Protein Info for Shew_3062 in Shewanella loihica PV-4

Annotation: glycine 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 962 PF02347: GDC-P" amino acids 17 to 439 (423 residues), 586.7 bits, see alignment E=4.2e-180 amino acids 462 to 740 (279 residues), 46.2 bits, see alignment E=4.8e-16 TIGR00461: glycine dehydrogenase" amino acids 18 to 955 (938 residues), 1534.1 bits, see alignment E=0 PF21478: GcvP2_C" amino acids 782 to 903 (122 residues), 201 bits, see alignment E=6.9e-64

Best Hits

Swiss-Prot: 72% identical to GCSP1_COLP3: Glycine dehydrogenase (decarboxylating) 1 (gcvP1) from Colwellia psychrerythraea (strain 34H / ATCC BAA-681)

KEGG orthology group: K00281, glycine dehydrogenase [EC: 1.4.4.2] (inferred from 70% identity to amc:MADE_00863)

MetaCyc: 67% identical to glycine decarboxylase (Escherichia coli K-12 substr. MG1655)
Glycine dehydrogenase (decarboxylating). [EC: 1.4.1.27, 1.4.4.2]

Predicted SEED Role

"Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)" in subsystem Glycine and Serine Utilization or Glycine cleavage system or Photorespiration (oxidative C2 cycle) (EC 1.4.4.2)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 1.4.1.27 or 1.4.4.2

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 A3QHI0 at UniProt or InterPro

Protein Sequence (962 amino acids)

>Shew_3062 glycine dehydrogenase (RefSeq) (Shewanella loihica PV-4)
MTTETLTQLEQHELFIRRHIGPDSADQQEMLNFVGAESLEDLTQQIVPESIRLGRDLAVG
SACGEAEGLASIRKYADKNKVFKSYIGMGYYGTIVPSVIQRNVFENPGWYTAYTPYQPEI
AQGRLEAILNFQQLSMDLTGLDLASASLLDEATAAAEAMALAKRVSKAKKANIFFIADDV
FPQTIDVVKTRAECFGFEIVVGPASEAVNYELFGALFQYTNHYGQITDFTELFAALQEKK
AVVTVAADIMSLVSLKSPGSMGADVVFGSAQRFGVPMGFGGPHAAFFVTRDQHKRSLPGR
IIGVSQDTRGNRALRMAMQTREQHIRREKANSNICTAQVLLANMASFYAVFHGPQGLKII
ADRIHRLADIFAAGLKAKGVELVNNTWFDTVSFKVADSAAAQARAIAGEVNLRIDSDGIL
GVAMAETTTREDVAQLFDIVLGEGHGLDVAAIDADIIANGSNSIPAELVRQDAILEHPTF
NRYHSETEMMRYIKRLENKDLALNHSMISLGSCTMKLNAATEMMPVSWPEFGNMHPFCPQ
DQAQGYAELIEELSNWLVDITGYDAMCMQPNSGASGEYAGLLAIKKYHESRGEGHRNVCL
IPQSAHGTNPASAQLAGMKIVVTACDKQGNVDMEDLKAKAAEVAENLSCIMVTYPSTHGV
YEETISEICEVIHQHGGQVYLDGANMNAQVGLTSPGSIGADVSHLNLHKTFAIPHGGGGP
GMGPIGVKAHLAPFVAGHAVVKHGRESDNNGAVSAAPYGSASILPITWMYIKLLGYQGLR
QSTQMALLNANYVMKKLSAHYPVLYTGRNDRVAHECIIDLRPLKEASGVTEMDIAKRLND
YGFHAPTMSFPVAGTLMIEPTESESKAELDRFIEAMVAIRGEIAKVEAGEWPADNNPLHN
APHTMADIMDSEFDSRPYSRETAVFPTAAVKANKFWPTVNRIDDVYGDRNLMCSCAPIDD
YK