cynR2 protein (Komagataeibacter europaeus) - STRING interaction network

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:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

cynR2

HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family. (322 aa)

Predicted Functional Partners:

cynR5

0.763

yofA2

0.761

gltC4

0.755

hcaR

0.753

gltR

0.753

gltC5

0.750

benM2

0.750

oxyR3

0.748

cynR4

0.747

cmpR

0.738

Your Current Organism:

Komagataeibacter europaeus

NCBI taxonomy Id: 33995
Other names: ATCC 51845, Acetobacter europaeus, DSM 6160, Gluconacetobacter europaeus, K. europaeus, LMG 18890, LMG:18890, strain DES 11

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 protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
benM2	cynR2	KOEU_31090	KOEU_05460	HTH-type transcriptional regulator BenM; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.750
benM2	gltR	KOEU_31090	KOEU_29410	HTH-type transcriptional regulator BenM; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator GltR; Belongs to the LysR transcriptional regulatory family.	0.768
benM2	yofA2	KOEU_31090	KOEU_31690	HTH-type transcriptional regulator BenM; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator YofA; Belongs to the LysR transcriptional regulatory family.	0.758
cmpR	cynR2	KOEU_01390	KOEU_05460	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.738
cmpR	cynR4	KOEU_01390	KOEU_18320	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.764
cmpR	gltR	KOEU_01390	KOEU_29410	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator GltR; Belongs to the LysR transcriptional regulatory family.	0.770
cmpR	yofA2	KOEU_01390	KOEU_31690	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator YofA; Belongs to the LysR transcriptional regulatory family.	0.754
cynR2	benM2	KOEU_05460	KOEU_31090	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator BenM; Belongs to the LysR transcriptional regulatory family.	0.750
cynR2	cmpR	KOEU_05460	KOEU_01390	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	0.738
cynR2	cynR4	KOEU_05460	KOEU_18320	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.747
cynR2	cynR5	KOEU_05460	KOEU_18450	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.763
cynR2	gltC4	KOEU_05460	KOEU_14220	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator GltC; Belongs to the LysR transcriptional regulatory family.	0.755
cynR2	gltC5	KOEU_05460	KOEU_24110	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator GltC; Belongs to the LysR transcriptional regulatory family.	0.750
cynR2	gltR	KOEU_05460	KOEU_29410	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator GltR; Belongs to the LysR transcriptional regulatory family.	0.753
cynR2	hcaR	KOEU_05460	KOEU_10810	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	Hca operon transcriptional activator; Belongs to the LysR transcriptional regulatory family.	0.753
cynR2	oxyR3	KOEU_05460	KOEU_24210	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	Hydrogen peroxide-inducible activator protein; Belongs to the LysR transcriptional regulatory family.	0.748
cynR2	yofA2	KOEU_05460	KOEU_31690	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator YofA; Belongs to the LysR transcriptional regulatory family.	0.761
cynR4	cmpR	KOEU_18320	KOEU_01390	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional activator CmpR; Belongs to the LysR transcriptional regulatory family.	0.764
cynR4	cynR2	KOEU_18320	KOEU_05460	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.747
cynR4	cynR5	KOEU_18320	KOEU_18450	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	HTH-type transcriptional regulator CynR; Belongs to the LysR transcriptional regulatory family.	0.771

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

14

PPI enrichment p-value:

1.11e-16

your network has significantly more interactions
than expected (what does that mean?)

Functional enrichments in your networkNote: some enrichments may be expected here (why?)
disable highlight explain columns

