(12 nodes) Nucleotide salvage network (Sordaria macrospora)

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:
	SMAC_00470	WGS project CABT00000000 data, contig 2.1. (1023 aa)
	SMAC_07177	Uridine kinase; Belongs to the uridine kinase family. (486 aa)
	SMAC_06915	WGS project CABT00000000 data, contig 2.38. (221 aa)
	SMAC_07016	WGS project CABT00000000 data, contig 2.36. (244 aa)
	SMAC_03751	WGS project CABT00000000 data, contig 2.16. (375 aa)
	SMAC_08849	WGS project CABT00000000 data, contig 2.13. (348 aa)
	SMAC_02799	WGS project CABT00000000 data, contig 2.12. (246 aa)
	SMAC_02704	WGS project CABT00000000 data, contig 2.11. (577 aa)
	SMAC_02584	WGS project CABT00000000 data, contig 2.11. (246 aa)
	SMAC_04987	WGS project CABT00000000 data, contig 2.8. (226 aa)
	SMAC_01875	WGS project CABT00000000 data, contig 2.5. (345 aa)
	SMAC_01649	WGS project CABT00000000 data, contig 2.4. (519 aa)

Your Current Organism:

Sordaria macrospora

NCBI taxonomy Id: 771870
Other names: S. macrospora k-hell, Sordaria macrospora k-hell

Send network to Cytoscape

Export your current network:

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file format is 'PNG': portable network graphic

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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:

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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
SMAC_00470	SMAC_01875	F7VL76	F7VS42	WGS project CABT00000000 data, contig 2.1.	WGS project CABT00000000 data, contig 2.5.	0.581
SMAC_00470	SMAC_04987	F7VL76	F7VUN2	WGS project CABT00000000 data, contig 2.1.	WGS project CABT00000000 data, contig 2.8.	0.980
SMAC_00470	SMAC_08849	F7VL76	F7VYP7	WGS project CABT00000000 data, contig 2.1.	WGS project CABT00000000 data, contig 2.13.	0.972
SMAC_01875	SMAC_00470	F7VS42	F7VL76	WGS project CABT00000000 data, contig 2.5.	WGS project CABT00000000 data, contig 2.1.	0.581
SMAC_01875	SMAC_04987	F7VS42	F7VUN2	WGS project CABT00000000 data, contig 2.5.	WGS project CABT00000000 data, contig 2.8.	0.721
SMAC_01875	SMAC_08849	F7VS42	F7VYP7	WGS project CABT00000000 data, contig 2.5.	WGS project CABT00000000 data, contig 2.13.	0.961
SMAC_04987	SMAC_00470	F7VUN2	F7VL76	WGS project CABT00000000 data, contig 2.8.	WGS project CABT00000000 data, contig 2.1.	0.980
SMAC_04987	SMAC_01875	F7VUN2	F7VS42	WGS project CABT00000000 data, contig 2.8.	WGS project CABT00000000 data, contig 2.5.	0.721
SMAC_04987	SMAC_08849	F7VUN2	F7VYP7	WGS project CABT00000000 data, contig 2.8.	WGS project CABT00000000 data, contig 2.13.	0.979
SMAC_07016	SMAC_07177	F7W6U8	F7W7R0	WGS project CABT00000000 data, contig 2.36.	Uridine kinase; Belongs to the uridine kinase family.	0.900
SMAC_07177	SMAC_07016	F7W7R0	F7W6U8	Uridine kinase; Belongs to the uridine kinase family.	WGS project CABT00000000 data, contig 2.36.	0.900
SMAC_08849	SMAC_00470	F7VYP7	F7VL76	WGS project CABT00000000 data, contig 2.13.	WGS project CABT00000000 data, contig 2.1.	0.972
SMAC_08849	SMAC_01875	F7VYP7	F7VS42	WGS project CABT00000000 data, contig 2.13.	WGS project CABT00000000 data, contig 2.5.	0.961
SMAC_08849	SMAC_04987	F7VYP7	F7VUN2	WGS project CABT00000000 data, contig 2.13.	WGS project CABT00000000 data, contig 2.8.	0.979