def protein (Mycoplasma californicum) - 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

def

formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology. (195 aa)

Predicted Functional Partners:

rplV

0.986

rplQ

0.984

tig

0.981

rpsT

0.981

rpsF

0.978

rpsP

0.976

rplU

0.976

rpmA

0.976

rpmB

0.976

rplI

0.975

Your Current Organism:

Mycoplasma californicum

NCBI taxonomy Id: 2113
Other names: ATCC 33461, DSM 21477, M. californicum, NCTC 10189, strain ST-6

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Export your current network:

... as a bitmap image:

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file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

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same PNG format, but at higher resolution

... as a vector graphic:

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

... as short tabular text output:

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

... as tabular text output:

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

... as an XML summary:

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

... protein node degrees:

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

... network coordinates:

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

... protein sequences:

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

... protein annotations:

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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
def	rplI	MCFN_03360	MCFN_00895	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.975
def	rplQ	MCFN_03360	MCFN_01700	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L17; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.984
def	rplU	MCFN_03360	MCFN_00835	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L21; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.976
def	rplV	MCFN_03360	MCFN_02395	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L22; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.986
def	rpmA	MCFN_03360	MCFN_00840	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L27; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.976
def	rpmB	MCFN_03360	MCFN_01020	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L28; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.976
def	rpsF	MCFN_03360	MCFN_02040	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S6.	0.978
def	rpsP	MCFN_03360	MCFN_00265	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S16; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.976
def	rpsT	MCFN_03360	MCFN_03290	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S20; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.981
def	tig	MCFN_03360	MCFN_00210	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Peptidylprolyl isomerase (trigger factor); Derived by automated computational analysis using gene prediction method: Protein Homology.	0.981
rplI	def	MCFN_00895	MCFN_03360	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	formylmethionyl-tRNA deformylase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.975
rplI	rplQ	MCFN_00895	MCFN_01700	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L17; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.998
rplI	rplU	MCFN_00895	MCFN_00835	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L21; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.998
rplI	rplV	MCFN_00895	MCFN_02395	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L22; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.998
rplI	rpmA	MCFN_00895	MCFN_00840	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L27; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.998
rplI	rpmB	MCFN_00895	MCFN_01020	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	50S ribosomal protein L28; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.997
rplI	rpsF	MCFN_00895	MCFN_02040	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S6.	0.998
rplI	rpsP	MCFN_00895	MCFN_00265	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S16; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.998
rplI	rpsT	MCFN_00895	MCFN_03290	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	30S ribosomal protein S20; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.992
rplI	tig	MCFN_00895	MCFN_00210	50S ribosomal protein L9; Derived by automated computational analysis using gene prediction method: Protein Homology.	Peptidylprolyl isomerase (trigger factor); Derived by automated computational analysis using gene prediction method: Protein Homology.	0.931