Protein Info for Shew_3731 in Shewanella loihica PV-4

Annotation: DNA topoisomerase type IA Zn finger domain-containing protein (RefSeq)

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 50 100 150 187 PF01396: Zn_ribbon_Top1" amino acids 21 to 55 (35 residues), 45 bits, see alignment 3.7e-16 amino acids 69 to 104 (36 residues), 57.7 bits, see alignment 4e-20 amino acids 112 to 149 (38 residues), 43.9 bits, see alignment 8.2e-16 amino acids 153 to 186 (34 residues), 13.5 bits, see alignment 2.5e-06

Best Hits

Swiss-Prot: 47% 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 slo:Shew_3731)

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)

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 A3QJE9 at UniProt or InterPro

Protein Sequence (187 amino acids)

>Shew_3731 DNA topoisomerase type IA Zn finger domain-containing protein (RefSeq) (Shewanella loihica PV-4)
MSKIDDQLFSSHEHALEKEYELCPKCGCELSVKNSKHGGFIGCNNYPCCDYTRPLVHHES
IETQVIEGSECPECGAELAVKSGRFGIFIGCTRYPDCKHIEKQDQEDPAEAVTCPSCHKG
VMEHRTSRFGKSFYACSAYPKCKFLVNYPPVQEACPDCGFGILVERKGAAGMRLECPQKS
CKYKRPL