Protein Info for DvMF_0274 in Desulfovibrio vulgaris Miyazaki F

Annotation: hydrogenase (NiFe) small subunit HydA (RefSeq)

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 50 100 150 200 250 317 signal peptide" amino acids 1 to 33 (33 residues), see Phobius details TIGR01409: Tat (twin-arginine translocation) pathway signal sequence" amino acids 3 to 23 (21 residues), 16.7 bits, see alignment (E = 7.2e-07) TIGR00391: hydrogenase (NiFe) small subunit (hydA)" amino acids 3 to 314 (312 residues), 243.4 bits, see alignment E=4.1e-76 PF01058: Oxidored_q6" amino acids 52 to 205 (154 residues), 105.9 bits, see alignment E=1.3e-34 PF14720: NiFe_hyd_SSU_C" amino acids 237 to 315 (79 residues), 90.8 bits, see alignment E=5.9e-30

Best Hits

KEGG orthology group: K06282, hydrogenase small subunit [EC: 1.12.99.6] (inferred from 100% identity to dvm:DvMF_0274)

MetaCyc: 81% identical to cytochrome-c3 [NiFe]-hydrogenase small subunit (Desulfovibrio vulgaris)
Cytochrome-c3 hydrogenase. [EC: 1.12.2.1]

Predicted SEED Role

"[Ni/Fe] hydrogenase, group 1, small subunit" in subsystem Hydrogenases

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.12.99.6

Use Curated BLAST to search for 1.12.2.1 or 1.12.99.6

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

See B0LPC7 at UniProt or InterPro

Protein Sequence (317 amino acids)

>DvMF_0274 hydrogenase (NiFe) small subunit HydA (RefSeq) (Desulfovibrio vulgaris Miyazaki F)
MSLNRRDFVKLCTGTVAGFGISQMFHPAVCEAISGSLNGERPPVLWLQGQGCTGCSVSLL
NSVHPTIADVLLKVISLEFHPTVMAWEGEPAMEHMMKIAEQYKGKYFVVVEGAVPTEADG
KYCIIGEAHHKEISMVDAMKSVAANAAAVLAVGTCAAYGGIPAAQGSETGAKSVSQFFKD
NGIATPVVNIPGCPPHPDWIVGTVVVALNAIKAKGLAAGLGDVVKLLDADGRPTPFYGRN
VHENCPYLEAYDAGKMCETFTKKEGCRYDLGCKGPMSMCDSFERKWNGGVNWCISNAVCI
GCVEPDFPDGKSPFYSA