Protein Info for Xcc-8004.140.1 in Xanthomonas campestris pv. campestris strain 8004

Annotation: ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku 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

1 100 200 300 400 500 600 700 800 900 1001 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 3 to 157 (155 residues), 237 bits, see alignment E=1.5e-74 PF13298: LigD_N" amino acids 35 to 140 (106 residues), 134.3 bits, see alignment E=3.7e-43 TIGR02779: DNA ligase D, ligase domain" amino acids 248 to 545 (298 residues), 353.5 bits, see alignment E=1.8e-109 PF01068: DNA_ligase_A_M" amino acids 260 to 427 (168 residues), 81.8 bits, see alignment E=1.1e-26 PF04679: DNA_ligase_A_C" amino acids 446 to 541 (96 residues), 87.2 bits, see alignment E=1.6e-28 TIGR02778: DNA ligase D, polymerase domain" amino acids 720 to 964 (245 residues), 340.8 bits, see alignment E=1e-105 PF21686: LigD_Prim-Pol" amino acids 737 to 989 (253 residues), 309.7 bits, see alignment E=3.5e-96

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 100% identity to xcb:XC_0109)

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)

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

See A0A0H2X2G3 at UniProt or InterPro

Protein Sequence (1001 amino acids)

>Xcc-8004.140.1 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD (Xanthomonas campestris pv. campestris strain 8004)
MSLRDYTRKRRFDQTPEPAEDAAATAHRQPIFVVQLHHASSRHYDFRLEADGVLKSWAVP
KGPSLRAGEKRLAVQVEDHPLAYAGFEGDIPQGQYGAGHVQVFDHGTWHCDGDALAALDA
GKLDFDLQGDKLRGGFALVRTRLRGRQPQWLLIKRDDAHAADLDADALVADSDATAQAIE
TPSAAAAPARRAKASRRRRTPAEALVTEKSASASRPRASAATQAHWRTRALALPGARDAA
CPTGLRAQLTLLRAEAPDGAQWPHEIKWDGYRLLTDLVDGRAQLRSRNDQAWTDSFPEVA
TAVQALPVRDARLDGELVVLDAQGRSDFSALQRAIDGTARQPLRYLVFDLLGVAGVDLRA
TPLLERKQLLRALLGETPGTLAYSAHVIGRGPEVFAASADKGWEGIVSKRADAPYRGGRS
ADWVKTKHEDSDEFVVVGYTDPKGARSGFGALLLAQLDGTQLRYVGRVGTGFDSALLGEI
TAQLQALHSPQPTLELPAHIPSRPRDVHWVRPVLIAEVAFRGWAKQGLLRQAAFKRLRED
KPMSDLGGDRATPGKSRGARTRTAAAAAGKASRAAATRTAAVSAGGSAAKPGKAGKSSTA
ADVSTPSRVAKQRVTPAASSAAKPGKPGKSSAAATGTASPRAAKRGAVSTASASSTPKSG
KRSVSSGSAASGKPAAPSKAASSKTARTPATSSARKTSTATAASSIRKARASASNAPDGV
AITHPERVVFPAAGISKGDVAAYYRAVAPLVLPEIARRPLSLLRCPDGAAGACFFQKHEG
RHLGAHIKAIPLKQKSGTEDYLYIEDVAGLLELVQMNTLELHPWGARVDDPEHPDRLVFD
LDPGEGVAWTQVVAAAREIRSKLRAAGLESAVRLSGGKGLHVVVPIVPQASWDQARDFCE
AFAQALATQAPERYVATMSKAKRHGVIFVDWLRNGRGNTSVCSWSLRAREHATVAVPLRW
EELGKLSGPDAFPLDKAVQRAKRQRNDPWADVLALKQVLPG