(47 nodes) Pentose and glucuronate interconversions network (Amycolatopsis pretoriensis)

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:
	xylB	Xylulokinase. (476 aa)
	SEF32263.1	Sugar phosphate isomerase/epimerase. (297 aa)
	xylA	Xylose isomerase; Belongs to the xylose isomerase family. (382 aa)
	SEF33175.1	Sugar phosphate isomerase/epimerase. (273 aa)
	SEF33189.1	Aldo/keto reductase. (277 aa)
	SEF35025.1	Ribulose-phosphate 3-epimerase; Belongs to the ribulose-phosphate 3-epimerase family. (228 aa)
	SEF35662.1	Hypothetical protein. (313 aa)
	rnc	Ribonuclease-3; Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. (249 aa)
	SEF36478.1	Glycosyl hydrolases family 2, TIM barrel domain; Belongs to the glycosyl hydrolase 2 family. (831 aa)
	SEF36809.1	Chitosanase of glycosyl hydrolase group 75. (355 aa)
	SEF37050.1	Hypothetical protein. (153 aa)
	SEF37051.1	Glycosyl hydrolases family 2, TIM barrel domain. (375 aa)
	SEF36918.1	Sugar lactone lactonase YvrE. (271 aa)
	SEF37185.1	Parallel beta-helix repeat (two copies). (724 aa)
	SEF37745.1	Sugar lactone lactonase YvrE. (297 aa)
	SEF37262.1	Dihydroxy-acid dehydratase; Belongs to the IlvD/Edd family. (570 aa)
	SEF22021.1	WD40-like Beta Propeller Repeat. (1337 aa)
	SEF22350.1	Aldo/keto reductase. (257 aa)
	SEF20443.1	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family. (338 aa)
	SEF20842.1	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family. (516 aa)
	SEF20962.1	UDPglucose 6-dehydrogenase. (434 aa)
	araB	L-ribulokinase. (546 aa)
	SEF21256.1	L-ribulose-5-phosphate 4-epimerase. (225 aa)
	araA	L-arabinose isomerase; Catalyzes the conversion of L-arabinose to L-ribulose. (499 aa)
	SEF21320.1	Xylitol oxidase. (412 aa)
	SEF21327.1	Pectate lyase. (321 aa)
	SEF21350.1	Pectate lyase. (424 aa)
	SEF21352.1	Hypothetical protein. (71 aa)
	SEF21354.1	Pectate lyase. (160 aa)
	SEF21357.1	Pectinesterase/pectate lyase. (335 aa)
	SEF21558.1	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family. (369 aa)
	SEF21656.1	L-rhamnose isomerase / sugar isomerase. (388 aa)
	SEF21660.1	L-arabinose isomerase; Catalyzes the conversion of L-arabinose to L-ribulose. (473 aa)
	SEF21662.1	Rhamnulokinase. (469 aa)
	SEF25141.1	Hypothetical protein. (331 aa)
	SEF25184.1	Hypothetical protein. (87 aa)
	SEF23500.1	Glycosyl hydrolases family 2; Belongs to the glycosyl hydrolase 2 family. (937 aa)
	SEF24009.1	Gluconate 5-dehydrogenase. (242 aa)
	SEF24164.1	2-dehydro-3-deoxy-D-arabinonate dehydratase. (291 aa)
	SEF24171.1	Glycosyl hydrolases family 2; Belongs to the glycosyl hydrolase 2 family. (1044 aa)
	SEF23213.1	2,5-diketo-D-gluconate reductase A. (277 aa)
	SEF26333.1	Xylulokinase; Belongs to the FGGY kinase family. (494 aa)
	SEF27161.1	Glycosyl hydrolases family 28; Belongs to the glycosyl hydrolase 28 family. (454 aa)
	SEF27585.1	UTP--glucose-1-phosphate uridylyltransferase. (301 aa)
	SEF30253.1	FAD-linked oxidoreductase. (431 aa)
	SEF30276.1	UDPglucose 6-dehydrogenase. (434 aa)
	SEF31146.1	Chitosanase of glycosyl hydrolase group 75. (230 aa)

