Protein Info for CSW01_02985 in Vibrio cholerae E7946 ATCC 55056
Annotation: inner membrane protein YpjD
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
Best Hits
Swiss-Prot: 51% identical to YPJD_ECOLI: Inner membrane protein YpjD (ypjD) from Escherichia coli (strain K12)
KEGG orthology group: None (inferred from 100% identity to vcm:VCM66_0517)Predicted SEED Role
"Glutamate synthase [NADPH] small chain (EC 1.4.1.13)" in subsystem Ammonia assimilation or Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis (EC 1.4.1.13)
MetaCyc Pathways
- ammonia assimilation cycle III (3/3 steps found)
- L-glutamate biosynthesis I (2/2 steps found)
- L-glutamine degradation I (1/1 steps found)
- L-glutamine degradation II (1/1 steps found)
- L-citrulline biosynthesis (6/8 steps found)
- L-glutamate and L-glutamine biosynthesis (5/7 steps found)
- superpathway of L-citrulline metabolism (8/12 steps found)
- L-asparagine biosynthesis III (tRNA-dependent) (1/4 steps found)
- glutaminyl-tRNAgln biosynthesis via transamidation (1/4 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Glutamate metabolism
- Nitrogen metabolism
Isozymes
Compare fitness of predicted isozymes for: 1.4.1.13
Use Curated BLAST to search for 1.4.1.13
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
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 (264 amino acids)
>CSW01_02985 inner membrane protein YpjD (Vibrio cholerae E7946 ATCC 55056) MDNLIAIAAAMLYLLSIATIVPGLVNQTGIRAKTVFISAAIALLFHGWLLSDLILHSSGQ NLSILNVASLISFIISLAMSLAMFKTRLWFLLPVAYSFSAINLSAATFLPGTFITHLESD PKLLLHISLALFSYSTLSIGALYALQLAWLDHKLKSKKVFSINPNLPPLLLVERQLFKII LIGNLLLTGTLLTGFIFVQDMFAQGKAHKGILSFVAWIVYSILLWGHYRKGWRGKKVTWF AVAGATLLTLAYFGSRFVREIILR