Protein Info for GFF3828 in Xanthobacter sp. DMC5

Annotation: DNA 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 50 100 150 200 250 300 350 400 450 500 550 600 650 712 TIGR00575: DNA ligase, NAD-dependent" amino acids 28 to 707 (680 residues), 777 bits, see alignment E=7.7e-238 PF01653: DNA_ligase_aden" amino acids 86 to 336 (251 residues), 321.3 bits, see alignment E=1.7e-99 PF03120: DNA_ligase_OB" amino acids 339 to 415 (77 residues), 116.3 bits, see alignment E=1.6e-37 PF03119: DNA_ligase_ZBD" amino acids 426 to 458 (33 residues), 30.6 bits, see alignment (E = 8.5e-11) PF12826: HHH_2" amino acids 540 to 570 (31 residues), 38 bits, see alignment (E = 5.3e-13) PF00533: BRCT" amino acids 638 to 710 (73 residues), 57.7 bits, see alignment E=3.8e-19 PF12738: PTCB-BRCT" amino acids 648 to 703 (56 residues), 23.3 bits, see alignment 1.8e-08

Best Hits

Swiss-Prot: 84% identical to DNLJ_XANP2: DNA ligase (ligA) from Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)

KEGG orthology group: K01972, DNA ligase (NAD+) [EC: 6.5.1.2] (inferred from 84% identity to xau:Xaut_1762)

Predicted SEED Role

"DNA ligase (EC 6.5.1.2)" in subsystem DNA Repair Base Excision (EC 6.5.1.2)

MetaCyc Pathways

Isozymes

No predicted isozymes

Use Curated BLAST to search for 6.5.1.2

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 (712 amino acids)

>GFF3828 DNA ligase (Xanthobacter sp. DMC5)
MTKPALPLRSLTVEDLSPSDAAAEHAALAEEIKGHDAAYYREDAPVVSDAEYDALRRRYE
AIEARFPGLVGEDSLSAKVGAAPSEKFGKVVHGVPMLSLSSVFTDDAIFEFVARVKRFLS
VNSDDQIAFTCEPKIDGLSCSLRYENGRLTVAATRGDGRQGEDVTENVRTIDDVPQQLFT
NDVPELIDVRGEVYMAKADFEALNARQSALGERVFANPRNAAAGSLRQLDPSVTASRPLK
FFAYAWGEASALPADTQNGMLNAFDRWGFCINRLVTVARNAGELIDHYRKIEELRASLPY
DIDGVVYKVNRLDLRERLGFVSRTPRWAIAHKFPAEQATTVLEAIDIQVGRTGALTPVAK
LLPVTVGGVVVANATLHNEDEIARKDIRVGDTVVVQRAGDVIPQVVRVITEKRPAGSKPY
EFPTLCPACGSHAVREVDTKTGKVDAVRRCTGGLICPAQMVERLRHFVSRNAFDIEGLGE
KQVRAFYDWGLIASPADIFTLEARNKEGLQRLENREGWGKTSAANLFVAIQSRRNVAVDR
FVFALGIRHVGETNAKRLMRHYGTVEALEAGALAAAIPGEEHPKGNDAWQEMLAIDGVGD
VVAEAVIEFFHEPRNREVVAALLAEVTPAPMERVAAESPVAGKTVVFTGSLEKMTRDEAK
AMAERLGAKVAGSVSAKTDLVVAGPGAGSKLEKAQALGVKVITEDEWFELVG