Protein Info for Shew_0065 in Shewanella loihica PV-4

Annotation: formate dehydrogenase, gamma subunit (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 50 100 150 200 250 300 330 signal peptide" amino acids 1 to 27 (27 residues), see Phobius details transmembrane" amino acids 79 to 101 (23 residues), see Phobius details amino acids 125 to 150 (26 residues), see Phobius details amino acids 170 to 190 (21 residues), see Phobius details amino acids 202 to 217 (16 residues), see Phobius details amino acids 231 to 252 (22 residues), see Phobius details amino acids 264 to 287 (24 residues), see Phobius details TIGR01583: formate dehydrogenase, gamma subunit" amino acids 116 to 321 (206 residues), 166.6 bits, see alignment E=3.6e-53 PF01292: Ni_hydr_CYTB" amino acids 118 to 294 (177 residues), 70.9 bits, see alignment E=6.2e-24

Best Hits

KEGG orthology group: K00127, formate dehydrogenase, gamma subunit [EC: 1.2.1.2] (inferred from 100% identity to slo:Shew_0065)

Predicted SEED Role

"Formate dehydrogenase -O, gamma subunit (EC 1.2.1.2)" in subsystem Anaerobic respiratory reductases or Formate hydrogenase (EC 1.2.1.2)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.2.1.2

Use Curated BLAST to search for 1.2.1.2

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 A3Q8Z0 at UniProt or InterPro

Protein Sequence (330 amino acids)

>Shew_0065 formate dehydrogenase, gamma subunit (RefSeq) (Shewanella loihica PV-4)
MNKWFKQFSVILALVIGTTFSALSFAHGDATDHTHAATEGQIWSEIQAGATGYTTSHGQF
HNQPINSYDLRVLELRSDWLAPALMAALFGMIIIFVLFIKVNGISKLHHGFSGKMVYRWS
KFDVSIHWLGAIPCLLLILTGLTLLAGRFFFQPYLGEGFWAGLVYGAKQIHDYMAIPFMI
GWALMTTLWAKNQLPKMYDVKWFLVVGGYINFGPFKGKHPDAGFANAGEKMWFWAFAFFG
LIISASGMLLLFPNLFEPSRTLSLIALVLHSVSAIVICAFSIVHIFMATVMSEGGMECMV
SGYCDENWATQHHNLWYDEIKANGTLKYKA