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
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[Homology]
Score
Pden_2804PFAM: pseudouridine synthase; KEGG: rsp:RSP_1506 pseudouridine synthase, Rlu. (215 aa)    
Predicted Functional Partners:
Pden_2805
PFAM: Lysine exporter protein (LYSE/YGGA); KEGG: rru:Rru_A3172 lysine exporter protein (LysE/YggA).
  
    0.802
Pden_2807
KEGG: rde:RD1_0024 hypothetical protein.
       0.757
rplC
LSU ribosomal protein L3P; 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.
 
 
 
 0.696
rplM
LSU ribosomal protein L13P; 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.
 
 
 0.672
mnmE
tRNA modification GTPase trmE; Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34; Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.
 
 
 0.665
Pden_2806
PFAM: glutathione-dependent formaldehyde-activating, GFA; KEGG: sit:TM1040_0070 glutathione-dependent formaldehyde-activating, GFA.
       0.655
rplQ
PFAM: ribosomal protein L17; KEGG: rde:RD1_1438 ribosomal protein L17.
 
   0.652
rplO
LSU ribosomal protein L15P; Binds to the 23S rRNA; Belongs to the universal ribosomal protein uL15 family.
 
 
 0.649
Pden_2518
TIGRFAM: iojap-like protein; PFAM: Iojap-related protein; KEGG: rsp:RSP_0865 hypothetical protein.
  
 
 0.642
rplN
LSU ribosomal protein L14P; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family.
 
 
   0.638
Your Current Organism:
Paracoccus denitrificans
NCBI taxonomy Id: 318586
Other names: P. denitrificans PD1222, Paracoccus denitrificans PD1222
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