Protein Info for Shew_3158 in Shewanella loihica PV-4

Annotation: polysulphide reductase, NrfD (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 50 100 150 200 250 313 transmembrane" amino acids 15 to 35 (21 residues), see Phobius details amino acids 48 to 70 (23 residues), see Phobius details amino acids 90 to 113 (24 residues), see Phobius details amino acids 140 to 167 (28 residues), see Phobius details amino acids 176 to 198 (23 residues), see Phobius details amino acids 213 to 235 (23 residues), see Phobius details amino acids 251 to 271 (21 residues), see Phobius details amino acids 283 to 304 (22 residues), see Phobius details TIGR03148: cytochrome c nitrite reductase, NrfD subunit" amino acids 2 to 311 (310 residues), 366.6 bits, see alignment E=5.6e-114 PF03916: NrfD" amino acids 3 to 311 (309 residues), 256 bits, see alignment E=3.4e-80

Best Hits

Swiss-Prot: 44% identical to NRFD_ECOLI: Protein NrfD (nrfD) from Escherichia coli (strain K12)

KEGG orthology group: K04015, formate-dependent nitrate reductase complex, transmembrane protein (inferred from 100% identity to slo:Shew_3158)

Predicted SEED Role

"NrfD protein" in subsystem Nitrate and nitrite ammonification

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 A3QHS6 at UniProt or InterPro

Protein Sequence (313 amino acids)

>Shew_3158 polysulphide reductase, NrfD (RefSeq) (Shewanella loihica PV-4)
MSAFHFEGLVWHWPIAIYLFLAGLSAGAVFFAIMLKHFKLSHEAWHSPFVQAAAIIAPVA
VFGGLGILVFDLTRPLDFWKILVFYNTSSVMSMGVLVLMAYQLVLFAWIACVFQRRITQL
LGKRLPIANRLLNWLVKQEAAITGVLVILAISLGAYTGFLLSALIGFPLLNNPVLPLLFL
ISGLSSGAAATLLGGVLLRGNPNGVEVRFIHGIEIPLILVEIGLLFTFFAGLILSGGQSQ
VAALNALGFGFWGWIFWAGVIGIGLTLPLAFNLWMKVSADRKFAYVAVTASFSLIGVFLL
RNFILYTGQMTGI