Protein Info for PP_0988 in Pseudomonas putida KT2440

Annotation: glycine dehydrogenase

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 951 transmembrane" amino acids 338 to 345 (8 residues), see Phobius details amino acids 744 to 760 (17 residues), see Phobius details TIGR00461: glycine dehydrogenase" amino acids 14 to 942 (929 residues), 1499.8 bits, see alignment E=0 PF02347: GDC-P" amino acids 14 to 438 (425 residues), 598.8 bits, see alignment E=9.1e-184 amino acids 458 to 731 (274 residues), 50.1 bits, see alignment E=3.1e-17 PF21478: GcvP2_C" amino acids 771 to 892 (122 residues), 207.6 bits, see alignment E=6.5e-66

Best Hits

Swiss-Prot: 100% identical to GCSP1_PSEPK: Glycine dehydrogenase (decarboxylating) 1 (gcvP1) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K00281, glycine dehydrogenase [EC: 1.4.4.2] (inferred from 62% identity to aha:AHA_1720)

MetaCyc: 64% 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

Compare fitness of predicted isozymes for: 1.4.4.2

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 Q88P65 at UniProt or InterPro

Protein Sequence (951 amino acids)

>PP_0988 glycine dehydrogenase (Pseudomonas putida KT2440)
MTINLGTANEFIARHIGPRAADEQAMLTALGFDSLDAMTAAVIPDSIKGTSVLGSHDGQS
EADALAALKAIAGKNQLFKSYIGQGYYNTHTPAPILRNLLENPAWYTAYTPYQPEISQGR
LEALLNFQTLISDLTGLPIANASLLDEATAAAEAMTFCKRLSKNKSSHAFFASVHCHPQT
LDVLRTRAEPLGIEVVVGDERELGDVSAFFGALLQYPASNGEVFDYREVVQRFHAANALV
AVAADLLALTLLTPPGEFDADVAIGSAQRFGVPLGFGGPHAAYFATRDAFKRDMPGRLVG
VSIDRFGKTALRLAMQTREQHIRREKATSNICTAQVLLANIASMFAVYHGPAGLKRIAER
THALTAILAAGLKALGVQVVGASAFDTLTLATGTATASLHDKARAQGINLRQIDAAHVGL
SLDETSTQADVESLWQLLGGEQAQPDFTALAASTGSLLPAALLRQSAILEHPVFNRYHSE
TELMRYLRRLADKDLALDRSMIPLGSCTMKLNAASEMIPVTWAEFGNLHPFAPAEQSQGY
LQMTTELEAMLCAATGYDAVSLQPNAGSQGEYAGLLAIRAYHRSRGEGHRDICLIPSSAH
GTNPATAHMAGMRVVVTACDARGNVDVEDLRAKAIEHRERLAAIMITYPSTHGVFEEAIG
EICAIIHDNGGQVYIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIG
VKSHLAPFLPGHAQLENTQGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQMAILNAN
YIARRLEEHYPVLYTGGNGLVAHECILDLRPLKDTSGISVDDVAKRLIDFGFHAPTMSFP
VAGTLMIEPTESESKEELDRFCNAMIQIREEIRAVEDGSLDKDDNPLKNAPHTAAELVGE
WTHGYSREQAVYPLASLVEGKYWPPVGRVDNVFGDRNLVCACPSIESYQDA