Your Current Organism:

Amycolatopsis pretoriensis

NCBI taxonomy Id: 218821
Other names: A. pretoriensis, Amycolatopsis pretoriensis Labeda et al. 2003, DSM 44654, JCM 12673, NRRL B-24133, strain ARC OV1 0181

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
SEF20443.1	SEF21558.1	SAMN05421837_101366	SAMN05421837_101932	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family.	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family.	0.506
SEF20443.1	SEF22350.1	SAMN05421837_101366	SAMN05421837_1011339	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family.	Aldo/keto reductase.	0.428
SEF20443.1	SEF23213.1	SAMN05421837_101366	SAMN05421837_10271	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family.	2,5-diketo-D-gluconate reductase A.	0.428
SEF20443.1	SEF33189.1	SAMN05421837_101366	SAMN05421837_106638	D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family.	Aldo/keto reductase.	0.428
SEF20842.1	SEF21327.1	SAMN05421837_101572	SAMN05421837_101816	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family.	Pectate lyase.	0.484
SEF20842.1	SEF21350.1	SAMN05421837_101572	SAMN05421837_101825	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family.	Pectate lyase.	0.484
SEF20842.1	SEF21357.1	SAMN05421837_101572	SAMN05421837_101828	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family.	Pectinesterase/pectate lyase.	0.828
SEF20842.1	SEF31146.1	SAMN05421837_101572	SAMN05421837_105605	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family.	Chitosanase of glycosyl hydrolase group 75.	0.484
SEF20842.1	SEF36809.1	SAMN05421837_101572	SAMN05421837_111230	Polygalacturonase; Belongs to the glycosyl hydrolase 28 family.	Chitosanase of glycosyl hydrolase group 75.	0.484
SEF20962.1	SEF27585.1	SAMN05421837_101641	SAMN05421837_103945	UDPglucose 6-dehydrogenase.	UTP--glucose-1-phosphate uridylyltransferase.	0.960
SEF20962.1	SEF30276.1	SAMN05421837_101641	SAMN05421837_105133	UDPglucose 6-dehydrogenase.	UDPglucose 6-dehydrogenase.	0.893
SEF20962.1	xylA	SAMN05421837_101641	SAMN05421837_106624	UDPglucose 6-dehydrogenase.	Xylose isomerase; Belongs to the xylose isomerase family.	0.639
SEF21256.1	SEF21660.1	SAMN05421837_101787	SAMN05421837_101991	L-ribulose-5-phosphate 4-epimerase.	L-arabinose isomerase; Catalyzes the conversion of L-arabinose to L-ribulose.	0.803
SEF21256.1	SEF21662.1	SAMN05421837_101787	SAMN05421837_101992	L-ribulose-5-phosphate 4-epimerase.	Rhamnulokinase.	0.750
SEF21256.1	SEF22350.1	SAMN05421837_101787	SAMN05421837_1011339	L-ribulose-5-phosphate 4-epimerase.	Aldo/keto reductase.	0.480
SEF21256.1	SEF23213.1	SAMN05421837_101787	SAMN05421837_10271	L-ribulose-5-phosphate 4-epimerase.	2,5-diketo-D-gluconate reductase A.	0.480
SEF21256.1	SEF26333.1	SAMN05421837_101787	SAMN05421837_103204	L-ribulose-5-phosphate 4-epimerase.	Xylulokinase; Belongs to the FGGY kinase family.	0.741
SEF21256.1	SEF32263.1	SAMN05421837_101787	SAMN05421837_106149	L-ribulose-5-phosphate 4-epimerase.	Sugar phosphate isomerase/epimerase.	0.488
SEF21256.1	SEF33175.1	SAMN05421837_101787	SAMN05421837_106632	L-ribulose-5-phosphate 4-epimerase.	Sugar phosphate isomerase/epimerase.	0.742
SEF21256.1	SEF33189.1	SAMN05421837_101787	SAMN05421837_106638	L-ribulose-5-phosphate 4-epimerase.	Aldo/keto reductase.	0.480