Protein Info for GFF242 in Xanthobacter sp. DMC5

Annotation: Multifunctional non-homologous end joining protein LigD

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 863 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 4 to 165 (162 residues), 236.5 bits, see alignment E=2.1e-74 PF13298: LigD_N" amino acids 41 to 146 (106 residues), 151.7 bits, see alignment E=1.4e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 262 to 562 (301 residues), 334.8 bits, see alignment E=9.2e-104 TIGR02776: DNA ligase D" amino acids 271 to 854 (584 residues), 648.7 bits, see alignment E=2.2e-198 PF01068: DNA_ligase_A_M" amino acids 274 to 443 (170 residues), 86 bits, see alignment E=5.9e-28 PF04679: DNA_ligase_A_C" amino acids 462 to 556 (95 residues), 90.7 bits, see alignment E=1.4e-29 TIGR02778: DNA ligase D, polymerase domain" amino acids 581 to 825 (245 residues), 293.2 bits, see alignment E=3.5e-91 PF21686: LigD_Prim-Pol" amino acids 597 to 850 (254 residues), 297.6 bits, see alignment E=1.7e-92

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 61% identity to gdj:Gdia_2239)

Predicted SEED Role

"ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD" in subsystem DNA Repair Base Excision (EC 6.5.1.1)

Isozymes

Compare fitness of predicted isozymes for: 6.5.1.1

Use Curated BLAST to search for 6.5.1.1

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 (863 amino acids)

>GFF242 Multifunctional non-homologous end joining protein LigD (Xanthobacter sp. DMC5)
MADLQRYRAKRDFAATPEPSGAARRKAKGEAARPEGSFVIQKHAARRLHYDFRLEMDGVL
KSWAVTRGPSLVPGEKRLAVHVEDHPLDYGSFEGTIPKGQYGGGSVIIWDRGTWTPIGDP
HKGYAKGHMEFTLDGEKLHGRWHLVRMAPRGGEKNENWLLIKAEDAFARPDGAPDILAEE
PLSVVSGRAVDALSPDDPAPKKRAAKSGATGAKKAAPKSPAAKFPTPPADDPPPDDTTGT
TGTPLTLPRGAKAAPLPAFIPPALATLATKAPAGTRYLHEIKFDGYRIQARVENGKVRLL
TRTGLDWTDRFGTGILAELNRFPIRTALFDGEIVVESGNGATDFSALQADLSEGRSDRFV
YYVFDLLHLDGHDLTPLPLKDRKDLLEKLVGQDGDKVRYSAHFEDDGALVLRHACRLSLE
GVVSKLKTAPYHSGRTRDWIKSKCLERQEFVVGGFVPSTTSRTAIGSLVLGVFEDGKLRY
VGRVGTGFTQRVAADLHKLLVSEKTDVCPFSGKLTAEEARGVSFVEPLHVAEVEFGAWTG
DGHLRHAAFRGLREDKPATEIVRESSSEPKASDPPAPKRRVRLTHPDRVYWPDVGLTKEG
LADYYAQVWRFMAPFVTGRPLALVRCPEGIDGQRFFQKHPWKGLDKNILQVPDPKAKDEA
PYLAIRDLDGLTALVQGAALEIHPFGATLADWERPDILTMDLDPGDDVPWGDVISAAEEV
RERIEKKGLSAFLKTSGGKGLHICAPLTPKADWARLKAFTKAMAEEMASDSPDRFVATIT
KSQRKGRILVDYLRNQRGATAVAPYSTRARPGAPVSMPLAWDELGEAIGPQHFNVGYALA
RLMNLGHDPWGDFRAAAVPLPGA