Protein Info for GFF35 in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868
Annotation: Lysine decarboxylase 2, constitutive (EC 4.1.1.18)
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: 91% identical to DCLZ_ECOLI: Constitutive lysine decarboxylase (ldcC) from Escherichia coli (strain K12)
KEGG orthology group: K01582, lysine decarboxylase [EC: 4.1.1.18] (inferred from 94% identity to cro:ROD_01941)MetaCyc: 91% identical to lysine decarboxylase 2 (Escherichia coli K-12 substr. MG1655)
Lysine decarboxylase. [EC: 4.1.1.18]
Predicted SEED Role
"Lysine decarboxylase 2, constitutive (EC 4.1.1.18)" in subsystem Lysine degradation (EC 4.1.1.18)
MetaCyc Pathways
- superpathway of arginine and polyamine biosynthesis (16/17 steps found)
- L-lysine degradation I (7/7 steps found)
- superpathway of polyamine biosynthesis I (7/8 steps found)
- aminopropylcadaverine biosynthesis (3/3 steps found)
- L-lysine degradation X (5/6 steps found)
- cadaverine biosynthesis (1/1 steps found)
- bisucaberin biosynthesis (1/5 steps found)
- desferrioxamine B biosynthesis (1/5 steps found)
- desferrioxamine E biosynthesis (1/5 steps found)
- lupanine biosynthesis (1/5 steps found)
- superpathway of L-lysine degradation (14/43 steps found)
KEGG Metabolic Maps
- Alkaloid biosynthesis II
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Lysine degradation
Isozymes
Compare fitness of predicted isozymes for: 4.1.1.18
Use Curated BLAST to search for 4.1.1.18
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 (713 amino acids)
>GFF35 Lysine decarboxylase 2, constitutive (EC 4.1.1.18) (Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868) MNIIAIMGPHGVYYKDEPIKELERALQSLGFQIIWPQNSVDLLKFIEHNPRICGVIFDWD EYSLDLCSEINQLNEYLPLYAFINTNSTLDVSVHDMRMALWFFEYALGLAEDIATRIHQY TNEYLDNITPPFTKALFTYAKEGKYTFCTPGHMAGTAYQKSPPGCLFYDFFGGNTLKADV SISVTELGSLLDHTGPHLEAEEYIARTFGAEQSYMVTNGTSTSNKIVGMYAAPAGSTLLI DRNCHKSLAHLLMMSDVVPLWLKPTRNALGILGGIPRREFTRASIESKIEETPQAQWPVH AVITNSTYDGLLYNTNWIKQMLDVPSIHFDSAWVPYTHFHPIYQGKSGMSGDRVPGKVIF ETQSTHKMLAAFSQASLIHIKGEYDEETFNEAFMMHTSTSPSYPIVASIETAAAMLRGNP GKRLINRSVERALHFRKEVQRLREESDSWFFDIWQPEEVDEAECWPVTPGETWHGFTDAD DDHMFLDPVKVTILTPGMDEQGNMSEEGIPAALVAKFLDERGVVVEKTGPYNLLFLFSIG IDKTRAMGLLRGLTEFKRAYDLNLRVKNMLPDLYAEDPDFYRNMRIQDLAQGIHKLIRQH DLPGLMLRAFEVLPEMIMTPHQAWQRQIKGEVETVALDQLPGRVSANMILPYPPGVPLLM PGERITQQSRAVLDFLLMLCSIGQHYPGFETDIHGAKRNEDGVYQVRVLKHAC