Protein Info for PP_4968 in Pseudomonas putida KT2440
Annotation: DNA ligase B
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
Best Hits
Swiss-Prot: 100% identical to LIGB_PSEPK: DNA ligase B (ligB) 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_4968)MetaCyc: 40% identical to DNA ligase B (Escherichia coli K-12 substr. MG1655)
DNA ligase (NAD(+)). [EC: 6.5.1.2, 6.5.1.6]
Predicted SEED Role
"DNA ligase (EC 6.5.1.2)" in subsystem DNA Repair Base Excision (EC 6.5.1.2)
MetaCyc Pathways
- NAD salvage pathway II (PNC IV cycle) (4/5 steps found)
- NAD salvage pathway III (to nicotinamide riboside) (2/3 steps found)
- NAD salvage pathway I (PNC VI cycle) (4/7 steps found)
- NAD salvage (plants) (4/11 steps found)
Isozymes
Compare fitness of predicted isozymes for: 6.5.1.2
Use Curated BLAST to search for 6.5.1.2 or 6.5.1.6
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
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 Q88D59 at UniProt or InterPro
Protein Sequence (566 amino acids)
>PP_4968 DNA ligase B (Pseudomonas putida KT2440) MPYLLLFALLFVLNTPLARAASCPHWNPQQAKAEVAQLRATLARWDEHYHRQGIALVADE LYDQSHERLNHLQQCFAVGTSPSPLASARGPVPHPVPHTGVDKLADRQAVARWMTGKTGV WVQPKVDGVAVSLTYQQGRLVQLTSRGDGVHGHDWSRHIPQLGAVTRQLPEAVDLHLQGE LYLRLDEHVQAKAGSANARGTVAGLLARKQLTGAQGNAIGLFVWGWPHGPEQQAERLAQL ARLGFPDSQLYSIAIDTLEDAAHWREHWYRSALPFATDGVILRQGSRPPAERWQAKAPYW IAAWKYPYAQALAEVRDVRFRVGRTGRVTPVLHVQPVTLDDRRITQVSLGSLARWQRLDI RPGDQVAISLAGLTIPRLEHVVHRAVERQPITAPAPDQHHAHSCWQASEGCDEQFIARLT WLGGKQGLALPRTGPGTWRRLVEAGLVTSMTDWLQLDAERLQQAPGISRLTATQMLGSFD QARSRPFDQWLRALGVPIGKHLPLTGNWQALASRSAGQWQTVPGIGAKRSRQLVEFFAAS EVQAIAAQLAEAGIEGFRTPPQRIEQ