SYNW2179 protein (Synechococcus sp. WH 8102)

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

SYNW2179

Putative HrpA-like helicase. (839 aa)

Predicted Functional Partners:

deaD

0.948

rpsD,rps4

0.928

rps11,

0.918

rnd

0.905

rps1b,

0.836

rps1a,

0.836

rpsE,rps5

0.815

fusA

0.768

rph

0.762

rps17,

0.742

Your Current Organism:

Synechococcus sp. WH 8102

NCBI taxonomy Id: 84588
Other names: S. sp. WH 8102, Synechococcus sp. WH8102

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 proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
SYNW2179	deaD	SYNW2179	SYNW0920	Putative HrpA-like helicase.	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	0.948
SYNW2179	fusA	SYNW2179	SYNW2137	Putative HrpA-like helicase.	Elongation factor EF-G; Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome; Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.	0.768
SYNW2179	rnd	SYNW2179	SYNW2036	Putative HrpA-like helicase.	Putative ribonuclease D.	0.905
SYNW2179	rph	SYNW2179	SYNW0276	Putative HrpA-like helicase.	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.	0.762
SYNW2179	rps11,	SYNW2179	SYNW2089	Putative HrpA-like helicase.	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.	0.918
SYNW2179	rps17,	SYNW2179	SYNW2076	Putative HrpA-like helicase.	30S ribosomal protein S17; One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.	0.742
SYNW2179	rps1a,	SYNW2179	SYNW1985	Putative HrpA-like helicase.	30S ribosomal protein S1, homolog A.	0.836
SYNW2179	rps1b,	SYNW2179	SYNW1740	Putative HrpA-like helicase.	30S ribosomal protein S1 homolog B, putative Nbp1; Citation: Sugita et al. (2000) Mol. Gen. Genet. 263:655-663.	0.836
SYNW2179	rpsD,rps4	SYNW2179	SYNW1694	Putative HrpA-like helicase.	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.	0.928
SYNW2179	rpsE,rps5	SYNW2179	SYNW2083	Putative HrpA-like helicase.	30S ribosomal protein S5; With S4 and S12 plays an important role in translational accuracy; Belongs to the universal ribosomal protein uS5 family.	0.815
deaD	SYNW2179	SYNW0920	SYNW2179	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	Putative HrpA-like helicase.	0.948
deaD	fusA	SYNW0920	SYNW2137	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	Elongation factor EF-G; Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome; Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. EF-G/EF-2 subfamily.	0.957
deaD	rnd	SYNW0920	SYNW2036	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	Putative ribonuclease D.	0.765
deaD	rph	SYNW0920	SYNW0276	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	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.	0.736
deaD	rps11,	SYNW0920	SYNW2089	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	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.	0.842
deaD	rps17,	SYNW0920	SYNW2076	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	30S ribosomal protein S17; One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.	0.493
deaD	rps1a,	SYNW0920	SYNW1985	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	30S ribosomal protein S1, homolog A.	0.755
deaD	rps1b,	SYNW0920	SYNW1740	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	30S ribosomal protein S1 homolog B, putative Nbp1; Citation: Sugita et al. (2000) Mol. Gen. Genet. 263:655-663.	0.755
deaD	rpsD,rps4	SYNW0920	SYNW1694	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	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.	0.886
deaD	rpsE,rps5	SYNW0920	SYNW2083	Probable ATP-dependent RNA helicase DeaD; DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation.	30S ribosomal protein S5; With S4 and S12 plays an important role in translational accuracy; Belongs to the universal ribosomal protein uS5 family.	0.861