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.
Node Color
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
Your Input:
Neighborhood
Gene Fusion
Co-occurrence
Co-expression
Experiments
Databases
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[Homology]
Score
Pden_3371KEGG: mes:Meso_2334 hypothetical protein. (166 aa)    
Predicted Functional Partners:
Pden_3373
Conjugation peptidase TraF, Serine peptidase, MEROPS family S26C; KEGG: mes:Meso_2333 conjugal transfer protein precursor.
 
     0.939
Pden_3374
PFAM: protein of unknown function DUF736; KEGG: mes:Meso_2332 protein of unknown function DUF736.
 
     0.903
Pden_3369
KEGG: nwi:Nwi_0845 hypothetical protein.
 
     0.864
Pden_3370
KEGG: nwi:Nwi_0846 possible replication protein A.
 
     0.839
Pden_3377
KEGG: bja:bll0044 hypothetical protein.
 
     0.833
Pden_3367
KEGG: nwi:Nwi_0844 hypothetical protein.
 
     0.808
Pden_3372
PFAM: C-5 cytosine-specific DNA methylase; KEGG: ngo:NGO1894 putative 5-methylcytosine methyltransferase; Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.
       0.778
Pden_0131
KEGG: nwi:Nwi_0845 hypothetical protein.
 
     0.775
Pden_3178
KEGG: mes:Meso_3841 putative transcriptional regulator.
 
     0.775
Pden_3187
KEGG: mes:Meso_3848 hypothetical protein.
 
     0.773
Your Current Organism:
Paracoccus denitrificans
NCBI taxonomy Id: 318586
Other names: P. denitrificans PD1222, Paracoccus denitrificans PD1222
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