Protein Info for Pf6N2E2_1216 in Pseudomonas fluorescens FW300-N2E2

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 878 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 6 to 164 (159 residues), 241.4 bits, see alignment E=7e-76 PF13298: LigD_N" amino acids 41 to 146 (106 residues), 150.5 bits, see alignment E=4e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 235 to 536 (302 residues), 359 bits, see alignment E=4.1e-111 PF01068: DNA_ligase_A_M" amino acids 238 to 415 (178 residues), 95.6 bits, see alignment E=8.4e-31 TIGR02776: DNA ligase D" amino acids 245 to 859 (615 residues), 734.4 bits, see alignment E=2.4e-224 PF04679: DNA_ligase_A_C" amino acids 434 to 530 (97 residues), 95 bits, see alignment E=7.5e-31 TIGR02778: DNA ligase D, polymerase domain" amino acids 588 to 830 (243 residues), 291.7 bits, see alignment E=1e-90 PF21686: LigD_Prim-Pol" amino acids 604 to 855 (252 residues), 279.2 bits, see alignment E=8.6e-87 PF01896: DNA_primase_S" amino acids 705 to 794 (90 residues), 29.1 bits, see alignment E=3.1e-10

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 93% identity to pba:PSEBR_a2838)

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

See A0A159ZV49 at UniProt or InterPro

Protein Sequence (878 amino acids)

>Pf6N2E2_1216 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD (Pseudomonas fluorescens FW300-N2E2)
MSSKTLDDYNRMRDFAATPEPAAKRSRQSAKTAHALQFCIQKHDASRLHYDFRLELDGAL
KSWAVPKGPSLDPKAKRLAVHVEDHPLDYATFEGNIPEGHYGAGDVIVWDRGVWIPQGDP
HEAYEKGRLKFELQGEKLSGLWNLVRTHMPGKQEQWFLIKHQDQAARPESEYDVVQAEPD
SVLSDRTLVPKRRGKAAAKAVKQPEKAVRPKSPKRPSKTTLSGAVAGPLPDTLKPELATL
VESAPDGEWLYEIKFDGYRVMARIENGDVRLLTRNGHDWTHKLPSQAEALAALGLESAWL
DGEMVVANDQGVPDFQALQNAFEAGSSGKIAYYLFDVPYLNGMDLRNVPVQERRAALAAV
LESNESPLLRFSDAFEENPEALLNSACQMQMEGLIGKRIGSTYVSRRSNDWIKLKCKNRQ
EFVVVGFSEPKGARSAFGALLLGLHDADSGQLRYAGKVGTGFNETTLKSIYQQLLPLETK
KAAVVNPPTGYEAKGVHWLEPKLLAEVAFAEMTKDGSVRHAVFHGLRDDKPAKDITQELA
KPVKKNATAKKAKAKAKAKAKAKDEPGATPARTKSKAKAKAPALDCKVRITHPERVIDAS
SGTTKLQLAEYYASVAEFILPELADRPVALVRAPDGIAGELFFQKNPERLAIPGITSLDK
ELTGQPVMIINNAEALIGAVQMSTVELHTWNATSVDLNKPDRFVLDLDPDPALPWKSMVE
ATQLTLSVLDELGLKAFLKTSGGKGIHVVVPLTRKLGWDEVKGFSHAIVSHMAKLLPDRF
SAVSGPKNRVGRIFIDYLRNGLGATTICAYAARTREGLPVSVPIFREEVAELKGANVWNV
HNVHERLAEVGHEPWAGLKRTRQSITAEMRRRIGMKKV