Protein Info for HSERO_RS08355 in Herbaspirillum seropedicae SmR1

Annotation: dioxygenase

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 50 100 150 217 transmembrane" amino acids 146 to 163 (18 residues), see Phobius details PF13532: 2OG-FeII_Oxy_2" amino acids 21 to 214 (194 residues), 217.3 bits, see alignment E=1.2e-68

Best Hits

Swiss-Prot: 57% identical to ALKB_ECOLI: Alpha-ketoglutarate-dependent dioxygenase AlkB (alkB) from Escherichia coli (strain K12)

KEGG orthology group: K03919, alkylated DNA repair protein [EC: 1.14.11.-] (inferred from 100% identity to hse:Hsero_1680)

MetaCyc: 57% 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)

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 D8IQT2 at UniProt or InterPro

Protein Sequence (217 amino acids)

>HSERO_RS08355 dioxygenase (Herbaspirillum seropedicae SmR1)
VTGDLFAGLERTPAVERITEGALLLRAFVDASEAAQLMRDIATVLAQSPLRHMQTPGGFR
MSVAMSNCGQYGWVTDRRGYRYQSLDPLSERDWPPMPASFLALAGRAAEAAGFAAFVPDA
CLVNRYEPGAKMSLHQDRNEIDMTQPIVSVSLGLPATFLFGGMERSDKAQRMRLDSGDVV
VWGGPARLAFHGVDTVRQAEHPLTGACRYNLTFRRAR