Protein Info for GFF3795 in Sphingobium sp. HT1-2

Annotation: Diaminopimelate decarboxylase (EC 4.1.1.20)

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 50 100 150 200 250 300 350 421 TIGR01048: diaminopimelate decarboxylase" amino acids 8 to 412 (405 residues), 442.6 bits, see alignment E=5.5e-137 PF00278: Orn_DAP_Arg_deC" amino acids 30 to 371 (342 residues), 89.7 bits, see alignment E=1.9e-29 PF02784: Orn_Arg_deC_N" amino acids 49 to 282 (234 residues), 177.7 bits, see alignment E=4.2e-56 PF01168: Ala_racemase_N" amino acids 53 to 235 (183 residues), 29.2 bits, see alignment E=1.1e-10

Best Hits

Swiss-Prot: 58% identical to DCDA_ZYMMO: Diaminopimelate decarboxylase (lysA) from Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

KEGG orthology group: K01586, diaminopimelate decarboxylase [EC: 4.1.1.20] (inferred from 88% identity to sch:Sphch_1731)

Predicted SEED Role

"Diaminopimelate decarboxylase (EC 4.1.1.20)" in subsystem Lysine Biosynthesis DAP Pathway (EC 4.1.1.20)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.1.1.20

Use Curated BLAST to search for 4.1.1.20

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

Find the best match in UniProt

Protein Sequence (421 amino acids)

>GFF3795 Diaminopimelate decarboxylase (EC 4.1.1.20) (Sphingobium sp. HT1-2)
LDHFDYVDGTMHVEQVPMTEIAQQVGTPVYVYSTATLERHVGVFREGLSQLDNPLIAFAV
KANPNAAVLATLAKLGLGADVVSGGELQRAVAAGIPADRIVFSGVGKTAEEMKLALELGI
FQFNLESEPEAEMLSEVALSMGRKAPVAYRINPDVDAGTHAKISTGKSENKFGIPYDRAL
DSYAAARDLPGLDVQGVAVHIGSQLTDLAPLEAAFVKVGALIAQLRAAGHDIRTADLGGG
LGVPYDPSQPLPPSPADYGAMVTRVTQGWDARLMFEPGRVIVGNAGVLLSQVIRVKQGAQ
APFVIVDAAMNDLMRPSLYDAWHDIRAVAPDGNRIASNVVGPVCETGDTFAMGRDMDVVA
AGDLLTFMTAGAYGATMAGTYNSRSLTPEVLVSGDKWAVVRARPPIEALIAGDHIPDWVA
G