(12 nodes) RNA degradation, and HRDC domain network (Pseudomonas sp. TCUHL1)

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:
	rhlB	ATP-dependent RNA helicase RhlB; DEAD-box RNA helicase involved in RNA degradation. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. Belongs to the DEAD box helicase family. RhlB subfamily. (491 aa)
	rnd	Ribonuclease D; Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides; Belongs to the RNase D family. (375 aa)
	rhlE	DEAD/DEAH box helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. (652 aa)
	rne	Ribonuclease E; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily. (1009 aa)
	pcnB	poly(A) polymerase; Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. (468 aa)
	pnp	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (702 aa)
	rnr	Exoribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (916 aa)
	THL1_5372	GTP-binding protein. (605 aa)
	rho	Transcription termination factor Rho; Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA- dependent ATPase activity, and release of the mRNA from the DNA template. (419 aa)
	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. (239 aa)
	THL1_882	ATP-dependent helicase. (840 aa)
	THL1_904	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family. (442 aa)

Your Current Organism:

Pseudomonas sp. TCUHL1

NCBI taxonomy Id: 1856685
Other names: P. sp. TCU-HL1, Pseudomonas sp. TCU-HL1

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
THL1_5372	THL1_904	THL1_5372	THL1_904	GTP-binding protein.	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	0.586
THL1_5372	pnp	THL1_5372	THL1_4916	GTP-binding protein.	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	0.473
THL1_5372	rhlB	THL1_5372	THL1_1283	GTP-binding protein.	ATP-dependent RNA helicase RhlB; DEAD-box RNA helicase involved in RNA degradation. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. Belongs to the DEAD box helicase family. RhlB subfamily.	0.577
THL1_5372	rhlE	THL1_5372	THL1_312	GTP-binding protein.	DEAD/DEAH box helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.581
THL1_882	THL1_904	THL1_882	THL1_904	ATP-dependent helicase.	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	0.650
THL1_882	rhlB	THL1_882	THL1_1283	ATP-dependent helicase.	ATP-dependent RNA helicase RhlB; DEAD-box RNA helicase involved in RNA degradation. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. Belongs to the DEAD box helicase family. RhlB subfamily.	0.666
THL1_882	rhlE	THL1_882	THL1_312	ATP-dependent helicase.	DEAD/DEAH box helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.660
THL1_882	rnd	THL1_882	THL1_1838	ATP-dependent helicase.	Ribonuclease D; Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides; Belongs to the RNase D family.	0.869
THL1_882	rph	THL1_882	THL1_5623	ATP-dependent 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.	0.679
THL1_904	THL1_5372	THL1_904	THL1_5372	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	GTP-binding protein.	0.586
THL1_904	THL1_882	THL1_904	THL1_882	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	ATP-dependent helicase.	0.650
THL1_904	pnp	THL1_904	THL1_4916	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	0.735
THL1_904	rhlE	THL1_904	THL1_312	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	DEAD/DEAH box helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.906
THL1_904	rnd	THL1_904	THL1_1838	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	Ribonuclease D; Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides; Belongs to the RNase D family.	0.527
THL1_904	rph	THL1_904	THL1_5623	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	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.	0.469
pcnB	pnp	THL1_4900	THL1_4916	poly(A) polymerase; Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	0.835
pcnB	rne	THL1_4900	THL1_3782	poly(A) polymerase; Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.	Ribonuclease E; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily.	0.505
pcnB	rnr	THL1_4900	THL1_5201	poly(A) polymerase; Adds poly(A) tail to the 3' end of many RNAs, which usually targets these RNAs for decay. Plays a significant role in the global control of gene expression, through influencing the rate of transcript degradation, and in the general RNA quality control. Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.	Exoribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.	0.569
pnp	THL1_5372	THL1_4916	THL1_5372	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	GTP-binding protein.	0.473
pnp	THL1_904	THL1_4916	THL1_904	Polynucleotide phosphorylase/polyadenylase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	DEAD/DEAH box helicase; Belongs to the DEAD box helicase family.	0.735