Biological Process (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0046653

Tetrahydrofolate metabolic process

8 of 33

2.83

9.02

2.97e-18

GO:0006730

One-carbon metabolic process

8 of 54

2.62

8.18

2.62e-17

GO:0019264

Glycine biosynthetic process from serine

6 of 9

3.27

8.07

1.48e-15

GO:0006565

L-serine catabolic process

6 of 9

3.27

8.07

1.48e-15

GO:0046655

Folic acid metabolic process

6 of 11

3.18

7.92

2.29e-15

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016742

Hydroxymethyl-, formyl- and related transferase activity

7 of 20

2.99

8.45

1.12e-16

GO:0070905

Serine binding

6 of 9

3.27

8.0

1.96e-15

GO:0004372

Glycine hydroxymethyltransferase activity

6 of 9

3.27

8.0

1.96e-15

GO:0030170

Pyridoxal phosphate binding

6 of 98

2.23

4.62

1.47e-10

GO:0016741

Transferase activity, transferring one-carbon groups

8 of 365

1.79

3.8

1.96e-11

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0009570

Chloroplast stroma

4 of 558

1.3

0.81

0.0128

GO:0005739

Mitochondrion

5 of 1344

1.02

0.66

0.0128

GO:0005737

Cytoplasm

11 of 10715

0.46

0.35

0.0070

GO:0043231

Intracellular membrane-bounded organelle

10 of 11116

0.4

0.28

0.0404

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:35599880

(2022) Glycine max Homologs of DOESNT MAKE INFECTIONS 1, 2, and 3 Function to Impair Heterodera glycines Parasitism While Also Regulating Mitogen Activated Protein Kinase Expression.

6 of 14

3.08

7.22

3.98e-14

PMID:34557481

(2021) Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals.

6 of 15

3.05

7.2

3.98e-14

PMID:24957993

(2013) Amino Acid biosynthesis pathways in diatoms.

6 of 127

2.12

3.97

2.31e-09

PMID:35033026

(2022) Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration.

2 of 10

2.75

1.26

0.0051

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:8212

Mixed, incl. Glycine metabolic process, and De novo IMP biosynthetic process

10 of 67

2.62

10.34

2.17e-22

CL:8266

De novo IMP biosynthetic process, and Serine hydroxymethyltransferase

8 of 22

3.01

10.16

4.59e-20

CL:8213

Serine family amino acid catabolic process, and De novo IMP biosynthetic process

9 of 50

2.7

9.83

1.28e-20

CL:8268

De novo IMP biosynthetic process

3 of 11

2.88

2.74

9.52e-06

CL:8294

One carbon pool by folate

2 of 5

3.05

1.55

0.0016

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

ppp00670

One carbon pool by folate

8 of 22

3.01

10.6

6.04e-21

ppp00460

Cyanoamino acid metabolism

6 of 17

3.0

7.78

2.48e-15

ppp00630

Glyoxylate and dicarboxylate metabolism

7 of 97

2.31

6.09

5.59e-14

ppp00260

Glycine, serine and threonine metabolism

6 of 71

2.37

5.55

2.89e-12

ppp01230

Biosynthesis of amino acids

6 of 258

1.81

3.33

3.01e-09

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-196757

Metabolism of folate and pterines

7 of 37

2.72

7.52

2.05e-15

MAP-196849

Metabolism of water-soluble vitamins and cofactors

7 of 177

2.05

4.47

3.32e-11

MAP-196854

Metabolism of vitamins and cofactors

7 of 201

1.99

4.27

5.28e-11

MAP-73817

Purine ribonucleoside monophosphate biosynthesis

4 of 25

2.65

3.94

3.56e-08

MAP-8956320

Nucleotide biosynthesis

4 of 29

2.59

3.83

5.10e-08

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0554

One-carbon metabolism

6 of 15

3.05

7.61

6.33e-15

KW-0663

Pyridoxal phosphate

6 of 64

2.42

5.45

7.60e-12

KW-0808

Transferase

6 of 941

1.25

1.37

3.37e-05

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00464

Serine hydroxymethyltransferase

4 of 7

3.2

4.5

6.46e-09

PF01212

Beta-eliminating lyase

2 of 12

2.67

1.06

0.0118

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR019798

Serine hydroxymethyltransferase, pyridoxal phosphate binding site

6 of 7

3.38

7.86

4.35e-15

IPR039429

Serine hydroxymethyltransferase-like domain

6 of 8

3.32

7.84

4.35e-15

IPR001085

Serine hydroxymethyltransferase

6 of 8

3.32

7.84

4.35e-15

IPR015422

Pyridoxal phosphate-dependent transferase, small domain

6 of 83

2.31

4.57

3.64e-10

IPR015424

Pyridoxal phosphate-dependent transferase

6 of 92

2.26

4.44

5.27e-10

(more ...)

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (22%) [HD]

Permalink

Network

Cooccurrence

Experiments

Neighborhood

Databases

Fusion

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About