Protein Info for Shew_1765 in Shewanella loihica PV-4

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 50 100 150 200 250 300 350 378 transmembrane" amino acids 48 to 60 (13 residues), see Phobius details amino acids 352 to 372 (21 residues), see Phobius details TIGR00391: hydrogenase (NiFe) small subunit (hydA)" amino acids 26 to 374 (349 residues), 502.7 bits, see alignment E=6.3e-155 TIGR01409: Tat (twin-arginine translocation) pathway signal sequence" amino acids 38 to 59 (22 residues), 18.9 bits, see alignment (E = 1.5e-07) PF10518: TAT_signal" amino acids 38 to 57 (20 residues), 30.3 bits, see alignment (E = 4.1e-11) PF01058: Oxidored_q6" amino acids 84 to 230 (147 residues), 98.9 bits, see alignment E=2.8e-32 PF14720: NiFe_hyd_SSU_C" amino acids 250 to 332 (83 residues), 110.7 bits, see alignment E=5.5e-36

Best Hits

Swiss-Prot: 66% identical to MBHS_WOLSU: Quinone-reactive Ni/Fe-hydrogenase small chain (hydA) from Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W)

KEGG orthology group: K05927, quinone-reactive Ni/Fe-hydrogenase small subunit [EC: 1.12.5.1] (inferred from 100% identity to slo:Shew_1765)

MetaCyc: 56% identical to Quinone-reactive Ni/Fe hydrogenase HydA (Helicobacter pylori 26695)
Hydrogen:quinone oxidoreductase. [EC: 1.12.5.1]

Predicted SEED Role

"Quinone-reactive Ni/Fe-hydrogenase small chain precursor (EC 1.12.5.1)" in subsystem Hydrogenases (EC 1.12.5.1)

MetaCyc Pathways

Isozymes

Compare fitness of predicted isozymes for: 1.12.5.1

Use Curated BLAST to search for 1.12.5.1

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 A3QDT3 at UniProt or InterPro

Protein Sequence (378 amino acids)

>Shew_1765 hydrogenase (NiFe) small subunit HydA (RefSeq) (Shewanella loihica PV-4)
MDTHAALYQQGQARLEELRRLAPRHAQTLQDKMEEHGITRRDFMKWSAAVTAMLALPLPF
STLVAEAAELADRVPLIWLHMAECTGCSESLVRADTPNLDSLIFDHVSLEYHETLMAAAG
WQAEENLEHALETYKGNYLLAVEGAIPTANNGAFLTVGCKGHTGLEIIKHAAEGAAAIIS
VGTCASFGGVQAAAPNPTGAKGVDKVVNKTVVNLGGCPPSEKNIVGTLMYFIMFGKLPAL
DMFNRPKWAYGARVHDNCERRGRFDAGEFVEQFGDEGAKEGYCLYKVGCKGPYTYNNCPT
ERFNHHTSWPVLAGHGCMGCSEPNFWDDMADFEKPLGRQLLHGLDATADTVGAVILGATA
VGIGAHAVASVFANSKED