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
RY70_58323S RNA-specific pseudouridylate synthase. (253 aa)    
Predicted Functional Partners:
smpB
SsrA-binding protein; Required for rescue of stalled ribosomes mediated by trans- translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to [...]
  
  
 0.731
RY70_1185
Putative Iojap protein.
  
 
 0.702
rplQ
50S ribosomal protein L17.
  
   0.686
rplU
50S ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family.
  
   0.684
RplO
50S ribosomal protein L15.
  
   0.683
rplC_1
50S ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.
   
 
 0.683
rplM_2
50S ribosomal protein L13; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.
  
 
 0.677
rplK
50S ribosomal protein L11; Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.
   
 
 0.659
rplN
50S ribosomal protein L14; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family.
   
   0.642
rplX
50S ribosomal protein L24; One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.
   
   0.634
Your Current Organism:
Bifidobacterium bifidum
NCBI taxonomy Id: 1681
Other names: AS 1.2212, ATCC 29521, Actinobacterium bifidum, Actinomyces bifidus, Actinomyces parabifidus, B. bifidum, BCRC 14615, Bacillus bifidus, Bacillus bifidus communis, Bacterium bifidum, Bacteroides bifidus, Bifidibacterium bifidum, CCRC 14615, CCRC:14615, CCUG 18364, CCUG 45217, CIP 56.7, Cohnistreptothrix bifidus, DSM 20456, IFO 14252, KCTC 3202, LMG 11041, LMG 8810, LMG:11041, LMG:8810, Lactobacillus bifidus type II, Lactobacillus parabifidus, NBRC 100015, NBRC 14252, NCFB 2715, NCIMB 702715, NCTC 13001, Nocardia bifida, Tissieria bifida, strain Ti
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