pchR protein (Oxobacter pfennigii) - 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

pchR

Regulatory protein PchR. (315 aa)

Predicted Functional Partners:

KPU43873.1

0.936

ecfT_1

0.933

ykoD_1

0.914

irtA_1

0.862

KPU43878.1

0.824

nifJ_1

0.749

nifJ_2

0.749

gltB_2

0.747

ribBA

0.681

KPU42996.1

0.670

Your Current Organism:

Oxobacter pfennigii

NCBI taxonomy Id: 36849
Other names: ATCC 43583, Clostridium pfennigii, DSM 3222, O. pfennigii, strain V5-2

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 protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
KPU42996.1	KPU43878.1	OXPF_34270	OXPF_25830	Hypothetical protein.	Putative multidrug export ATP-binding/permease protein.	0.747
KPU42996.1	ecfT_1	OXPF_34270	OXPF_25790	Hypothetical protein.	Energy-coupling factor transporter transmembrane protein EcfT.	0.786
KPU42996.1	irtA_1	OXPF_34270	OXPF_25820	Hypothetical protein.	Iron import ATP-binding/permease protein IrtA.	0.758
KPU42996.1	pchR	OXPF_34270	OXPF_25810	Hypothetical protein.	Regulatory protein PchR.	0.670
KPU42996.1	ribBA	OXPF_34270	OXPF_21680	Hypothetical protein.	Riboflavin biosynthesis protein RibBA; Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate; In the C-terminal section; belongs to the GTP cyclohydrolase II family.	0.736
KPU42996.1	ykoD_1	OXPF_34270	OXPF_25800	Hypothetical protein.	Putative HMP/thiamine import ATP-binding protein YkoD.	0.782
KPU43873.1	KPU43878.1	OXPF_25780	OXPF_25830	Hypothetical protein.	Putative multidrug export ATP-binding/permease protein.	0.912
KPU43873.1	ecfT_1	OXPF_25780	OXPF_25790	Hypothetical protein.	Energy-coupling factor transporter transmembrane protein EcfT.	0.952
KPU43873.1	irtA_1	OXPF_25780	OXPF_25820	Hypothetical protein.	Iron import ATP-binding/permease protein IrtA.	0.914
KPU43873.1	pchR	OXPF_25780	OXPF_25810	Hypothetical protein.	Regulatory protein PchR.	0.936
KPU43873.1	ribBA	OXPF_25780	OXPF_21680	Hypothetical protein.	Riboflavin biosynthesis protein RibBA; Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate; In the C-terminal section; belongs to the GTP cyclohydrolase II family.	0.736
KPU43873.1	ykoD_1	OXPF_25780	OXPF_25800	Hypothetical protein.	Putative HMP/thiamine import ATP-binding protein YkoD.	0.950
KPU43878.1	KPU42996.1	OXPF_25830	OXPF_34270	Putative multidrug export ATP-binding/permease protein.	Hypothetical protein.	0.747
KPU43878.1	KPU43873.1	OXPF_25830	OXPF_25780	Putative multidrug export ATP-binding/permease protein.	Hypothetical protein.	0.912
KPU43878.1	ecfT_1	OXPF_25830	OXPF_25790	Putative multidrug export ATP-binding/permease protein.	Energy-coupling factor transporter transmembrane protein EcfT.	0.918
KPU43878.1	irtA_1	OXPF_25830	OXPF_25820	Putative multidrug export ATP-binding/permease protein.	Iron import ATP-binding/permease protein IrtA.	0.822
KPU43878.1	pchR	OXPF_25830	OXPF_25810	Putative multidrug export ATP-binding/permease protein.	Regulatory protein PchR.	0.824
KPU43878.1	ykoD_1	OXPF_25830	OXPF_25800	Putative multidrug export ATP-binding/permease protein.	Putative HMP/thiamine import ATP-binding protein YkoD.	0.781
ecfT_1	KPU42996.1	OXPF_25790	OXPF_34270	Energy-coupling factor transporter transmembrane protein EcfT.	Hypothetical protein.	0.786
ecfT_1	KPU43873.1	OXPF_25790	OXPF_25780	Energy-coupling factor transporter transmembrane protein EcfT.	Hypothetical protein.	0.952

