GDI1906 protein (Gluconacetobacter diazotrophicus)

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

GDI1906

Conserved hypothetical protein. (182 aa)

Predicted Functional Partners:

pgl-2

0.625

GDI1905

0.623

grxC

0.573

GDI1903

0.519

GDI0739

0.505

imp

0.412

Your Current Organism:

Gluconacetobacter diazotrophicus

NCBI taxonomy Id: 272568
Other names: G. diazotrophicus PA1 5, Gluconacetobacter diazotrophicus ATCC 49037, Gluconacetobacter diazotrophicus BR 11281, Gluconacetobacter diazotrophicus CCUG 37298, Gluconacetobacter diazotrophicus CIP 103539, Gluconacetobacter diazotrophicus DSM 5601, Gluconacetobacter diazotrophicus LMG 7603, Gluconacetobacter diazotrophicus NCCB 89154, Gluconacetobacter diazotrophicus PA1 5, Gluconacetobacter diazotrophicus str. PA1 5, Gluconacetobacter diazotrophicus strain PA1 5

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
GDI0739	GDI1906	GDI0739	GDI1906	Conserved hypothetical protein.	Conserved hypothetical protein.	0.505
GDI0739	imp	GDI0739	GDI3327	Conserved hypothetical protein.	Organic solvent tolerance protein precursor; Involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane; Belongs to the LptD family.	0.734
GDI1903	GDI1905	GDI1903	GDI1905	Putative phosphoribosyltransferase.	Conserved hypothetical protein.	0.654
GDI1903	GDI1906	GDI1903	GDI1906	Putative phosphoribosyltransferase.	Conserved hypothetical protein.	0.519
GDI1903	grxC	GDI1903	GDI1904	Putative phosphoribosyltransferase.	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	0.731
GDI1905	GDI1903	GDI1905	GDI1903	Conserved hypothetical protein.	Putative phosphoribosyltransferase.	0.654
GDI1905	GDI1906	GDI1905	GDI1906	Conserved hypothetical protein.	Conserved hypothetical protein.	0.623
GDI1905	grxC	GDI1905	GDI1904	Conserved hypothetical protein.	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	0.729
GDI1905	pgl-2	GDI1905	GDI1907	Conserved hypothetical protein.	Putative 6-phosphogluconolactonase.	0.510
GDI1906	GDI0739	GDI1906	GDI0739	Conserved hypothetical protein.	Conserved hypothetical protein.	0.505
GDI1906	GDI1903	GDI1906	GDI1903	Conserved hypothetical protein.	Putative phosphoribosyltransferase.	0.519
GDI1906	GDI1905	GDI1906	GDI1905	Conserved hypothetical protein.	Conserved hypothetical protein.	0.623
GDI1906	grxC	GDI1906	GDI1904	Conserved hypothetical protein.	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	0.573
GDI1906	imp	GDI1906	GDI3327	Conserved hypothetical protein.	Organic solvent tolerance protein precursor; Involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane; Belongs to the LptD family.	0.412
GDI1906	pgl-2	GDI1906	GDI1907	Conserved hypothetical protein.	Putative 6-phosphogluconolactonase.	0.625
grxC	GDI1903	GDI1904	GDI1903	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	Putative phosphoribosyltransferase.	0.731
grxC	GDI1905	GDI1904	GDI1905	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	Conserved hypothetical protein.	0.729
grxC	GDI1906	GDI1904	GDI1906	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	Conserved hypothetical protein.	0.573
grxC	pgl-2	GDI1904	GDI1907	Glutaredoxin-3; Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins.	Putative 6-phosphogluconolactonase.	0.444
imp	GDI0739	GDI3327	GDI0739	Organic solvent tolerance protein precursor; Involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane; Belongs to the LptD family.	Conserved hypothetical protein.	0.734

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

27

average node degree:

4.91

avg. local clustering coefficient:

0.895

expected number of edges:

11

PPI enrichment p-value:

1.9e-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:0006412

Translation

10 of 100

1.34

2.22

1.96e-10

GO:0009059

Macromolecule biosynthetic process

11 of 164

1.17

1.72

1.96e-10

GO:0010467

Gene expression

11 of 187

1.11

1.57

1.96e-10

GO:0044271

Cellular nitrogen compound biosynthetic process

11 of 244

1.0

1.26

1.51e-09

GO:0044238

Primary metabolic process

11 of 736

0.52

0.45

0.00011

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003735

Structural constituent of ribosome

10 of 55

1.6

3.41

7.00e-13

GO:0019843

rRNA binding

8 of 41

1.64

3.03

5.68e-10

GO:0003723

RNA binding

9 of 99

1.3

1.97

4.42e-09

GO:0070180

Large ribosomal subunit rRNA binding

2 of 2

2.34

1.08

0.0103

GO:0000049

tRNA binding

3 of 24

1.44

0.83

0.0156

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005840

Ribosome

10 of 57

1.59

3.45

1.16e-13

GO:0044391

Ribosomal subunit

4 of 14

1.8

2.22

9.87e-06

GO:0015934

Large ribosomal subunit

3 of 8

1.92

1.89

0.00012

GO:0032991

Protein-containing complex

5 of 143

0.89

0.69

0.0026

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:27330141

(2016) Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.

7 of 26

1.78

2.96

3.35e-08

PMID:28977619

(2017) The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression.

8 of 51

1.54

2.45

3.35e-08

PMID:22043294

(2011) Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes.

4 of 8

2.04

1.98

0.00011

PMID:20019804

(2009) Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis.

6 of 65

1.31

1.32

0.00015

PMID:30779773

(2019) Multiplexing polysome profiling experiments to study translation in Escherichia coli.

3 of 7

1.98

1.24

0.0040

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:95

rRNA-binding

8 of 31

1.76

3.73

1.37e-11

CL:86

Ribosome, and Translational elongation

11 of 69

1.55

3.38

1.30e-14

CL:89

Ribosome

10 of 59

1.57

3.36

2.01e-13

CL:91

Ribosome

9 of 50

1.6

3.28

4.05e-12

CL:147

Large ribosomal subunit rRNA binding, and Translation regulation

4 of 5

2.25

3.03

9.25e-07

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

llm03010

Ribosome

10 of 55

1.6

3.53

9.24e-14

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0015934

Large ribosomal subunit

5 of 10

2.04

3.23

1.01e-07

GOCC:0005840

Ribosome

8 of 45

1.59

2.87

9.60e-10

GOCC:0022625

Cytosolic large ribosomal subunit

3 of 6

2.04

1.94

0.00013

GOCC:0043229

Intracellular organelle

10 of 224

0.99

1.19

5.88e-08

GOCC:0032991

Protein-containing complex

6 of 331

0.6

0.38

0.0297

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0689

Ribosomal protein

10 of 56

1.6

3.45

2.01e-13

KW-0699

rRNA-binding

8 of 39

1.66

3.24

9.68e-11

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (18%) [HD]

Permalink

Network

Neighborhood

Experiments

Cooccurrence

Databases

Fusion

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About