Protein Info for Shew_1187 in Shewanella loihica PV-4

Annotation: riboflavin biosynthesis protein RibD (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 50 100 150 200 250 300 350 386 PF00383: dCMP_cyt_deam_1" amino acids 10 to 107 (98 residues), 70.6 bits, see alignment E=1.4e-23 TIGR00326: riboflavin biosynthesis protein RibD" amino acids 15 to 371 (357 residues), 411.4 bits, see alignment E=3.1e-127 PF14437: MafB19-deam" amino acids 33 to 112 (80 residues), 31.4 bits, see alignment E=2.4e-11 TIGR00227: riboflavin-specific deaminase C-terminal domain" amino acids 154 to 375 (222 residues), 188.9 bits, see alignment E=9.2e-60 PF01872: RibD_C" amino acids 155 to 360 (206 residues), 157.1 bits, see alignment E=7.7e-50

Best Hits

KEGG orthology group: K11752, diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase [EC: 1.1.1.193 3.5.4.26] (inferred from 100% identity to slo:Shew_1187)

Predicted SEED Role

"Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26) / 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193)" in subsystem Riboflavin, FMN and FAD metabolism (EC 1.1.1.193, EC 3.5.4.26)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.193, 3.5.4.26

Use Curated BLAST to search for 1.1.1.193 or 3.5.4.26

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 A3QC59 at UniProt or InterPro

Protein Sequence (386 amino acids)

>Shew_1187 riboflavin biosynthesis protein RibD (RefSeq) (Shewanella loihica PV-4)
MAMSMAWSKFDSQMMARAIKLARKGQYTTSPNPNVGCVIVQGETLVGEGFHIAAGGPHAE
VHALRMAGDKAKGATAYVTLEPCSHYGRTPPCAEALIKAEVSRVVVAVTDPNPQVSGRGI
KMLQDAGILVEVGLHQEEAAALNPGFMKRMRSGLPWVGIKLATSLDGKTALSNGVSKWIT
GPEARRDVQRMRARFDAVVTGIETVLADDPSLNVRHLELGSLSEQLTEADIRQPLRVVLD
SRARLGAKAKLFETQSPVLLVSCQPYPEAVASAWPEQVSQLQLPSDNGQVPLKALLEHLG
SQLNSVMVEAGATLAGAFMAQGLADELVLYQAPKILGGHGRNLLALPDYTEMTQLPALKL
CDERAIGADRRLTFQLSHNHLPSDKE