Protein Info for PP_3260 in Pseudomonas putida KT2440

Annotation: DNA ligase D

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 833 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 5 to 160 (156 residues), 246.8 bits, see alignment E=1.5e-77 PF13298: LigD_N" amino acids 38 to 143 (106 residues), 149.1 bits, see alignment E=1.1e-47 TIGR02779: DNA ligase D, ligase domain" amino acids 219 to 520 (302 residues), 376.1 bits, see alignment E=2.4e-116 PF01068: DNA_ligase_A_M" amino acids 219 to 399 (181 residues), 100 bits, see alignment E=3.8e-32 TIGR02776: DNA ligase D" amino acids 228 to 816 (589 residues), 783.9 bits, see alignment E=2.5e-239 PF04679: DNA_ligase_A_C" amino acids 418 to 514 (97 residues), 91.5 bits, see alignment E=9.3e-30 TIGR02778: DNA ligase D, polymerase domain" amino acids 547 to 788 (242 residues), 292 bits, see alignment E=8e-91 PF21686: LigD_Prim-Pol" amino acids 562 to 812 (251 residues), 284.4 bits, see alignment E=2.3e-88 PF01896: DNA_primase_S" amino acids 663 to 782 (120 residues), 35.3 bits, see alignment E=3.9e-12

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 100% identity to ppu:PP_3260)

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)

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 Q88HU3 at UniProt or InterPro

Protein Sequence (833 amino acids)

>PP_3260 DNA ligase D (Pseudomonas putida KT2440)
MAKPLQEYARKRDFNATPEPSGKRKRGKRAHALQFCIQKHDASHLHYDFRLELDGTLKSW
AIPKGPSLDPKVRRLAVHVEDHPLDYADFEGHIPEGHYGAGDVIVWDRGIWEPEGDAHEA
YAKGKLRFRLLGEKLGGVWNLFRTHLAGKKEQWMLVKSHDAQACSETEYSIVEALPDSVL
SERTLVPCKSAAKKATAPRSSRKRADKVQAAPLPAQLQPQLATLVDSPPSGDWRYEVKFD
GYRILARIEGQDIRLFTRNGHDWSSKMPRQVAALRALGIDSAWLDGEMVVADENGMADFQ
ALQNAFDTEHDERITYYLFDLPFLGGQDLRQLPLQNRRNTLRQLLEHNHCDVIKYSADFD
EPVQSLLDSACRLKLEGLIGKRVDSVYSGRRSPDWIKLKCKQRQEFVIVGYTDPKGSRSG
FGALLLALHDNDSGQLRYAGKVGTGFNATTLASIHARLKPLEIARPALPSPPAGAEARGV
HWLRPQLLAEVAFAQMTRDGIVRHSVFHGLRDDKAATAIDLERAMPAKTVSNRNKQAKAS
ENLGELRLTHPDRVIDPTTGVTKREVAEYYAGISQWILPQLKHRPVALVRAPDGLGGELF
FQKNAGQLYIPNVLSYEKAEAGQAAMVINRADTLLGAVQMNMLELHTWNATDKDFDKPDR
FVLDLDPDPALPWKAMVEATQLTLTLLDELGLKVFLKTSGGKGIHVVVPLTRRAGWDEVK
DFSHAIVNYLAKLFPERLSAVSGPKNRVGRIFIDYLRNGKGATTACAYSLRARDGLPVSV
PIWREELAQIKAANQWNITNLHEHLAEVDDPWADMGKVRQSITARMRKQLGLE