STRINGSTRING
STRING protein interaction network
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.
Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
Others
textmining
co-expression
protein homology
Your Input:
Neighborhood
Gene Fusion
Cooccurrence
Coexpression
Experiments
Databases
Textmining
[Homology]
Score
rndPMID: 3041371 best DB hits: BLAST: gb:AAG56793.1; AE005403_4 (AE005403) RNase D, processes tRNA; E=2e-32 pir:A83483; ribonuclease D PA1294 [imported] - Pseudomonas; E=3e-32 swissprot:P09155; RND_ECOLI RIBONUCLEASE D (RNASE D) -----; E=7e-32 COG: PA1294; COG0349 Ribonuclease D; E=3e-33 aq_1967; COG0749 DNA polymerase I - 3'-5' exonuclease and polymerase; E=3e-08 PFAM: PF01612; 3'-5' exonuclease; E=2e-31 PF00570; HRDC domain; E=0.00016. (493 aa)    
Predicted Functional Partners:
rph
Ribonuclease PH; Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation.
   
 0.977
rtcA
RNA 3-terminal phosphate cyclase (RNA-3-phosphate cyclase); Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.
   
  0.973
rpsD
30S ribosomal protein S4; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.
   
  0.967
rpsK
30S ribosomal protein S11; Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine- Dalgarno cleft in the 70S ribosome; Belongs to the universal ribosomal protein uS11 family.
    
  0.966
rnr
Ribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.
   
 
 0.915
rpsA
30S ribosomal protein S1; PMID: 9823893 best DB hits: BLAST: gb:AAD29257.1; AF107093_2 (AF107093) ribosomal protein S1; E=3e-48 gb:AAF64246.1; (AF045481) 30S ribosomal protein S1; E=2e-45 swissprot:Q9ZD28; RS1_RICPR 30S RIBOSOMAL PROTEIN S1 -----; E=3e-45 COG: RP521; COG0539 Ribosomal protein S1; E=3e-46 PFAM: PF00575; S1 RNA binding domain; E=3.6e-06.
   
 0.883
RB2543
30S ribosomal protein S1; PMID: 10871362 best DB hits: BLAST: swissprot:Q9Z8M3; RS1_CHLPN 30S RIBOSOMAL PROTEIN S1 -----; E=1e-139 swissprot:O84100; RS1_CHLTR 30S RIBOSOMAL PROTEIN S1 -----; E=1e-138 pir:A81710; ribosomal protein S1 TC0373 [imported] - Chlamydia; E=1e-137 COG: CPn0315; COG0539 Ribosomal protein S1; E=1e-140 PFAM: PF00575; S1 RNA binding domain; E=0.0018 PF01479; S4 domain; E=0.83 PF00575; S1 RNA binding domain; E=1.4e-24.
   
 0.883
hrpB
ATP-dependent helicase; PMID: 10322435 PMID: 9862990 best DB hits: BLAST: pir:B83150; probable ATP-dependent helicase PA3961 [imported] -; E=1e-113 gb:AAC45544.1; (U49051) HelO [Sinorhizobium meliloti]; E=1e-110 pir:E82708; ATP-dependent helicase XF1229 [imported] - Xylella; E=1e-107 COG: PA3961; COG1643 HrpA-like helicases; E=1e-114 PFAM: PF00270; DEAD/DEAH box helicase; E=0.19 PF00271; Helicase conserved C-terminal; E=3.7e-12.
  
 0.883
rpsG
30S ribosomal protein S7; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA; Belongs to the universal ribosomal protein uS7 family.
  
   0.877
rplD
50S ribosomal protein L4; One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
    
  0.877
Your Current Organism:
Rhodopirellula baltica
NCBI taxonomy Id: 243090
Other names: Pirellula sp. 1, R. baltica SH 1, Rhodopirellula baltica SH 1, Rhodopirellula baltica str. SH 1, Rhodopirellula baltica strain SH 1
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