGGNGAAPAGEVKNPLLVALGDRVRNLRAQRGLTRKAVALSAEV
SERHLANLEYGIGNASILVLQQVAGALHCSLAELVGDVTTSSPEWLLIRELLEHRSEADL
RRVRVALGELLGTASVDPARHRRIALVGLRGAGKSTLGQMLAEDLEIPFIELSREIEKLA
GCSVREIHDLYGTNAYRRYERRALEEAVQIYSEVVIATPGGIVSDPATFNELLAHCTTVW
LQAAPEEHMGRVAAQGDTRPMAASKEAMEDLRRILNGRAAFYSKADLSVDTSGRTLSQSF
QALRAATRQSMGLA