GAT88622.1 protein (Paenarthrobacter nicotinovorans)

Nodes:

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splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

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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:

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Gene Fusion

Cooccurrence

Coexpression

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Databases

Textmining

[Homology]

Score

GAT88622.1

Oxidoreductase. (373 aa)

Predicted Functional Partners:

GAT88621.1

0.982

GAT87980.1

0.810

GAT88620.1

0.735

GAT88885.1

0.722

GAT87924.1

0.721

GAT88619.1

0.691

GAT89808.1

0.636

GAT87749.1

0.618

GAT87827.1

0.560

GAT88617.1

0.514

Your Current Organism:

Paenarthrobacter nicotinovorans

NCBI taxonomy Id: 29320
Other names: ATCC 49919, Arthrobacter nicotinivorans, Arthrobacter nicotinovorans, Arthrobacter oxydans DSM 420, CIP 106990, DSM 420, IFO 15511, JCM 3874, LMG 16253, LMG:16253, NBRC 15511, P. nicotinovorans

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
GAT87749.1	GAT87827.1	CVCC1112_2408	CVCC1112_2485	Sugar phosphate isomerase.	Hypothetical protein.	0.565
GAT87749.1	GAT88619.1	CVCC1112_2408	CVCC1112_3278	Sugar phosphate isomerase.	Dehydrogenase.	0.717
GAT87749.1	GAT88622.1	CVCC1112_2408	CVCC1112_3281	Sugar phosphate isomerase.	Oxidoreductase.	0.618
GAT87749.1	GAT89808.1	CVCC1112_2408	CVCC1112_4467	Sugar phosphate isomerase.	Dehydrogenase.	0.952
GAT87827.1	GAT87749.1	CVCC1112_2485	CVCC1112_2408	Hypothetical protein.	Sugar phosphate isomerase.	0.565
GAT87827.1	GAT88622.1	CVCC1112_2485	CVCC1112_3281	Hypothetical protein.	Oxidoreductase.	0.560
GAT87827.1	GAT89808.1	CVCC1112_2485	CVCC1112_4467	Hypothetical protein.	Dehydrogenase.	0.641
GAT87924.1	GAT87980.1	CVCC1112_2583	CVCC1112_2639	Glutamine amidotransferase.	Xylose isomerase.	0.540
GAT87924.1	GAT88621.1	CVCC1112_2583	CVCC1112_3280	Glutamine amidotransferase.	Hypothetical protein.	0.686
GAT87924.1	GAT88622.1	CVCC1112_2583	CVCC1112_3281	Glutamine amidotransferase.	Oxidoreductase.	0.721
GAT87980.1	GAT87924.1	CVCC1112_2639	CVCC1112_2583	Xylose isomerase.	Glutamine amidotransferase.	0.540
GAT87980.1	GAT88619.1	CVCC1112_2639	CVCC1112_3278	Xylose isomerase.	Dehydrogenase.	0.409
GAT87980.1	GAT88621.1	CVCC1112_2639	CVCC1112_3280	Xylose isomerase.	Hypothetical protein.	0.539
GAT87980.1	GAT88622.1	CVCC1112_2639	CVCC1112_3281	Xylose isomerase.	Oxidoreductase.	0.810
GAT87980.1	GAT88885.1	CVCC1112_2639	CVCC1112_3544	Xylose isomerase.	Glutamine amidotransferase.	0.553
GAT88617.1	GAT88619.1	CVCC1112_3276	CVCC1112_3278	ABC transporter.	Dehydrogenase.	0.631
GAT88617.1	GAT88620.1	CVCC1112_3276	CVCC1112_3279	ABC transporter.	AP endonuclease.	0.642
GAT88617.1	GAT88621.1	CVCC1112_3276	CVCC1112_3280	ABC transporter.	Hypothetical protein.	0.537
GAT88617.1	GAT88622.1	CVCC1112_3276	CVCC1112_3281	ABC transporter.	Oxidoreductase.	0.514
GAT88619.1	GAT87749.1	CVCC1112_3278	CVCC1112_2408	Dehydrogenase.	Sugar phosphate isomerase.	0.717

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:

20

PPI enrichment p-value:

8.9e-11

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:0000463

Maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

5 of 23

2.29

3.8

2.05e-08

GO:0006364

rRNA processing

10 of 205

1.64

3.59

3.74e-13

GO:0042254

Ribosome biogenesis

11 of 267

1.57

3.44

2.58e-14

GO:0042273

Ribosomal large subunit biogenesis

6 of 64

1.92

3.32

1.82e-08

GO:0000466

Maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

5 of 47

1.98

2.93

3.83e-07

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003723

RNA binding

8 of 537

1.13

1.22

1.78e-05

GO:0043021

Ribonucleoprotein complex binding

3 of 39

1.84

1.13

0.0059

GO:0070180

Large ribosomal subunit rRNA binding

2 of 8

2.35

0.93

0.0193

GO:0005488

Binding

11 of 4312

0.36

0.26

0.0342

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030687

Preribosome, large subunit precursor

7 of 30

2.32

5.68

7.77e-13

GO:0030684

Preribosome

8 of 89

1.91

4.38

2.91e-12

GO:0005730

Nucleolus

10 of 232

1.59

3.35

5.86e-13

GO:1990904

Ribonucleoprotein complex

10 of 436

1.31

2.16

7.08e-11

GO:0005732

sno(s)RNA-containing ribonucleoprotein complex

2 of 24

1.87

0.92

0.0169

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:4359

Preribosome, large subunit precursor, and Maturation of LSU-rRNA

7 of 30

2.32

5.55

1.64e-12

CL:4363

Preribosome, large subunit precursor, and Ribosomal protein L10

6 of 19

2.45

5.44

1.02e-11

CL:4368

Preribosome, large subunit precursor

4 of 5

2.86

4.26

1.24e-08

CL:4188

Nucleolus

9 of 149

1.73

3.84

1.72e-12

CL:4177

Ribosome biogenesis, and tRNA modification

10 of 198

1.66

3.68

2.64e-13

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03008

Ribosome biogenesis in eukaryotes

4 of 93

1.59

1.47

0.00041

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-6791226

Major pathway of rRNA processing in the nucleolus and cytosol

6 of 132

1.61

2.15

2.74e-06

MAP-8868773

rRNA processing in the nucleus and cytosol

6 of 136

1.6

2.13

2.74e-06

MAP-72312

rRNA processing

6 of 141

1.58

2.1

2.74e-06

MAP-8953854

Metabolism of RNA

8 of 553

1.11

1.28

3.44e-06

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005730

Nucleolus

5 of 120

1.57

1.85

2.10e-05

GOCC:0031981

Nuclear lumen

9 of 510

1.2

1.58

1.38e-07

GOCC:0005732

Small nucleolar ribonucleoprotein complex

2 of 21

1.93

0.87

0.0217

GOCC:0005634

Nucleus

10 of 1299

0.84

0.85

3.04e-06

GOCC:1990904

Ribonucleoprotein complex

5 of 415

1.03

0.74

0.0061

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0698

rRNA processing

3 of 19

2.15

1.77

0.00037

KW-0690

Ribosome biogenesis

3 of 21

2.11

1.76

0.00037

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR030378

Circularly permuted (CP)-type guanine nucleotide-binding (G) domain

2 of 4

2.65

0.73

0.0482

IPR023179

GTP-binding protein, orthogonal bundle domain superfamily

2 of 4

2.65

0.73

0.0482

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