Protein Info for GFF4416 in Pseudomonas sp. DMC3

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

1 50 100 150 200 250 324 TIGR01205: D-alanine--D-alanine ligase" amino acids 19 to 311 (293 residues), 353.4 bits, see alignment E=4.9e-110 PF01820: Dala_Dala_lig_N" amino acids 67 to 101 (35 residues), 43.6 bits, see alignment 1.3e-14 PF02655: ATP-grasp_3" amino acids 110 to 281 (172 residues), 26.8 bits, see alignment E=1.6e-09 PF02786: CPSase_L_D2" amino acids 111 to 302 (192 residues), 43.6 bits, see alignment E=7.8e-15 PF07478: Dala_Dala_lig_C" amino acids 119 to 310 (192 residues), 188.9 bits, see alignment E=2.5e-59 PF02222: ATP-grasp" amino acids 119 to 279 (161 residues), 37.1 bits, see alignment E=7.8e-13 PF13535: ATP-grasp_4" amino acids 146 to 281 (136 residues), 32.5 bits, see alignment E=1.9e-11

Best Hits

Swiss-Prot: 94% identical to DDL_PSEPF: D-alanine--D-alanine ligase (ddl) from Pseudomonas fluorescens (strain Pf0-1)

KEGG orthology group: K01921, D-alanine-D-alanine ligase [EC: 6.3.2.4] (inferred from 94% identity to pfo:Pfl01_4671)

Predicted SEED Role

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

MetaCyc Pathways

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)

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 (324 amino acids)

>GFF4416 D-alanine--D-alanine ligase (Pseudomonas sp. DMC3)
MTAAYAKLFSTIAPKDFGRVAVLFGGLSAEREVSLKSGNAVLEALQSAGVDAFGIDVGED
FLQRLLSEKIDRAFIILHGRGGEDGSMQGLLECAGIPYTGSGILASALAMDKLRTKQVWH
SLGIPTPRHAVLCSEADCISAATELGLPLIVKPAHEGSSIGMAKVNSASELIDAWKAAST
YDSQVLVEQWIQGPEFTIATLRDQVLPPIALGTPHTFYDYDAKYIANDTQYRIPCGLDAA
KEQELMELTAKACEALGIAGWGRADVMQDADGQFWFLEVNTAPGMTDHSLVPMAARAAGL
DFQQLVLAILAASVEDAGATEARG