Protein Info for PFR28_00508 in Pseudomonas sp. RS175

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 50 100 150 200 250 300 350 400 450 500 562 TIGR04120: DNA ligase, ATP-dependent, PP_1105 family" amino acids 2 to 561 (560 residues), 708.4 bits, see alignment E=3.5e-217 PF04675: DNA_ligase_A_N" amino acids 2 to 161 (160 residues), 49.8 bits, see alignment E=7.3e-17 PF01068: DNA_ligase_A_M" amino acids 231 to 430 (200 residues), 84.2 bits, see alignment E=1.6e-27 PF04679: DNA_ligase_A_C" amino acids 451 to 546 (96 residues), 34.9 bits, see alignment E=2.6e-12

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 91% identity to pba:PSEBR_a1156)

Predicted SEED Role

"ATP-dependent DNA ligase (EC 6.5.1.1) LigC" 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 (562 amino acids)

>PFR28_00508 DNA ligase (Pseudomonas sp. RS175)
MKAFAELYADLDATTSSNAKLAAMRGYFTQASPQDAAWAVYFLSGGRPRQLVPVKILREL
AVQVSGLSSWLFEESYQAVGDLAETISLVLPESPHRSDEGLAAWIEEKLLPLRGEPPEVL
AARLPALWAQLDRPSLMLCIKLITGSFRVGVSKLLVTRALAGLAGLDSKRVAQRLVGYTD
LSHRPTADSFLKLIAAESDDEHAQRGGQPYPFFLAHALSASVEQFDTLLGPASDWQVEWK
WDGIRAQLVKRDGQLWVWSRGEELVTERFPELHALAGALPDGTVIDGEIVVWKTPLPLTD
EAFDADAPLQPAVQPFALLQQRIGRKTLSKKVLEDAPVVVMAYDLLEWQGEDWRSRPQAE
RRECLEALVTRCHNPVLLPSPIVTGRDWPDLARQREASRSLGVEGMMLKARDALYGVGRT
KDMGVWWKWKIDPFSVDAVLIYAQRGHGRRASLYSDYTFAVWDNPPGSRERSLVPFAKAY
SGLTDEEMRQVDSIVRKTTVEKFGPVSSVKPTLVFELGFEGIALSKRHKSGIAVRFPRML
RWRQDKTVEDADTLATLQDLLK