Protein Info for b3283 in Escherichia coli BW25113

Name: yrdD
Annotation: predicted DNA topoisomerase (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

1 50 100 150 180 PF01396: zf-C4_Topoisom" amino acids 13 to 49 (37 residues), 59.1 bits, see alignment 1.5e-20 amino acids 62 to 98 (37 residues), 64.4 bits, see alignment 3.3e-22 amino acids 104 to 142 (39 residues), 57.6 bits, see alignment 4.2e-20 amino acids 145 to 167 (23 residues), 11.7 bits, see alignment (E = 9.5e-06)

Best Hits

Swiss-Prot: 100% identical to YRDD_ECOLI: Uncharacterized protein YrdD (yrdD) from Escherichia coli (strain K12)

KEGG orthology group: K07479, putative DNA topoisomerase (inferred from 100% identity to eco:b3283)

Predicted SEED Role

"Similar to C-terminal Zn-finger domain of DNA topoisomerase I" in subsystem Conserved gene cluster associated with Met-tRNA formyltransferase or DNA topoisomerases, Type I, ATP-independent

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search 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 P45771 at UniProt or InterPro

Protein Sequence (180 amino acids)

>b3283 predicted DNA topoisomerase (NCBI) (Escherichia coli BW25113)
MAKSALFTVRNNESCPKCGAELVIRSGKHGPFLGCSQYPACDYVRPLKSSADGHIVKVLE
GQVCPACGANLVLRQGRFGMFIGCINYPECEHTELIDKPDETAITCPQCRTGHLVQRRSR
YGKTFHSCDRYPECQFAINFKPIAGECPECHYPLLIEKKTAQGVKHFCASKQCGKPVSAE