Protein Info for ABID97_RS24835 in Variovorax sp. OAS795

Annotation: DNA oxidative demethylase AlkB

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 50 100 150 219 transmembrane" amino acids 21 to 43 (23 residues), see Phobius details amino acids 56 to 73 (18 residues), see Phobius details amino acids 145 to 166 (22 residues), see Phobius details PF13532: 2OG-FeII_Oxy_2" amino acids 45 to 216 (172 residues), 191 bits, see alignment E=1.4e-60

Best Hits

Swiss-Prot: 57% identical to ALKB_SALTY: Alpha-ketoglutarate-dependent dioxygenase AlkB (alkB) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: K03919, alkylated DNA repair protein [EC: 1.14.11.-] (inferred from 89% identity to vap:Vapar_4650)

MetaCyc: 56% identical to DNA oxidative demethylase (Escherichia coli K-12 substr. MG1655)
RXN-21233 [EC: 1.14.11.54]; 1.14.11.54 [EC: 1.14.11.54]; RXN-18737 [EC: 1.14.11.54, 1.14.11.33]; 1.14.11.33 [EC: 1.14.11.54, 1.14.11.33]; 1.14.11.33 [EC: 1.14.11.54, 1.14.11.33]; 1.14.11.33 [EC: 1.14.11.54, 1.14.11.33]; 1.14.11.33 [EC: 1.14.11.54, 1.14.11.33]; 1.14.11.- [EC: 1.14.11.54, 1.14.11.33]; RXN0-7275 [EC: 1.14.11.54, 1.14.11.33]

Predicted SEED Role

"Alkylated DNA repair protein AlkB" in subsystem DNA repair, bacterial

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.14.11.-

Use Curated BLAST to search for 1.14.11.- or 1.14.11.33 or 1.14.11.54

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 (219 amino acids)

>ABID97_RS24835 DNA oxidative demethylase AlkB (Variovorax sp. OAS795)
MTRDLFSDAPDAEPPRGKEAIGPASFVLRGFALPFADALLPALGEVERRAGFRHLVTPGG
FTMSVAMTNCGRLGWISDRRGYRYGEHDPATGAQWPAMPAVFERLAQAAAAEAGFEGFRP
DACLVNRYEPGTRLSLHQDKDERDYAAPIVSVSLGMPATFLFGGLARSDKAARIPLVHGD
VVVWGGPDRLRYHGVLPLEDRAHALLGSRRINLTFRKAG