(6 nodes) Mixed, incl. RNA helicase, DEAD-box type, Q motif, and rRNA (uridine) methyltransferase activity network (Hydrogenovibrio crunogenus)

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:
	Tcr_0230	KEGG: mca:MCA2826 hypothetical protein. (167 aa)
	rhlE	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. (445 aa)
	rlmE	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. (206 aa)
	Tcr_1015	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family. (393 aa)
	Tcr_1054	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily. (315 aa)
	map	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily. (268 aa)

Your Current Organism:

Hydrogenovibrio crunogenus

NCBI taxonomy Id: 317025
Other names: H. crunogenus XCL-2, Hydrogenovibrio crunogenus XCL-2, Thiomicrospira crunogena XCL-2

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
Tcr_0230	Tcr_1054	Tcr_0230	Tcr_1054	KEGG: mca:MCA2826 hypothetical protein.	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	0.898
Tcr_0230	map	Tcr_0230	Tcr_1286	KEGG: mca:MCA2826 hypothetical protein.	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	0.860
Tcr_1015	Tcr_1054	Tcr_1015	Tcr_1054	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	0.773
Tcr_1015	rhlE	Tcr_1015	Tcr_0779	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.903
Tcr_1015	rlmE	Tcr_1015	Tcr_0811	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	0.525
Tcr_1054	Tcr_0230	Tcr_1054	Tcr_0230	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	KEGG: mca:MCA2826 hypothetical protein.	0.898
Tcr_1054	Tcr_1015	Tcr_1054	Tcr_1015	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	0.773
Tcr_1054	map	Tcr_1054	Tcr_1286	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	0.858
Tcr_1054	rhlE	Tcr_1054	Tcr_0779	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.773
Tcr_1054	rlmE	Tcr_1054	Tcr_0811	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	0.888
map	Tcr_0230	Tcr_1286	Tcr_0230	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	KEGG: mca:MCA2826 hypothetical protein.	0.860
map	Tcr_1054	Tcr_1286	Tcr_1054	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	0.858
map	rlmE	Tcr_1286	Tcr_0811	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	0.667
rhlE	Tcr_1015	Tcr_0779	Tcr_1015	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	0.903
rhlE	Tcr_1054	Tcr_0779	Tcr_1054	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	0.773
rhlE	rlmE	Tcr_0779	Tcr_0811	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	0.525
rlmE	Tcr_1015	Tcr_0811	Tcr_1015	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	PFAM: helicase-like DEAD/DEAH box helicase-like; KEGG: vfi:VF1790 ATP-dependent RNA helicase; Belongs to the DEAD box helicase family.	0.525
rlmE	Tcr_1054	Tcr_0811	Tcr_1054	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	Ras superfamily GTP-binding protein YlqF; Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity; Belongs to the TRAFAC class YlqF/YawG GTPase family. MTG1 subfamily.	0.888
rlmE	map	Tcr_0811	Tcr_1286	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	Methionine aminopeptidase, type I; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed; Belongs to the peptidase M24A family. Methionine aminopeptidase type 1 subfamily.	0.667
rlmE	rhlE	Tcr_0811	Tcr_0779	Ribosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.	ATP-dependent RNA helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA.	0.525