Protein Info for HMPREF1078_RS03855 in Parabacteroides merdae CL09T00C40
Annotation: GDP-mannose 4,6-dehydratase
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: 60% identical to GMD1_CAEBR: GDP-mannose 4,6 dehydratase 1 (CBG21737) from Caenorhabditis briggsae
KEGG orthology group: K01711, GDPmannose 4,6-dehydratase [EC: 4.2.1.47] (inferred from 86% identity to pdi:BDI_2203)MetaCyc: 58% identical to GDP-mannose 4,6-dehydratase (Escherichia coli K-12 substr. MG1655)
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 (9/11 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)
- 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 GDP-mannose-derived O-antigen building blocks biosynthesis (8/14 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
Find the best match in UniProt
Protein Sequence (362 amino acids)
>HMPREF1078_RS03855 GDP-mannose 4,6-dehydratase (Parabacteroides merdae CL09T00C40) MKKALITGITGQDGSFLAEFLLGKGYDVHGTIRRSSVDYRERIAHLEGHPNFHLHYADLG DSMSILQVVKKVKPTEIYNLAAQSHVQVSFDAPEFTADVDATGVLRILEAVRQCDLIDTC RIYQASTSELYGKVEEVPQNEKTPFHPYSPYAVAKLYGYWIVKEYREAYNMFCCSGILFN HESERRGETFVTRKITLAAARISQGKQDCLYLGNLDSLRDWGYAKDYVECMWLILQHDTP EDFVIATGVQHTVREFATLAFRYAGIELRWEGEGVQEKGIDAKTGKTVVAVSEDFYRPTD VVNLWGDPTKAKNELGWNPQSTSFEELVRIMVTHDMQKVAAEHVTSVMRTNLAEYLEKGI VK