Protein Info for DDA3937_RS06485 in Dickeya dadantii 3937
Annotation: cytochrome d ubiquinol oxidase subunit II
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: 78% identical to CYDB_ECOLI: Cytochrome bd-I ubiquinol oxidase subunit 2 (cydB) from Escherichia coli (strain K12)
KEGG orthology group: K00426, cytochrome bd-I oxidase subunit II [EC: 1.10.3.-] (inferred from 100% identity to ddd:Dda3937_01883)MetaCyc: 78% identical to cytochrome bd-I subunit 2 (Escherichia coli K-12 substr. MG1655)
RXN0-5266 [EC: 7.1.1.7]; 1.11.1.- [EC: 7.1.1.7]; 1.11.1.- [EC: 7.1.1.7]
Predicted SEED Role
"Cytochrome d ubiquinol oxidase subunit II (EC 1.10.3.-)" in subsystem Bacterial RNA-metabolizing Zn-dependent hydrolases or Conserved gene cluster associated with Met-tRNA formyltransferase or Terminal cytochrome d ubiquinol oxidases or Terminal cytochrome oxidases (EC 1.10.3.-)
MetaCyc Pathways
- NADH to cytochrome bd oxidase electron transfer I (2/2 steps found)
- NADH to cytochrome bd oxidase electron transfer II (2/2 steps found)
- succinate to cytochrome bd oxidase electron transfer (2/2 steps found)
- pyruvate to cytochrome bd oxidase electron transfer (1/2 steps found)
Isozymes
Compare fitness of predicted isozymes for: 1.10.3.-
Use Curated BLAST to search for 1.10.3.- or 7.1.1.7
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
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 E0SEZ9 at UniProt or InterPro
Protein Sequence (379 amino acids)
>DDA3937_RS06485 cytochrome d ubiquinol oxidase subunit II (Dickeya dadantii 3937) MFDYEVLRFVWWLLIGVLLIGFAVTDGFDMGVGVLVRLMGRNDVERRVMINSIAPHWDGN QVWLITAGGALFAAWPMVYAAAFSGFYIAMILVLASLYFRPVGFDYRSKIEDPRWRNMWD WGIFIGSFVPPVVIGVAFGNLLQGVPFHVDEYLRLYYTGNFFQLLNPFGLLAGVVSLSMI VAQGSTYLVMRTSGDLHFRAKKVAQFSSLALTVTFALAGVWVVYGIDGYAVTSVMNTAAE SNPLHKEVARQAGAWLVNFNNHPVLWAVPLLGVVLPLMTAVMARAEKGAMAFLFSSLSIA CVILTAGIAMFPFIMPSVTVPNVSLTVWDATSSLLTLRVMTVVAIIFVPIVLSYTIWCYY KMFGRITKEHVEQNSHSLY