Protein Info for PFR28_02106 in Pseudomonas sp. RS175

Annotation: Multifunctional non-homologous end joining 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 880 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 7 to 165 (159 residues), 239.8 bits, see alignment E=2.1e-75 PF13298: LigD_N" amino acids 42 to 147 (106 residues), 150.3 bits, see alignment E=4.8e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 237 to 538 (302 residues), 356.4 bits, see alignment E=2.4e-110 PF01068: DNA_ligase_A_M" amino acids 240 to 417 (178 residues), 93.3 bits, see alignment E=4.2e-30 TIGR02776: DNA ligase D" amino acids 247 to 858 (612 residues), 741.8 bits, see alignment E=1.4e-226 PF04679: DNA_ligase_A_C" amino acids 436 to 532 (97 residues), 92.5 bits, see alignment E=4.4e-30 TIGR02778: DNA ligase D, polymerase domain" amino acids 588 to 830 (243 residues), 291.3 bits, see alignment E=1.3e-90 PF21686: LigD_Prim-Pol" amino acids 604 to 855 (252 residues), 282.6 bits, see alignment E=8.3e-88 PF01896: DNA_primase_S" amino acids 705 to 795 (91 residues), 29.2 bits, see alignment E=2.9e-10

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 89% 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)

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

Find the best match in UniProt

Protein Sequence (880 amino acids)

>PFR28_02106 Multifunctional non-homologous end joining protein LigD (Pseudomonas sp. RS175)
MMASKTLDDYNRMRDFAATPEPAAKRSRRAKKAAHALQFCIQKHDATRLHYDFRLELDGA
LKSWAVPKGPSLDPKAKRLAVHVEDHPLDYATFEGSIPEGHYGAGDVIVWDRGVWIPQGD
PHEAYEKGRLKFELQGEKLAGLWNLVRTHMPGKQEQWFLIKHQDEAARPQSEYDVVQAEP
DSVLSDRTIIPKRRGKAAAAKAVKQPEKASPQKSSKKASGTTLSGAVPGPIPKTLKPELA
TLVQSAPDGEWLYEIKFDGYRVMARIEDGDVRLITRNGHDWTHKLPRQAEALAGLGLESA
WLDGEMVVANEDGVPDFQALQNAFDAGSSGKIAYYLFDLPYLNGMDLRKVPVQERRAALA
AVLERNRDPLLHFSDAFEETPEALLNSACQMRMEGLIGKRMGSAYVSRRSNDWIKLKCKN
RQEFVVVGFSEPKGARSAFGALLLGLHDADSGELRYAGKVGTGFNETTLKSIYQQLLPLE
TKKAAVVNPPTGYEAKGVHWLEPSLLAEVAFAEMTKEGSVRHAVFHGLRNDKPAKDITQE
KARPVKKSADTKKAKAAEAQSAPARAPDKPKAKGKAKASAAQGMEGKVRITHPDRIIDAT
SGTTKLQLAEYYASVAEFILPELAERPVALVRAPDGIAGELFFQKNAERLAIPGITSLDK
SVTGHPVMIINNPEALIGAVQMSTVELHTWNATTVDLDKPDRFVLDLDPDPALPWKSMVE
ATQLTLSVLDELGLKAFLKTSGGKGIHVVVPLTRKAGWDEVKGFSHAIVSHMAKLLPDRF
SAVSGPKNRVGRIFIDYLRNGLGATTICAYAARTREGLPVSVPIYREEVAELKGANLWNI
HNVHERLAEVGHEPWTELRKTRQSITADMRRRIGMKKAGK