Protein Info for Shew_2360 in Shewanella loihica PV-4

Updated annotation (from data): D-hydroxyproline dehydrogenase
Rationale: Specific phenotype: utilization of Gelatin. L-hydroxyproline is a major component of gelatin and converted to D-hydroxyproline by Shew_2363 (PMC4113996). Shew_2360 is 44% identical to the D-hydroxyproline dehydrogenase from Pseudomonas putida (PMC3463351). The P.putida enzyme was studied with an artificial electron acceptor and the in vivo acceptor does not seem to be known. Some related enzymes are D-amino acid oxidases (using O2 as the acceptor) but we suspect that Shew_2360 is not an oxidase.
Original annotation: D-amino-acid dehydrogenase (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 50 100 150 200 250 300 350 400 446 PF01266: DAO" amino acids 30 to 427 (398 residues), 205 bits, see alignment E=3.9e-64 PF00890: FAD_binding_2" amino acids 30 to 70 (41 residues), 21.6 bits, see alignment 1.7e-08 PF13450: NAD_binding_8" amino acids 33 to 68 (36 residues), 24.4 bits, see alignment 4.4e-09

Best Hits

KEGG orthology group: K00285, D-amino-acid dehydrogenase [EC: 1.4.99.1] (inferred from 100% identity to slo:Shew_2360)

Predicted SEED Role

"D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster" in subsystem Proline, 4-hydroxyproline uptake and utilization or Respiratory dehydrogenases 1 (EC 1.4.99.1)

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 1.4.99.1

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Search 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 A3QFH8 at UniProt or InterPro

Protein Sequence (446 amino acids)

>Shew_2360 D-hydroxyproline dehydrogenase (Shewanella loihica PV-4)
MIEANHMTKHELTGQDKGSQTCAASTQNADVTVIGAGVVGLANAIALQQAGFSVRVIDKQ
GVAAGASFGNAGHFATEQMFPLADPAMLFKLPGMLLDPLGPFRIQPRYFLKALPWFMRFL
VNMLPARRAHNSAAIKALNQKSIQAWQQLVSECGCSELLKLEGSLLVFEQTPFIEVERVY
KSYRDAGVAVKLLSGEEVRTLEPDLSPNINHGLWFTQVGHTPDPAELCHRLATQFEKLGG
ELVIAEVIQLAAECKGDNKEKGVNVSVASGVTYQSDKLLLSAGAWSKPLAQQLGFKVPLE
TERGYHLMMPQQSRLQRPVASFERKFIITPMNRGTCLAGTVEFGGLKAPLIEARADCLLP
HAKALLPDVLASAKTSQGERWMGFRPSLPDSLPVLGASPKSDKIFFAFGHQHLGLSWAAF
SAQLMAETIKGEEVTVDMTPYRIDRF