Protein Info for SO2091 in Shewanella oneidensis MR-1

Name: hypD
Annotation: hydrogenase expression/formation protein HypD (NCBI ptt file)

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 50 100 150 200 250 300 350 379 TIGR00075: hydrogenase expression/formation protein HypD" amino acids 6 to 371 (366 residues), 509.2 bits, see alignment E=2.9e-157 PF01924: HypD" amino acids 16 to 369 (354 residues), 500.1 bits, see alignment E=1.8e-154

Best Hits

Swiss-Prot: 52% identical to HYPD2_BRADU: Hydrogenase maturation factor HypD2 (hypD2) from Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)

KEGG orthology group: K04654, hydrogenase expression/formation protein HypD (inferred from 100% identity to son:SO_2091)

MetaCyc: 43% identical to Fe-(CN)2CO cofactor assembly scaffold protein HypD (Escherichia coli K-12 substr. MG1655)
RXN-22646; RXN-22647

Predicted SEED Role

"[NiFe] hydrogenase metallocenter assembly protein HypD" in subsystem NiFe hydrogenase maturation

MetaCyc Pathways

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

See Q8EF94 at UniProt or InterPro

Protein Sequence (379 amino acids)

>SO2091 hydrogenase expression/formation protein HypD (NCBI ptt file) (Shewanella oneidensis MR-1)
MLELKQLYQGFRDPQTIASLAQDIAKVARTLKEPINIMEVCGGHTHTIMKYGLLDLLPDN
IEFIHGPGCPVCIMPKERIDQAAVLAQQEDVILVTLGDMIRVPGSKGSLASFRAKGCDIR
PIYDPLDTLKIARDNPHKTVVFFAIGFETSTPMTAVLLQLAEQQKLANVFFHINHVLVPP
AIDAVMHDPNARVNAFIGPAHVSVISGAKIYRPAVEQYGTPVVVSGFEPVDVMESILRIM
RQKAAGKAELDIQYSRAVSEQGNLAAQAKVEQFFQIRPQFRWRGLGPIPNSALQLKPEYA
HRDAELRFKNCLPVKEIDDHKACQCGDILRGLAKPKDCKVFGRGCNPETPLGSCMVSSEG
ACNAYYRYQGIDSKEQHHG