Protein Info for GFF2383 in Variovorax sp. SCN45

Annotation: Oxygen-independent coproporphyrinogen-III oxidase-like protein YggW

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 50 100 150 200 250 300 350 420 TIGR00539: putative oxygen-independent coproporphyrinogen III oxidase" amino acids 38 to 383 (346 residues), 351.1 bits, see alignment E=3.6e-109 PF04055: Radical_SAM" amino acids 41 to 215 (175 residues), 88.2 bits, see alignment E=7.2e-29 PF06969: HemN_C" amino acids 344 to 407 (64 residues), 41.4 bits, see alignment E=1.2e-14

Best Hits

KEGG orthology group: K02495, oxygen-independent coproporphyrinogen III oxidase [EC: 1.3.99.22] (inferred from 93% 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)

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 (420 amino acids)

>GFF2383 Oxygen-independent coproporphyrinogen-III oxidase-like protein YggW (Variovorax sp. SCN45)
MATVFPIQPAQPTGAPQANDVLHWMRPGPLQLSALPPLSLYIHLPWCLRKCPYCDFNSHE
WRAASEADIDGIPEQAYIDALVADLDAALPLIWGRTVHTIFIGGGTPSLFSPQAIDRLLG
DVRARLKLAPDCEITLEANPGTFERNRFRAYRAAGVTRLSVGVQSFNDEHLKALGRVHDR
AQAIAAVEEAASAFDTFNLDLMYALPGQTLEGLDADLSQALSLAPPHLSVYHLTIEPNTW
FAKFPPTLPEDDIAYEMLDRITERTSAAGMTRYEVSAYAREGHACGHNRNYWEFGDYLGI
GAGAHSKLSFAHRIVRQVRYREPRLYMENARAGAAVSQSDEVALADLPFEFMLNALRLKA
GFTLPQFSERTGLAMTAIQRGLEEAERKGLLARDLFRVWPTERGLDFLSDLQAMFLPDGE