(37 nodes) (2018) The Phenylpropanoid Case - It Is Transport That Matters. network (Nicotiana tabacum)

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:
	LOC107767884	4-coumarate--CoA ligase 2-like. (549 aa)
	AN9	Glutathione S-transferase F11-like; Belongs to the GST superfamily. (229 aa)
	PDR3	Pleiotropic drug resistance protein 3; May be a general defense protein. (1447 aa)
	NtPAL	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton; Belongs to the PAL/histidase family. (712 aa)
	PALA	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton. (712 aa)
	TPA1	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton; Belongs to the PAL/histidase family. (715 aa)
	4CL2	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family. (542 aa)
	NtDFR2	Dihydroflavonol-4-reductase-like. (382 aa)
	pal4	Phenylalanine ammonia-lyase. (717 aa)
	NtFLS	Flavonol synthase/flavanone 3-hydroxylase-like; Belongs to the iron/ascorbate-dependent oxidoreductase family. (346 aa)
	NtF3H	Naringenin,2-oxoglutarate 3-dioxygenase; Belongs to the iron/ascorbate-dependent oxidoreductase family. (369 aa)
	Dfr2	Dihydroflavonol 4-reductase. (381 aa)
	LOC107831218	4-coumarate--CoA ligase 2-like. (569 aa)
	LOC107831213	Phenylalanine ammonia-lyase. (719 aa)
	LOC107826655	4-coumarate--CoA ligase-like 6 isoform X1. (565 aa)
	LOC107820497	Phenylalanine ammonia-lyase. (717 aa)
	LOC107814113	4-coumarate--CoA ligase-like 1. (551 aa)
	LOC107810554	4-coumarate--CoA ligase 2-like. (558 aa)
	LOC107806462	Naringenin,2-oxoglutarate 3-dioxygenase-like; Belongs to the iron/ascorbate-dependent oxidoreductase family. (369 aa)
	LOC107803965	4-coumarate--CoA ligase 2-like. (447 aa)
	LOC107803813	4-coumarate--CoA ligase-like 1. (551 aa)
	LOC107803673	4-coumarate--CoA ligase 1. (547 aa)
	LOC107802063	Phenylalanine ammonia-lyase. (717 aa)
	LOC107798422	4-coumarate--CoA ligase-like 7. (538 aa)
	LOC107797035	4-coumarate--CoA ligase-like 7. (538 aa)
	LOC107794811	Glutathione S-transferase; Belongs to the GST superfamily. (213 aa)
	LOC107794305	Flavonol synthase/flavanone 3-hydroxylase; Belongs to the iron/ascorbate-dependent oxidoreductase family. (338 aa)
	LOC107793030	4-coumarate--CoA ligase-like 6. (565 aa)
	LOC107792668	Phenylalanine ammonia-lyase. (712 aa)
	LOC107790326	4-coumarate--CoA ligase-like 9. (549 aa)
	LOC107787414	4-coumarate--CoA ligase-like 9. (549 aa)
	LOC107786762	Phenylalanine ammonia-lyase. (712 aa)
	LOC107761111	4-coumarate--CoA ligase 2-like. (546 aa)
	LOC107761482	Phenylalanine ammonia-lyase. (715 aa)
	LOC107766072	4-coumarate--CoA ligase 2-like. (542 aa)
	LOC107785405	4-coumarate--CoA ligase 1-like. (547 aa)
	LOC107769758	4-coumarate--CoA ligase 2-like. (571 aa)

Your Current Organism:

Nicotiana tabacum

NCBI taxonomy Id: 4097
Other names: American tobacco, N. tabacum, Nicotiana tabacum L., common tobacco, tobacco

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
4CL2	Dfr2	O24146	A3RK77	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Dihydroflavonol 4-reductase.	0.700
4CL2	LOC107761482	O24146	A0A1S3X5R5	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.917
4CL2	LOC107786762	O24146	A0A1S3ZH48	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.786
4CL2	LOC107792668	O24146	A0A1S4A1B2	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.786
4CL2	LOC107794305	O24146	A0A1S4A6K1	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Flavonol synthase/flavanone 3-hydroxylase; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.698
4CL2	LOC107802063	O24146	A0A1S4AWI6	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.913
4CL2	LOC107806462	O24146	A0A1S4BAY8	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Naringenin,2-oxoglutarate 3-dioxygenase-like; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.763
4CL2	LOC107820497	O24146	A0A1S4CMI5	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.913
4CL2	LOC107831213	O24146	A0A1S4DM00	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.929
4CL2	NtDFR2	O24146	J7MFT7	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Dihydroflavonol-4-reductase-like.	0.696
4CL2	NtF3H	O24146	A9ZMI9	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Naringenin,2-oxoglutarate 3-dioxygenase; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.802
4CL2	NtFLS	O24146	A9ZMJ0	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Flavonol synthase/flavanone 3-hydroxylase-like; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.711
4CL2	NtPAL	O24146	P45733	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton; Belongs to the PAL/histidase family.	0.933
4CL2	PALA	O24146	P35513	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.	0.922
4CL2	TPA1	O24146	P25872	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase; This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton; Belongs to the PAL/histidase family.	0.775
4CL2	pal4	O24146	C6ZIA5	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	Phenylalanine ammonia-lyase.	0.929
AN9	LOC107806462	A0A193KWR1	A0A1S4BAY8	Glutathione S-transferase F11-like; Belongs to the GST superfamily.	Naringenin,2-oxoglutarate 3-dioxygenase-like; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.509
AN9	NtF3H	A0A193KWR1	A9ZMI9	Glutathione S-transferase F11-like; Belongs to the GST superfamily.	Naringenin,2-oxoglutarate 3-dioxygenase; Belongs to the iron/ascorbate-dependent oxidoreductase family.	0.501
AN9	PDR3	A0A193KWR1	Q5W274	Glutathione S-transferase F11-like; Belongs to the GST superfamily.	Pleiotropic drug resistance protein 3; May be a general defense protein.	0.473
Dfr2	4CL2	A3RK77	O24146	Dihydroflavonol 4-reductase.	4-coumarate--CoA ligase 2; Belongs to the ATP-dependent AMP-binding enzyme family.	0.700