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
ycfD50S ribosomal protein L16 arginine hydroxylase. (374 aa)    
Predicted Functional Partners:
rplP
50S ribosomal protein L16; Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs; Belongs to the universal ribosomal protein uL16 family.
    
 
 0.713
mnmA
tRNA-specific 2-thiouridylase MnmA; Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation of s(2)U34, the first step of tRNA-mnm(5)s(2)U34 synthesis. Sulfur is provided by IscS, via a sulfur-relay system. Binds ATP and its substrate tRNAs; Belongs to the MnmA/TRMU family.
     
 0.589
hflD
High frequency lysogenization protein HflD.
  
  
 0.535
rluE
Ribosomal large subunit pseudouridine synthase E; Belongs to the pseudouridine synthase RsuA family.
 
    0.504
purB_2
Adenylosuccinate lyase; Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily.
     
 0.504
APC13417.1
Hypothetical protein.
  
     0.501
phoQ
Virulence sensor histidine kinase PhoQ.
       0.496
phoP
Virulence transcriptional regulatory protein PhoP.
       0.441
nudJ
Phosphatase NudJ; Belongs to the Nudix hydrolase family. NudJ subfamily.
       0.423
ycaO
Ribosomal protein S12 methylthiotransferase accessory factor YcaO.
 
   
 0.406
Your Current Organism:
Providencia rettgeri
NCBI taxonomy Id: 587
Other names: ATCC 29944, Bacterium rettgeri, CCUG 14804, CIP 103182, DSM 4542, LMG 3259, LMG:3259, NCTC 11801, P. rettgeri, Proteus rettgeri, Shigella rettgeri
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