Protein Info for GFF3256 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB

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 50 100 150 200 250 300 350 400 425 TIGR00539: putative oxygen-independent coproporphyrinogen III oxidase" amino acids 46 to 399 (354 residues), 348.7 bits, see alignment E=1.9e-108 PF04055: Radical_SAM" amino acids 49 to 225 (177 residues), 89.2 bits, see alignment E=3.6e-29 PF06969: HemN_C" amino acids 349 to 414 (66 residues), 47.6 bits, see alignment E=1.4e-16

Best Hits

KEGG orthology group: K02495, oxygen-independent coproporphyrinogen III oxidase [EC: 1.3.99.22] (inferred from 76% identity to vpe:Varpa_4955)

Predicted SEED Role

"Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB" in subsystem Heat shock dnaK gene cluster extended or Heme and Siroheme Biosynthesis or Queuosine-Archaeosine Biosynthesis

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.3.99.22

Use Curated BLAST to search for 1.3.99.22

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

Find the best match in UniProt

Protein Sequence (425 amino acids)

>GFF3256 Radical SAM family enzyme, similar to coproporphyrinogen III oxidase, oxygen-independent, clustered with nucleoside-triphosphatase RdgB (Hydrogenophaga sp. GW460-11-11-14-LB1)
MSEPTGVPMSWPGGQPAAAGQADPAWNDVRHWMRPGTLQLQSLPPLSLYIHLPWCLKKCP
YCDFNSHEWSATAAPGEALPETAYLEALRADLAASLPLIWGRTVHSVFIGGGTPSLFSPA
AIDRLLGDVRAMLRLEADAEITLEANPGTFEKDRFRAFRDAGVTRLSIGVQSFNDAHLKA
LGRVHDRAQALAAVEEAAQAFDTFNLDLMYALPGQTLADCEADVRTALSFAPPHISIYHL
TLEPNTYFAKYPPALPPEDEAWDMLDRITELTAEAGMRRYEVSAYAREGHQCWHNLNYWQ
FGDYLGIGAGAHSKLSFAHRVARPVRVREPRLYMERALVGNAVVSADEVSRKALPFEFML
NALRLKDGFTLLQFMERTGLPLSSIAPALAQAEQKGLIARDATRVWPTERGFDFLSDLQE
LFLAD