(7 nodes) Outer membrane efflux protein network (Rhodoferax saidenbachensis)

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:
	APW41592.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (460 aa)
	APW42042.1	Channel protein TolC; Derived by automated computational analysis using gene prediction method: Protein Homology. (452 aa)
	APW42913.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (426 aa)
	APW43288.1	RND transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (492 aa)
	APW43320.1	RND transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (475 aa)
	APW43541.1	Multidrug transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (476 aa)
	APW44904.1	RND transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (457 aa)

Your Current Organism:

Rhodoferax saidenbachensis

NCBI taxonomy Id: 1484693
Other names: CCUG 57711, DSM 22694, R. saidenbachensis, Rhodoferax saidenbachensis Kaden et al. 2014, strain ED16

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

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

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

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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:

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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
APW41592.1	APW42042.1	RS694_02830	RS694_05500	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Channel protein TolC; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.908
APW41592.1	APW43541.1	RS694_02830	RS694_14030	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Multidrug transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.911
APW42042.1	APW41592.1	RS694_05500	RS694_02830	Channel protein TolC; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.908
APW42042.1	APW43541.1	RS694_05500	RS694_14030	Channel protein TolC; Derived by automated computational analysis using gene prediction method: Protein Homology.	Multidrug transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.908
APW43541.1	APW41592.1	RS694_14030	RS694_02830	Multidrug transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.911
APW43541.1	APW42042.1	RS694_14030	RS694_05500	Multidrug transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Channel protein TolC; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.908