SFN04045.1 protein (Thermodesulforhabdus norvegica)

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

SFN04045.1

ATP-binding cassette, subfamily F, member 3. (657 aa)

Predicted Functional Partners:

rplW

0.978

rplD

0.977

rplU

0.975

rpsO

0.975

rplM

0.974

rplT

0.974

rplC

0.974

rpmA

0.973

rpsD

0.973

rplP

0.973

Your Current Organism:

Thermodesulforhabdus norvegica

NCBI taxonomy Id: 39841
Other names: DSM 9990, Desulforhabdus acetothermus, T. norvegica, Thermodesulforhabdus norvegicus, strain A8444

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
SFN04045.1	rplC	SAMN05660836_02438	SAMN05660836_02391	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	0.974
SFN04045.1	rplD	SAMN05660836_02438	SAMN05660836_02390	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L4P; Forms part of the polypeptide exit tunnel.	0.977
SFN04045.1	rplM	SAMN05660836_02438	SAMN05660836_00021	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L13P; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.	0.974
SFN04045.1	rplP	SAMN05660836_02438	SAMN05660836_02384	ATP-binding cassette, subfamily F, member 3.	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.	0.973
SFN04045.1	rplT	SAMN05660836_02438	SAMN05660836_01062	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L20P; Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.	0.974
SFN04045.1	rplU	SAMN05660836_02438	SAMN05660836_01746	ATP-binding cassette, subfamily F, member 3.	Large subunit ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family.	0.975
SFN04045.1	rplW	SAMN05660836_02438	SAMN05660836_02389	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L23P; One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome; Belongs to the universal ribosomal protein uL23 family.	0.978
SFN04045.1	rpmA	SAMN05660836_02438	SAMN05660836_01745	ATP-binding cassette, subfamily F, member 3.	LSU ribosomal protein L27P; Belongs to the bacterial ribosomal protein bL27 family.	0.973
SFN04045.1	rpsD	SAMN05660836_02438	SAMN05660836_02366	ATP-binding cassette, subfamily F, member 3.	SSU ribosomal protein S4P; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.	0.973
SFN04045.1	rpsO	SAMN05660836_02438	SAMN05660836_02353	ATP-binding cassette, subfamily F, member 3.	SSU ribosomal protein S15P; Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.	0.975
rplC	SFN04045.1	SAMN05660836_02391	SAMN05660836_02438	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	ATP-binding cassette, subfamily F, member 3.	0.974
rplC	rplD	SAMN05660836_02391	SAMN05660836_02390	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	LSU ribosomal protein L4P; Forms part of the polypeptide exit tunnel.	0.999
rplC	rplM	SAMN05660836_02391	SAMN05660836_00021	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	LSU ribosomal protein L13P; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.	0.999
rplC	rplP	SAMN05660836_02391	SAMN05660836_02384	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 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
rplC	rplT	SAMN05660836_02391	SAMN05660836_01062	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	LSU ribosomal protein L20P; Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.	0.998
rplC	rplU	SAMN05660836_02391	SAMN05660836_01746	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Large subunit ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family.	0.998
rplC	rplW	SAMN05660836_02391	SAMN05660836_02389	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	LSU ribosomal protein L23P; One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome; Belongs to the universal ribosomal protein uL23 family.	0.999
rplC	rpmA	SAMN05660836_02391	SAMN05660836_01745	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	LSU ribosomal protein L27P; Belongs to the bacterial ribosomal protein bL27 family.	0.998
rplC	rpsD	SAMN05660836_02391	SAMN05660836_02366	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	SSU ribosomal protein S4P; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.	0.998
rplC	rpsO	SAMN05660836_02391	SAMN05660836_02353	LSU ribosomal protein L3P; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	SSU ribosomal protein S15P; Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.	0.998