Protein Info for Psest_2179 in Pseudomonas stutzeri RCH2

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 854 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 3 to 160 (158 residues), 237.9 bits, see alignment E=8e-75 PF13298: LigD_N" amino acids 37 to 142 (106 residues), 149.9 bits, see alignment E=6.4e-48 PF01068: DNA_ligase_A_M" amino acids 232 to 415 (184 residues), 99.9 bits, see alignment E=4.2e-32 TIGR02779: DNA ligase D, ligase domain" amino acids 235 to 535 (301 residues), 362.6 bits, see alignment E=3.2e-112 TIGR02776: DNA ligase D" amino acids 245 to 835 (591 residues), 742.5 bits, see alignment E=8.8e-227 PF04679: DNA_ligase_A_C" amino acids 434 to 529 (96 residues), 99.5 bits, see alignment E=2.9e-32 TIGR02778: DNA ligase D, polymerase domain" amino acids 562 to 806 (245 residues), 295.3 bits, see alignment E=7.9e-92 PF21686: LigD_Prim-Pol" amino acids 579 to 828 (250 residues), 293.4 bits, see alignment E=4.1e-91 PF01896: DNA_primase_S" amino acids 681 to 800 (120 residues), 36.4 bits, see alignment E=1.8e-12

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 92% identity to psa:PST_2130)

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 L0GIZ3 at UniProt or InterPro

Protein Sequence (854 amino acids)

>Psest_2179 DNA ligase D (Pseudomonas stutzeri RCH2)
MALEDYQRMRDFAATPEPAGKARPKSRKTQALQYCIQKHDATRLHYDFRLELDGTLKSWA
IPKGPSLDPSVRRLAVHVEDHPLEYATFEGSIPAGHYGAGDVIVWDRGVWIPEGDPRDAY
RKGKLKFALEGEKLAGSWNLVRTQMDGKKEQWFLIKSRDEAARDESDYDIVAAEPDSVLS
DRTLVPRKRGAKARVAESPPSPVKAPAKQRAPRKQKEKVALDGALPAKLPESFKPQLATL
VDSVPAGDWRYEIKFDGYRMLARIDAGEVRLFTRNGHDWTAKMPQQAAALAGLGLESGWL
DGEVVVPNEEGTPDFQALQNAFEAGRSGNILYYLFDIPYLNGMDLRDVPLEQRRAALREV
LERSDSELLRFSEDFTEQPDSILESACQMKLEGLIGKRAGSTYTSKRSSSWVKIKCSNRQ
EFIIVGYTQPKGTRTGFGALLLGLHDEKGKLLYAGKVGTGFNQATLQGLHKQLKKLETDK
SPLDKAAPAADVRGAQWLKPELMCEVAYAEMTRQGVVRHSVFHGLRSDKPAEAITHERAK
PVASQTKASAARQPDSIGSARIKISNPERVIDPSSGISKIELARFYAQIAPWALPQLQNR
PLALVRAPEGITGELFFQKHADKLAIPHITQLDPALDPKHGALLVIDSVEALVGAAQMGT
IELHSWNAVAPDLEHPDRFVLDLDPDPALPWKRMLEATQLTQTLLDEIGLASFLKTSGGK
GLHIVVPLDSVHDWTEVKSFSQAIARYLAKLLPSHFSAVSGPKNRVGRIFIDYLRNSRGA
STVAPYSVRAREGLPVSVPIHREELADLKGANLWTVRNLLERLQELGDDDPWANIGTTRQ
RLTKQMRERLGVKD