Protein Info for GFF4478 in Variovorax sp. SCN45

Annotation: UDP-N-acetylmuramoyl-dipeptide--2,6-diaminopimela te ligase (EC 6.3.2.13)

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 50 100 150 200 250 300 350 400 450 518 PF01225: Mur_ligase" amino acids 24 to 67 (44 residues), 25.8 bits, see alignment 1.8e-09 PF08245: Mur_ligase_M" amino acids 109 to 334 (226 residues), 137.3 bits, see alignment E=1e-43 TIGR01085: UDP-N-acetylmuramyl-tripeptide synthetase" amino acids 151 to 512 (362 residues), 347.9 bits, see alignment E=5e-108 PF02875: Mur_ligase_C" amino acids 358 to 488 (131 residues), 100.6 bits, see alignment E=1.9e-32

Best Hits

KEGG orthology group: K01928, UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase [EC: 6.3.2.13] (inferred from 88% identity to vpe:Varpa_0974)

Predicted SEED Role

"UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (EC 6.3.2.13)" in subsystem Methicillin resistance in Staphylococci or Peptidoglycan Biosynthesis (EC 6.3.2.13)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 6.3.2.13

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 (518 amino acids)

>GFF4478 UDP-N-acetylmuramoyl-dipeptide--2,6-diaminopimela te ligase (EC 6.3.2.13) (Variovorax sp. SCN45)
MLTFTSPQLVAAWLKERAPQAAMHADSRAVGAGDIFVAWPGAATDGRKHVASALAQGAAV
CLVEHEGVEPFGFDGDERIVSYPGLKAATGPIASAFYDNPSALLDVLAVTGTNGKTSTAW
WLAESLSTLRAAGGVRVMKPDGTMQRDAPSPCAVMGTLGVGVPPELTYTGLTTPDPVMMQ
RELRSLVERGFGACAIEASSIGIAERRLDGAQIAVAVFTNFTQDHLDYHGSMDAYWQAKA
ELFRWPGLRAAVINIDDTHGASLCANLIDAGIGALDVWTVSAGGKPARLVARDIGYDAQG
LQFSVAEHGTAAVERLSTGLIGQYNVANLLGVLGTLRALGLTLAQAAAACANLTSVPGRM
DRAGTGDGAPLAVVDYAHTPDALDKALIGLRPLAQQRGGALWCLFGCGGDRDPIKRPMMA
AVAERQADRVIVTSDNPRSEKPDAIISQVLLGFSRPEVAQVQPDRALAIADAIAQAAPQD
VVLIAGKGHEAWQEIAGQRIEFSDKTHALQALAKRGGA