Nodes:
Network nodes represent proteins
splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
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colored nodes:
query proteins and first shell of interactors
white nodes:
second shell of interactors
Node Content
empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
Edges:
Edges represent protein-protein associations
associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.
Knowledge-based Evidence
from curated databases
textmining
Assay-based Predictions
experimentally determined
co-expression
Genomic Predictions
gene neighborhood
gene co-occurrence
gene fusions
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[Homology]
Score
ligDCOG1793 ATP-dependent DNA ligase. (578 aa)    
Predicted Functional Partners:
ku
Hypothetical protein; With LigD forms a non-homologous end joining (NHEJ) DNA repair enzyme, which repairs dsDNA breaks with reduced fidelity. Binds linear dsDNA with 5'- and 3'- overhangs but not closed circular dsDNA nor ssDNA. Recruits and stimulates the ligase activity of LigD. Belongs to the prokaryotic Ku family.
 
  
 0.986
dnaN
DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]
   
 0.918
polA
DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.
  
 0.912
ADC48704.1
Hypothetical protein; COG1796 DNA polymerase IV (family X).
  
 0.902
ADC51801.1
COG0258 5'-3' exonuclease (including N-terminal domain of PolI).
  
 0.742
ADC51758.1
Exodeoxyribonuclease; COG0708 Exonuclease III.
  
 
 0.678
polY2
DNA polymerase IV; Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII.
  
 
 0.506
ADC51954.1
COG0420 DNA repair exonuclease.
  
 0.496
ADC51667.1
Lesion bypass phage DNA polymerase; COG0389 Nucleotidyltransferase/DNA polymerase involved in DNA repair; Belongs to the DNA polymerase type-Y family.
  
 
 0.454
ADC48787.1
Hypothetical protein; COG0419 ATPase involved in DNA repair.
   
 0.445
Your Current Organism:
Bacillus pseudofirmus
NCBI taxonomy Id: 398511
Other names: B. pseudofirmus OF4, Bacillus pseudofirmus OF4, Bacillus pseudofirmus str. OF4, Bacillus pseudofirmus strain OF4
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