Protein Info for GFF58 in Xanthobacter sp. DMC5

Annotation: Oxygen-dependent coproporphyrinogen-III oxidase

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

Best Hits

Swiss-Prot: 72% identical to HEM6_BRADU: Oxygen-dependent coproporphyrinogen-III oxidase (hemF) from Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)

KEGG orthology group: K00228, coproporphyrinogen III oxidase [EC: 1.3.3.3] (inferred from 83% identity to xau:Xaut_2954)

Predicted SEED Role

"Coproporphyrinogen III oxidase, aerobic (EC 1.3.3.3)" in subsystem Experimental tye or Heme and Siroheme Biosynthesis (EC 1.3.3.3)

MetaCyc Pathways

superpathway of heme b biosynthesis from glycine (7/8 steps found)
heme b biosynthesis I (aerobic) (3/4 steps found)
heme b biosynthesis V (aerobic) (3/4 steps found)
superpathway of heme b biosynthesis from glutamate (7/10 steps found)
superpathway of heme b biosynthesis from uroporphyrinogen-III (4/6 steps found)
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent) (2/9 steps found)
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent) (2/9 steps found)

KEGG Metabolic Maps

Porphyrin and chlorophyll metabolism

Isozymes

No predicted isozymes

Use Curated BLAST to search for 1.3.3.3

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 (315 amino acids)

>GFF58 Oxygen-dependent coproporphyrinogen-III oxidase (Xanthobacter sp. DMC5)
MENPKPAATEPAAPAEPGNALLDARRAGARAWFEELQGRIIAAFEALEEAADPALYGPSP
ARFVRTPWSRTDHTGAPGGGGTMALMRGRLFEKVGVHTSTVFGEFAPEFRAQIPGAAEDP
RFWASGISLIAHMANPHVPAVHMNTRFVVTTKAWFGGGADLTPVLARRRTQEDEDTIAFH
KAFEAACTAHKVADYARYKAWCDDYFFLKHRNEMRGIGGIFYDYLDSAAAGTGRWEDDLA
FTRDVGLAFLDVYPRLVRANMATPWTPEDREEQLIRRGRYVEFNLLYDRGTIFGLKTGGN
VDSILSSMPPVVKWP