Protein Info for LRK54_RS12250 in Rhodanobacter denitrificans FW104-10B01

Annotation: D-alanine--D-alanine ligase

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: 71% identical to DDLB_XANCP: D-alanine--D-alanine ligase B (ddlB) from Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)

KEGG orthology group: K01921, D-alanine-D-alanine ligase [EC: 6.3.2.4] (inferred from 70% identity to xcv:XCV0832)

Predicted SEED Role

"D-alanine--D-alanine ligase (EC 6.3.2.4)" in subsystem Peptidoglycan Biosynthesis (EC 6.3.2.4)

MetaCyc Pathways

peptidoglycan biosynthesis I (meso-diaminopimelate containing) (10/12 steps found)
UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) (7/8 steps found)
UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing) (6/8 steps found)
UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-diaminopimelate containing) (6/8 steps found)
peptidoglycan biosynthesis III (mycobacteria) (10/15 steps found)
peptidoglycan biosynthesis II (staphylococci) (11/17 steps found)
peptidoglycan biosynthesis IV (Enterococcus faecium) (11/17 steps found)
peptidoglycan biosynthesis V (β-lactam resistance) (10/17 steps found)

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 6.3.2.4

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search 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 (311 amino acids)

>LRK54_RS12250 D-alanine--D-alanine ligase (Rhodanobacter denitrificans FW104-10B01)
MKVTDPVRFGRVAVVMGGSSAEREVSLDSGRNVLEALQARGVDAHAVDGIPALLDALRSE
RFARVFNILHGQHGGGEDGVLQGALEALGVPYTGSGVLGSALSMDKPRSKRVWQSLGLPT
PKFVALPRGADVHAAAKQVGFPLIVKPACEGSSVGVTRVFEEAQLDQAVELAARYPGDLL
METLIEGDELTVGILGREVLPSIHIVPKGAFYDYNAKYIAEDTLYLCPGLEGDAEAELRA
LALAAFDALGCQGWGRVDVMRDRQGRNWLLEVNTAPGMTSHSLVPKAAKAAGIDYQELCW
RVLETSFRESL