SDD05293.1 protein (Peptococcus niger) - STRING 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

SDD05293.1

Helix-turn-helix domain-containing protein. (152 aa)

Predicted Functional Partners:

rpmC

0.799

rplB

0.790

rpsE

0.790

rpsJ

0.789

rpsS

0.781

rpsC

0.781

rplX

0.781

rpsB

0.781

rpsM

0.777

rplP

0.776

Your Current Organism:

Peptococcus niger

NCBI taxonomy Id: 2741
Other names: ATCC 27731, DSM 20475, JCM 6506, Micrococcus niger, NCTC 11805, P. niger, VPI 7953

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
SDD05293.1	rplB	SAMN04489866_10156	SAMN04489866_102115	Helix-turn-helix domain-containing protein.	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	0.790
SDD05293.1	rplP	SAMN04489866_10156	SAMN04489866_102119	Helix-turn-helix domain-containing protein.	LSU ribosomal protein L16P; 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.	0.776
SDD05293.1	rplX	SAMN04489866_10156	SAMN04489866_102123	Helix-turn-helix domain-containing protein.	LSU ribosomal protein L24P; One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.	0.781
SDD05293.1	rpmC	SAMN04489866_10156	SAMN04489866_102120	Helix-turn-helix domain-containing protein.	LSU ribosomal protein L29P; Belongs to the universal ribosomal protein uL29 family.	0.799
SDD05293.1	rpsB	SAMN04489866_10156	SAMN04489866_11012	Helix-turn-helix domain-containing protein.	SSU ribosomal protein S2P; Belongs to the universal ribosomal protein uS2 family.	0.781
SDD05293.1	rpsC	SAMN04489866_10156	SAMN04489866_102118	Helix-turn-helix domain-containing protein.	SSU ribosomal protein S3P; Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation; Belongs to the universal ribosomal protein uS3 family.	0.781
SDD05293.1	rpsE	SAMN04489866_10156	SAMN04489866_102129	Helix-turn-helix domain-containing protein.	SSU ribosomal protein S5P; Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Belongs to the universal ribosomal protein uS5 family.	0.790
SDD05293.1	rpsJ	SAMN04489866_10156	SAMN04489866_102111	Helix-turn-helix domain-containing protein.	SSU ribosomal protein S10P; Involved in the binding of tRNA to the ribosomes. Belongs to the universal ribosomal protein uS10 family.	0.789
SDD05293.1	rpsM	SAMN04489866_10156	SAMN04489866_102136	Helix-turn-helix domain-containing protein.	Small subunit ribosomal protein S13; Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Belongs to the universal ribosomal protein uS13 family.	0.777
SDD05293.1	rpsS	SAMN04489866_10156	SAMN04489866_102116	Helix-turn-helix domain-containing protein.	SSU ribosomal protein S19P; Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.	0.781
rplB	SDD05293.1	SAMN04489866_102115	SAMN04489866_10156	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	Helix-turn-helix domain-containing protein.	0.790
rplB	rplP	SAMN04489866_102115	SAMN04489866_102119	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	LSU ribosomal protein L16P; 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.	0.999
rplB	rplX	SAMN04489866_102115	SAMN04489866_102123	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	LSU ribosomal protein L24P; One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.	0.999
rplB	rpmC	SAMN04489866_102115	SAMN04489866_102120	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	LSU ribosomal protein L29P; Belongs to the universal ribosomal protein uL29 family.	0.999
rplB	rpsB	SAMN04489866_102115	SAMN04489866_11012	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	SSU ribosomal protein S2P; Belongs to the universal ribosomal protein uS2 family.	0.998
rplB	rpsC	SAMN04489866_102115	SAMN04489866_102118	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	SSU ribosomal protein S3P; Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation; Belongs to the universal ribosomal protein uS3 family.	0.999
rplB	rpsE	SAMN04489866_102115	SAMN04489866_102129	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	SSU ribosomal protein S5P; Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Belongs to the universal ribosomal protein uS5 family.	0.999
rplB	rpsJ	SAMN04489866_102115	SAMN04489866_102111	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	SSU ribosomal protein S10P; Involved in the binding of tRNA to the ribosomes. Belongs to the universal ribosomal protein uS10 family.	0.999
rplB	rpsM	SAMN04489866_102115	SAMN04489866_102136	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	Small subunit ribosomal protein S13; Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Belongs to the universal ribosomal protein uS13 family.	0.999
rplB	rpsS	SAMN04489866_102115	SAMN04489866_102116	LSU ribosomal protein L2P; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family.	SSU ribosomal protein S19P; Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.	0.999