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:

32

PPI enrichment p-value:

6.32e-05

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:0000103

Sulfate assimilation

4 of 8

2.53

2.87

3.84e-06

GO:0006790

Sulfur compound metabolic process

5 of 139

1.39

1.14

0.0016

GO:0019379

Sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin)

2 of 3

2.66

0.93

0.0203

GO:0070814

Hydrogen sulfide biosynthetic process

2 of 5

2.44

0.91

0.0213

GO:0042128

Nitrate assimilation

2 of 6

2.36

0.88

0.0243

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0020037

Heme binding

6 of 53

1.89

2.99

1.13e-07

GO:0043546

Molybdopterin cofactor binding

3 of 4

2.71

2.47

2.83e-05

GO:0030151

Molybdenum ion binding

3 of 5

2.61

2.39

3.62e-05

GO:0050464

Nitrate reductase (NADPH) activity

2 of 2

2.83

1.42

0.0027

GO:0004783

Sulfite reductase (NADPH) activity

2 of 2

2.83

1.42

0.0027

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0009337

Sulfite reductase complex (NADPH)

2 of 2

2.83

1.13

0.0089

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:9918

Mixed, incl. Nitrate metabolic process, and Sulfate assimilation

10 of 26

2.42

8.8

2.34e-20

CL:9920

Nitrate metabolic process, and O2/CO2 exchange in erythrocytes

5 of 10

2.53

4.57

1.30e-09

CL:9947

Sulfate assimilation

4 of 5

2.74

3.9

5.12e-08

CL:9923

Nitrate reductase activity, and Nitrate import

3 of 5

2.61

2.56

1.71e-05

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00920

Sulfur metabolism

6 of 31

2.12

4.18

6.17e-10

map01100

Metabolic pathways

9 of 1782

0.54

0.4

0.0061

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-1480926

O2/CO2 exchange in erythrocytes

2 of 6

2.36

0.71

0.0497

MAP-1237044

Erythrocytes take up carbon dioxide and release oxygen

2 of 6

2.36

0.71

0.0497

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0500

Molybdenum

3 of 6

2.53

2.49

2.21e-05

KW-0408

Iron

5 of 60

1.75

2.29

4.18e-06

KW-0349

Heme

3 of 24

1.93

1.63

0.00051

KW-0274

FAD

3 of 36

1.75

1.39

0.0012

KW-0560

Oxidoreductase

4 of 156

1.24

0.99

0.0022

(more ...)

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00175

Oxidoreductase NAD-binding domain

4 of 8

2.53

3.15

1.07e-06

PF03404

Mo-co oxidoreductase dimerisation domain

3 of 3

2.83

2.56

2.04e-05

PF00174

Oxidoreductase molybdopterin binding domain

3 of 3

2.83

2.56

2.04e-05

PF00970

Oxidoreductase FAD-binding domain

3 of 5

2.61

2.45

2.85e-05

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR001433

Oxidoreductase FAD/NAD(P)-binding

4 of 8

2.53

2.92

3.08e-06

IPR017938

Riboflavin synthase-like beta-barrel

4 of 13

2.32

2.65

7.38e-06

IPR017927

FAD-binding domain, ferredoxin reductase-type

4 of 15

2.26

2.61

8.00e-06

IPR039261

Ferredoxin-NADP reductase (FNR), nucleotide-binding domain

4 of 17

2.21

2.55

9.25e-06

IPR036374

Oxidoreductase, molybdopterin-binding domain superfamily

3 of 3

2.83

2.53

2.34e-05

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM01117

Cytochrome b5-like Heme/Steroid binding domain

3 of 21

1.99

1.47

0.0013

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (20%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About