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
Textmining
[Homology]
Score
DvMF_1011PFAM: transcriptional regulator TrmB; KEGG: dde:Dde_2665 hypothetical protein. (257 aa)    
Predicted Functional Partners:
topA
DNA topoisomerase I; Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA- (5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supe [...]
   
    0.815
DvMF_1106
KEGG: dde:Dde_2556 phage uncharacterized protein-like.
  
     0.678
DvMF_2978
KEGG: dde:Dde_1354 hypothetical protein.
  
     0.631
lysA-2
Diaminopimelate decarboxylase; Specifically catalyzes the decarboxylation of meso- diaminopimelate (meso-DAP) to L-lysine.
     
 0.621
DvMF_3051
PFAM: protein of unknown function DUF88; KEGG: dde:Dde_2484 hypothetical protein.
  
     0.581
DvMF_0651
KEGG: dde:Dde_2862 hypothetical protein.
  
     0.484
DvMF_3114
KEGG: dde:Dde_2414 hypothetical protein.
 
   
 0.456
DvMF_0067
PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein; KEGG: dde:Dde_2274 reductase, iron-sulfur binding subunit, putative.
   
    0.451
DvMF_0319
PFAM: 4Fe-4S ferredoxin iron-sulfur binding domain protein; KEGG: dde:Dde_1075 iron-sulfur cluster-binding protein.
   
    0.451
DvMF_0644
KEGG: sfu:Sfum_0037 formate dehydrogenase, beta subunit, putative.
   
    0.451
Your Current Organism:
Desulfovibrio vulgaris Miyazaki
NCBI taxonomy Id: 883
Other names: D. vulgaris str. 'Miyazaki F', Desulfovibrio vulgaris (strain Miyazaki), Desulfovibrio vulgaris str. 'Miyazaki F'
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