Protein Info for PP_3255 in Pseudomonas putida KT2440

Annotation: non-homologous end joining protein

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 50 100 150 200 273 signal peptide" amino acids 1 to 25 (25 residues), see Phobius details TIGR02772: Ku protein" amino acids 2 to 263 (262 residues), 327.3 bits, see alignment E=3.5e-102 PF02735: Ku" amino acids 11 to 194 (184 residues), 170.6 bits, see alignment E=1.9e-54

Best Hits

Swiss-Prot: 74% identical to KU_PSEAE: Non-homologous end joining protein Ku (ku) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K10979, DNA end-binding protein Ku (inferred from 100% identity to ppu:PP_3255)

Predicted SEED Role

"Ku domain protein" in subsystem DNA Repair Base Excision

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 Q88HU8 at UniProt or InterPro

Protein Sequence (273 amino acids)

>PP_3255 non-homologous end joining protein (Pseudomonas putida KT2440)
MARAIWKGAISFGLVHIPVALNTAVRTERVDFDWLDKRSMEPVGYKRVNKVTGKEIDKDN
IVKGVEFEKGRYVVISEEEIRKARPETTQTIDIFSFVEAGDIPLQHFDTPYYLTPDRRGG
KVYALLRETLEKTGKVALATVVLHTRQHLALLRPLDHALVMITLRWPEEVRGLETLELDA
SVTDSKVEKRELEMAKRLVEDMSGPWKPEDYHDAFRQTIMDLVEEKASKGKIEAVEKGDT
GAAEKGADILDLTELLKRSLGGKKPVKKTRKAS