Protein Info for PP_4274 in Pseudomonas putida KT2440

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 776 PF22745: Nlig-Ia" amino acids 5 to 53 (49 residues), 34 bits, see alignment 1.1e-11 TIGR00575: DNA ligase, NAD-dependent" amino acids 10 to 604 (595 residues), 741.2 bits, see alignment E=5.2e-227 PF01653: DNA_ligase_aden" amino acids 67 to 315 (249 residues), 331.9 bits, see alignment E=8.5e-103 PF03120: DNA_ligase_OB" amino acids 320 to 395 (76 residues), 120.9 bits, see alignment E=4.8e-39 PF12826: HHH_2" amino acids 520 to 583 (64 residues), 68.7 bits, see alignment E=1.2e-22 PF00533: BRCT" amino acids 697 to 765 (69 residues), 44.1 bits, see alignment E=6e-15

Best Hits

Swiss-Prot: 100% identical to DNLJ_PSEPK: DNA ligase (ligA) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K01972, DNA ligase (NAD+) [EC: 6.5.1.2] (inferred from 100% identity to ppu:PP_4274)

Predicted SEED Role

"DNA ligase (EC 6.5.1.2)" in subsystem DNA Repair Base Excision (EC 6.5.1.2)

MetaCyc Pathways

Isozymes

Compare fitness of predicted isozymes for: 6.5.1.2

Use Curated BLAST to search for 6.5.1.2

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 Q88F25 at UniProt or InterPro

Protein Sequence (776 amino acids)

>PP_4274 DNA ligase (Pseudomonas putida KT2440)
MTAETRILELRAELDQHNYRYYVLDEPSVPDAEYDRLFNELKALEAEHPHLVTPDSPTQR
VGGAALAAFSQVRHEVPMLSLGNAFEEADLREFGRRVVEGLDQPGAVDYSCEPKLDGLAV
SLLYRDGQLVQGATRGDGTTGEDISANVRTVRNIPLKLQGKGWPAVLEVRGEVYMSKAGF
DRLNAAQAEAGGKTFANPRNAAAGSLRQLDSKITASRPLEFCCYGVGQVSESIGDSHIGI
LEQLKAWGLPISRELKHAAGIEECLAYYRDIGERRNSLPYEIDGVVFKVNSLAAQRELGF
RAREPRWAIAHKFPAMEELTEVLDVEFQVGRTGAVTPVARLKPVKVAGVTVSNATLHNMD
EIARLGLRIGDTVIIRRAGDVIPQVMQVVLERRPQGARPVEVPSACPVCGSQVERTRLVK
RSKGKETTSEGAVYRCVGRLACGAQLKQAIIHYVSRRAMDIDGLGEKSVEQLVDEGLIGS
PADLYKLQFEQVVGLEGFAEVSTQKLLDAIEASKRPSLARFIYALGIPDVGEETAKVLAR
SLGSLARVQQALPQVLTYLPDIGLEVAYEIHNFFEDEHNQKVIQQLLDSGMQLQDEGELA
AEFAASTTLAGMIAKLDIASVGPTGAEKLVARLDSLDKIIAADGIDLRQALAAKQADAVR
EFFKDEANQKLARDIEAQLLAFGMHWSSEKKVAEGLPLAGQTWVLTGTLERMSRDIAKDK
LESLGAKVAGSVSGKTHCVVAGPGAGSKLAKAAELGVKVLDEDAFVTFLAEQGIAV