Protein Info for GFF6242 in Variovorax sp. SCN45

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 845 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 12 to 167 (156 residues), 220 bits, see alignment E=2.6e-69 PF13298: LigD_N" amino acids 43 to 148 (106 residues), 147.5 bits, see alignment E=3.5e-47 TIGR02779: DNA ligase D, ligase domain" amino acids 226 to 526 (301 residues), 338.6 bits, see alignment E=6.6e-105 PF01068: DNA_ligase_A_M" amino acids 239 to 408 (170 residues), 83.7 bits, see alignment E=3.7e-27 TIGR02776: DNA ligase D" amino acids 240 to 827 (588 residues), 680.7 bits, see alignment E=4.4e-208 PF04679: DNA_ligase_A_C" amino acids 427 to 520 (94 residues), 98 bits, see alignment E=8.9e-32 TIGR02778: DNA ligase D, polymerase domain" amino acids 556 to 798 (243 residues), 289.8 bits, see alignment E=3.9e-90 PF21686: LigD_Prim-Pol" amino acids 571 to 823 (253 residues), 295.5 bits, see alignment E=9.1e-92 PF01896: DNA_primase_S" amino acids 674 to 795 (122 residues), 32.3 bits, see alignment E=3.1e-11

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 83% identity to vpe:Varpa_0532)

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 (845 amino acids)

>GFF6242 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD (Variovorax sp. SCN45)
MGTTASTARKALARYHGKRDFSRTPEPKTGGRAGKGVLSFVIQKHHASHLHYDFRLELDG
TLKSWAVPKGPCLDPAVKRMAVHVEDHPISYAGFEGTIPPKQYGAGTVIVWDRGDWLPDG
DARKSLAAGKLKFELRGEKLHGHWTLVRMHGKGDESHEPWLLIKERDAEARALDDYDVLE
EQPASVLSGRGVDDVAQPAKKMPAKAPAKVQAKAPKKVALPATLQPQLATLAASPPASPG
DWLYELKFDGYRLLARIDKGKVRCFTRNGHDWTAKLPALAEALAKLSTGAAWLDGEITVE
GENGAPDFQALQNAFDRGATSAIVYWLFDAPFLDGEDLRELPVEERRARLAKLLGKKPPA
PLRLSEAFDAAPRDLLASSARIGFEGIVCKRKGSPYVPRRSPDWIKLKNQQRQEFVIGGY
TAPKGARAGFGALLLGVHDEATGRLRYCGNVGTGFDAKRLADIKARLDRLATDDCPFSPQ
PRGVKAQWVKPSLVAEVSFGEWTREDRVRQAVFQGLRADKPARDIRRERPKEAGEIEADA
SSPAKKKGKPAPMAQKITHADRVIDKHSGITKGQLAAYYDSVATLMLPHLRGRPVSLVRA
PEGVGGELFFQKHVQNREIPGVRLLDPALDPGHEPLLQIDTRTGLLGAAQMNVIELHTWN
ATSRAIGKPDRMTFDLDPGEGVAWPRIQEAAMLVRTLLDELGLPSFLKTSGGKGLHVVVP
LRRQYDWDAVKGFSQAVVAHLAETIPSRFVAKSGPRNRVGKVFVDYLRNGFGATTVSAWS
ARSRPGLGVSVPLAWEELPVVTAADQWNVGNAAERFAIGNKPWAAMERSRKGLAAAMKLL
GYSSK