Protein Info for DvMF_1732 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 50 100 150 200 250 322 signal peptide" amino acids 1 to 15 (15 residues), see Phobius details transmembrane" amino acids 24 to 46 (23 residues), see Phobius details TIGR00391: hydrogenase (NiFe) small subunit (hydA)" amino acids 14 to 313 (300 residues), 360.4 bits, see alignment E=1.1e-111 TIGR01409: Tat (twin-arginine translocation) pathway signal sequence" amino acids 19 to 48 (30 residues), 25.8 bits, see alignment (E = 9.8e-10) PF01058: Oxidored_q6" amino acids 65 to 212 (148 residues), 93.5 bits, see alignment E=9e-31 PF14720: NiFe_hyd_SSU_C" amino acids 230 to 311 (82 residues), 106.6 bits, see alignment E=6.9e-35

Best Hits

Swiss-Prot: 72% identical to PHNS2_DESVH: Periplasmic [NiFe] hydrogenase small subunit 2 (hynB2) from Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)

KEGG orthology group: K06282, hydrogenase small subunit [EC: 1.12.99.6] (inferred from 100% identity to dvm:DvMF_1732)

MetaCyc: 59% identical to periplasmic [NiFe] hydrogenase 1 small subunit (Desulfovibrio vulgaris)
Cytochrome-c3 hydrogenase. [EC: 1.12.2.1]

Predicted SEED Role

"Uptake hydrogenase small subunit precursor (EC 1.12.99.6)" in subsystem Hydrogenases or Membrane-bound Ni, Fe-hydrogenase (EC 1.12.99.6)

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 B8DM33 at UniProt or InterPro

Protein Sequence (322 amino acids)

>DvMF_1732 hydrogenase (NiFe) small subunit HydA (RefSeq) (Desulfovibrio vulgaris Miyazaki F)
MNALAQLVARRAEAEERGVSRRDFLKFCGMVAVAMGLEASMGAQIARALEGKKKPSVVYM
HGAECTGCTEALLRLVDPYFDVLIMEVVSLDYCETVMAAAGHAAHAALQKAIRNPDGYFC
VIEGAIPTRDGGVYGQVGGQTMLSLFTEVAGKAKGVIAMGSCASYGGIQAAAPNPSRAIG
VGAALKPLGIAPINLPGCPPNPVNFVGTVVHLLTKGLPDLDTSGRPRLFYGKTVHDMCER
RPHFDKGEFAPAFSSQQARDGWCLHKLGCRGPWTYNNCPTALFNQTTWPVRSGAPCIGCS
EPGFWDQLAPFNRDVREKGDDA