Protein Info for GFF5134 in Sphingobium sp. HT1-2

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 837 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 7 to 162 (156 residues), 225.5 bits, see alignment E=5.2e-71 PF13298: LigD_N" amino acids 37 to 143 (107 residues), 151 bits, see alignment E=2.9e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 240 to 541 (302 residues), 313.9 bits, see alignment E=2.1e-97 TIGR02776: DNA ligase D" amino acids 250 to 821 (572 residues), 612.8 bits, see alignment E=1.6e-187 PF01068: DNA_ligase_A_M" amino acids 252 to 425 (174 residues), 105.7 bits, see alignment E=6.9e-34 PF04679: DNA_ligase_A_C" amino acids 444 to 536 (93 residues), 87.7 bits, see alignment E=1.4e-28 TIGR02778: DNA ligase D, polymerase domain" amino acids 556 to 801 (246 residues), 308.9 bits, see alignment E=5.7e-96 PF21686: LigD_Prim-Pol" amino acids 572 to 818 (247 residues), 299.4 bits, see alignment E=6.2e-93 PF01896: DNA_primase_S" amino acids 676 to 797 (122 residues), 29.8 bits, see alignment E=1.9e-10

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 77% identity to sch:Sphch_2999)

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 (837 amino acids)

>GFF5134 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD (Sphingobium sp. HT1-2)
MSRNNPLASYNAKRDFNRTSEPAGKIAKKGGNSFIVQKHAATRLHWDFRLEVDGVLKSWA
VTKGPSLDPDDKRLAVRTEDHPLSYGSFEGNIPKGEYGGGTVMLWDRGWWEPIAGKSAKN
IEDGHLHFILHGERMKGEWLLVRMKGRAGEKRENWLLRKIDDGEARRNGDLVERALTSVL
TDRSMAQIAGDIAGTQSLKGANGKTFADRMQAANAHNARIGKTKGRAKARTEAMPRFIKP
QLATLVDNVPVGNEWMHEIKYDGYRALVAVSGEAIKIYTRSGLDWTDKFSPLAGAIKALD
LPPALIDGEIIAFDADGNPSFSALQAVLKRGHGAERADTPFHFFAFDLLSLDGMDLKSLP
AIERKERLEALLADAEQPIHVADHLIGSGEKLYRSLCQAGQEGIIAKRVDAPYRSGRTRA
WVKVKCTRRQEFVIVGWTRSKAKGRAFSSLLLGQHEGSELVYKGKVGTGFDAATMTDLAE
AMGPISTGTPQVIISAREARDVQWVEPRLVAEVSFAEFTGEGRVRHGSFLGLRSDKLAKT
VKPEKAAPTPPSATVIKISNRARVIFPESGQTKGVLADYYARIAPLMLSFAANRPISLVR
CPQGRAKKCFFQKHDSGAFGDHVRHVAIREKNGGSEDYLYVDDTDGLIACVQMGTIEFHG
WASRADAVEKPDRMIFDLDPDEGMDFAQVSQAAKDIRDHLREIGLISFAMLSGGKGVHVV
VPLSPTHDWDAHKDFAARFAQALSAAEPDRFVATMSKAKRKDRIFIDWLRNQRGSTAILP
YSARARAGAPVAIPVDWNELNDLQDAHPFDIGDVEMLWERASKLKGWGFAAQALPDL