(2 nodes) (2018) Development of a strictly regulated xylose-induced expression system in Streptomyces. network (Streptomyces coelicolor)

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:
	SCO1171	SCG11A.02, possible xylose repressor, len: 402 aa; similar to SW:XYLR_BACSU (EMBL:M27248) Bacillus subtilis xylose repressor xylR, 384 aa; fasta scores: opt: 612 z-score: 642.4 E(): 2.1e-28; 29.4% identity in 381 aa overlap. Contains match to Pfam entry PF00480 ROK, ROK family and a possible helix-turn-helix motif at residues 43..64 (+3.15 SD). (402 aa)
	SCO1170	Xylulose kinase; Catalyzes the phosphorylation of D-xylulose to D-xylulose 5- phosphate; Belongs to the FGGY kinase family. (481 aa)

Your Current Organism:

Streptomyces coelicolor

NCBI taxonomy Id: 100226
Other names: S. coelicolor A3(2), Streptomyces coelicolor A3(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
SCO1170	SCO1171	gene:17758753	gene:17758754	Xylulose kinase; Catalyzes the phosphorylation of D-xylulose to D-xylulose 5- phosphate; Belongs to the FGGY kinase family.	SCG11A.02, possible xylose repressor, len: 402 aa; similar to SW:XYLR_BACSU (EMBL:M27248) Bacillus subtilis xylose repressor xylR, 384 aa; fasta scores: opt: 612 z-score: 642.4 E(): 2.1e-28; 29.4% identity in 381 aa overlap. Contains match to Pfam entry PF00480 ROK, ROK family and a possible helix-turn-helix motif at residues 43..64 (+3.15 SD).	0.924
SCO1171	SCO1170	gene:17758754	gene:17758753	SCG11A.02, possible xylose repressor, len: 402 aa; similar to SW:XYLR_BACSU (EMBL:M27248) Bacillus subtilis xylose repressor xylR, 384 aa; fasta scores: opt: 612 z-score: 642.4 E(): 2.1e-28; 29.4% identity in 381 aa overlap. Contains match to Pfam entry PF00480 ROK, ROK family and a possible helix-turn-helix motif at residues 43..64 (+3.15 SD).	Xylulose kinase; Catalyzes the phosphorylation of D-xylulose to D-xylulose 5- phosphate; Belongs to the FGGY kinase family.	0.924