Protein Info for GFF3837 in Xanthobacter sp. DMC5
Annotation: Diaminopimelate decarboxylase
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
Best Hits
Swiss-Prot: 47% identical to DCDA_AQUAE: Diaminopimelate decarboxylase (lysA) from Aquifex aeolicus (strain VF5)
KEGG orthology group: K01586, diaminopimelate decarboxylase [EC: 4.1.1.20] (inferred from 89% identity to xau:Xaut_1740)Predicted SEED Role
"Diaminopimelate decarboxylase (EC 4.1.1.20)" in subsystem Lysine Biosynthesis DAP Pathway (EC 4.1.1.20)
MetaCyc Pathways
- aspartate superpathway (22/25 steps found)
- L-lysine biosynthesis I (9/9 steps found)
- superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (15/18 steps found)
- superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (12/15 steps found)
- L-lysine biosynthesis III (6/7 steps found)
- L-lysine biosynthesis VI (6/7 steps found)
- L-lysine biosynthesis II (7/9 steps found)
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 (422 amino acids)
>GFF3837 Diaminopimelate decarboxylase (Xanthobacter sp. DMC5) MHHFDYRNGRLHAEDVDLTSLAAEVGTPFYCYATATLERHYRVFMEAFAGRDVLLCYALK ANSNQSVISTLARLGAGADIVSAGELMRARAAGVPGERIVFSGVGKTREEMAQALDAGIL CFNVESEPELDALSEVALSKGVKAPVSIRVNPDVDAKTHKKISTGKSATKFGIPISRARD VYDFAARLPGLAISGVDMHIGSQITDMAPFENAVTLLAELARDLMAAGHRLHHMDLGGGL GVPYAASDPVPPSPAAYAEVVGRALGDLKLPLVFEMGRMLVANAGILVTRVIYVKKGEGK TFVVVDAAMNDLIRPTLYEAHHDIVPVAEPAAGAAMVVADVVGPVCETGDFLALDRLLPE VKPGDLLAVMTAGAYGAVQSGTYNTRALVPEVLVRGPEAAVVRPRVDPAALIALDRPAPW LG