Protein Info for PP_5192 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 957 PF02347: GDC-P" amino acids 18 to 441 (424 residues), 602.1 bits, see alignment E=9.1e-185 amino acids 452 to 728 (277 residues), 33.2 bits, see alignment E=4.2e-12 TIGR00461: glycine dehydrogenase" amino acids 19 to 950 (932 residues), 1539.8 bits, see alignment E=0 PF01212: Beta_elim_lyase" amino acids 546 to 714 (169 residues), 32.1 bits, see alignment E=1.1e-11 PF21478: GcvP2_C" amino acids 779 to 900 (122 residues), 195.8 bits, see alignment E=2.8e-62

Best Hits

Swiss-Prot: 100% identical to GCSP2_PSEPK: Glycine dehydrogenase (decarboxylating) 2 (gcvP2) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K00281, glycine dehydrogenase [EC: 1.4.4.2] (inferred from 81% identity to avn:Avin_47260)

MetaCyc: 65% 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 Q88CI9 at UniProt or InterPro

Protein Sequence (957 amino acids)

>PP_5192 glycine dehydrogenase (Pseudomonas putida KT2440)
MSQSPSLHQLQELNPFLRRHLGPDATEQQAMLNALGIASRNELIEQTVPPDIRLNRPLDL
PAALDEQAALAKLAGYAEQNQVWTSLIGMGYHGTITPTVILRNVLENPGWYTAYTPYQPE
IAQGRLEALLNFQQMVIDLTGLPLANASLLDEATAAAEAMALAKRVARNKSNAFFADEHC
HPQTLSVLKTRAEGFGFELIVDSVDNLAKHSVFGALLQYPDTHGEVRDLRPLIDQLHSQQ
ALACVAADLLSLVVLAPPGELGADVVLGSTQRFGVPMGYGGPHAAYFACRDDYKRAMPGR
IIGVSRDARGNTALRMALQTREQHIRREKANSNICTAQVLLANIAGFYAVYHGPEGLQRI
AQRVHRLTFILAAGLEAKGIKRLNQHFFDTLTLNVGGAQAAIIESAEAAHINLRILGRGH
LGVSLDETCTEQTVLRLLDIFLGVDHGLEITALDQLALPEGIPASLVRRTPFLAHPVFNL
HHSETEMLRYLKQLENKDLALNQSMIPLGSCTMKLNATSEMIPITWPGFAQLHPFAPAAQ
AAGYKAMIDELESWLCAITGFDAICMQPNSGAQGEYAGLMAITRYHCSRHQPMRTLCLIP
SSAHGTNPASAQMAGMEVVIVDCDNDGNVDLADLKAKAHAAGERLSCLMITYPSTHGVYE
EGIREICDVVHQYGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGM
GPIGIRAHLKPFVASHPVVPVPGLDPNNSAVSAAPWGSASILPISWMYIAMMGPQLADAS
EVAILSANYLASQLGAAFPVLYRGRNQRVAHECILDLRPLKALTGISEEDVAKRLMDYGF
HAPTMSFPVPGTLMVEPTESESKAELDRFVEAMLAIRAEIDEVQQGNWPAENNPLKHAPH
TLADVLGVWDRPYSLEQAVAPSAHVRQHKYWPAVNRVDNVYGDRNLFCACVPVEAYR