Protein Info for GFF4444 in Xanthobacter sp. DMC5

Annotation: Uptake hydrogenase small subunit

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 50 100 150 200 250 300 368 signal peptide" amino acids 1 to 45 (45 residues), see Phobius details TIGR00391: hydrogenase (NiFe) small subunit (hydA)" amino acids 4 to 356 (353 residues), 563 bits, see alignment E=2.9e-173 TIGR01409: Tat (twin-arginine translocation) pathway signal sequence" amino acids 15 to 44 (30 residues), 29.3 bits, see alignment (E = 7.3e-11) PF01058: Oxidored_q6" amino acids 61 to 206 (146 residues), 93.3 bits, see alignment E=1e-30 PF14720: NiFe_hyd_SSU_C" amino acids 226 to 306 (81 residues), 110.9 bits, see alignment E=3.2e-36

Best Hits

Swiss-Prot: 84% identical to MBHS_ALCHY: Uptake hydrogenase small subunit (hupS) from Alcaligenes hydrogenophilus

KEGG orthology group: K06282, hydrogenase small subunit [EC: 1.12.99.6] (inferred from 94% identity to xau:Xaut_2173)

MetaCyc: 82% identical to hydrogenase small subunit (Cupriavidus necator)
Hydrogenase (acceptor). [EC: 1.12.99.6]

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 1.12.99.6

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

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

Find the best match in UniProt

Protein Sequence (368 amino acids)

>GFF4444 Uptake hydrogenase small subunit (Xanthobacter sp. DMC5)
MALETFYEVMRRQGITRRSFLKYCSLTAAALGLGPEFAPQIAMAMETKPRTPVLWLHGLE
CTCCSESFIRSAHPLVKDVVLSMISLDYDDTLMASAGHQAEAILDEVMTKYKGNYILAVE
GNPPLNEDGMYCIIGGKPFVDQLKKVAKDAKAIISWGSCASYGCVQAARPNPTRATPVHE
VIFDKPIIKVPGCPPIAEVMTGVITYMLTFDQLPALDRQGRPLMFYSQRIHDKCYRRPHF
DAGQYVESFDDEGARKGYCLYKVGCKGPTTYNACSTVRWNDGVSFPIQAGHGCIGCSEDG
FWDKGSWYARLADLKGSGFGVEANADQVGLVAAGAVGAGVAAHAAISALKRAQHKNTDGA
TKTEGGEK