Protein Info for Rru_A0253 in Rhodospirillum rubrum S1H

Annotation: GDP-mannose 4,6-dehydratase (NCBI)

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: 74% identical to GM4D_SINFN: GDP-mannose 4,6-dehydratase (gmd) from Sinorhizobium fredii (strain NBRC 101917 / NGR234)

KEGG orthology group: K01711, GDPmannose 4,6-dehydratase [EC: 4.2.1.47] (inferred from 100% identity to rru:Rru_A0253)

MetaCyc: 67% identical to GDP-mannose 4,6-dehydratase monomer (Escherichia coli O157:H7)
GDP-mannose 4,6-dehydratase. [EC: 4.2.1.47]

Predicted SEED Role

"GDP-mannose 4,6-dehydratase (EC 4.2.1.47)" in subsystem Capsular heptose biosynthesis or Colanic acid biosynthesis (EC 4.2.1.47)

MetaCyc Pathways

colanic acid building blocks biosynthesis (11/11 steps found)
GDP-L-fucose biosynthesis I (from GDP-D-mannose) (3/3 steps found)
GDP-6-deoxy-D-talose biosynthesis (1/2 steps found)
GDP-D-perosamine biosynthesis (1/2 steps found)
GDP-D-rhamnose biosynthesis (1/2 steps found)
GDP-L-colitose biosynthesis (3/5 steps found)
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis (9/14 steps found)
GDP-N-acetyl-α-D-perosamine biosynthesis (1/3 steps found)
GDP-N-formyl-α-D-perosamine biosynthesis (1/3 steps found)
GDP-mycosamine biosynthesis (1/3 steps found)
superpathway of candicidin biosynthesis (4/11 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.2.1.47

Use Curated BLAST to search for 4.2.1.47

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 Q2RXT7 at UniProt or InterPro

Protein Sequence (356 amino acids)

>Rru_A0253 GDP-mannose 4,6-dehydratase (NCBI) (Rhodospirillum rubrum S1H)
MAAKVALITGVTGQDGAYLAEFLLGKGYEVHGIKRRSSSLNTGRIDPLYQDPHDPDRTFF
LHYGDMTDSANLIGLVQAIQPDEIYNLAAQSHVQVSFEIPEYTANADAVGTLRLLEAIRL
LGLTDKTRFYQASTSELYGKVRETPQSETTPFYPRSPYAAAKLYAYWITVNYREAYGIHA
SNGILFNHESPLRGETFVTRKITRAVAAIHLGLQDVLYLGNLDSWRDWGHARDYVKGMWA
MLQQPRPDDYVLATGVVHSVRAFVEMAFSKLGRRVTWQGEGVDEIGIDSASGAKLVAIDP
RYFRPTEVEFLQGDPTKARERLGWVAETPLAELVAEMVAADLAVLKRTQESLITND