GCA_001559865_01025 protein (Abyssisolibacter fermentans)

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.

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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

GCA_001559865_01025

Unannotated protein. (321 aa)

Predicted Functional Partners:

GCA_001559865_03017

0.961

GCA_001559865_02304

0.946

GCA_001559865_03313

0.946

GCA_001559865_03367

0.927

GCA_001559865_03335

0.922

GCA_001559865_02305

0.907

GCA_001559865_00120

0.891

GCA_001559865_00251

0.878

GCA_001559865_01516

0.876

GCA_001559865_00640

0.870

Your Current Organism:

Abyssisolibacter fermentans

NCBI taxonomy Id: 1766203
Other names: A. fermentans, Clostridiales bacterium MCWD3, KCTC 15524, strain MCWD3

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Browse interactions in tabular form:

node1	node2	node1 annotation	node2 annotation	score
GCA_001559865_00120	GCA_001559865_00251	Unannotated protein.	Unannotated protein.	0.770
GCA_001559865_00120	GCA_001559865_00640	Unannotated protein.	Unannotated protein.	0.965
GCA_001559865_00120	GCA_001559865_01025	Unannotated protein.	Unannotated protein.	0.891
GCA_001559865_00120	GCA_001559865_03335	Unannotated protein.	Unannotated protein.	0.972
GCA_001559865_00251	GCA_001559865_00120	Unannotated protein.	Unannotated protein.	0.770
GCA_001559865_00251	GCA_001559865_00640	Unannotated protein.	Unannotated protein.	0.568
GCA_001559865_00251	GCA_001559865_01025	Unannotated protein.	Unannotated protein.	0.878
GCA_001559865_00251	GCA_001559865_03335	Unannotated protein.	Unannotated protein.	0.547
GCA_001559865_00640	GCA_001559865_00120	Unannotated protein.	Unannotated protein.	0.965
GCA_001559865_00640	GCA_001559865_00251	Unannotated protein.	Unannotated protein.	0.568
GCA_001559865_00640	GCA_001559865_01025	Unannotated protein.	Unannotated protein.	0.870
GCA_001559865_00640	GCA_001559865_01516	Unannotated protein.	Unannotated protein.	0.788
GCA_001559865_00640	GCA_001559865_03017	Unannotated protein.	Unannotated protein.	0.576
GCA_001559865_00640	GCA_001559865_03335	Unannotated protein.	Unannotated protein.	0.951
GCA_001559865_01025	GCA_001559865_00120	Unannotated protein.	Unannotated protein.	0.891
GCA_001559865_01025	GCA_001559865_00251	Unannotated protein.	Unannotated protein.	0.878
GCA_001559865_01025	GCA_001559865_00640	Unannotated protein.	Unannotated protein.	0.870
GCA_001559865_01025	GCA_001559865_01516	Unannotated protein.	Unannotated protein.	0.876
GCA_001559865_01025	GCA_001559865_02304	Unannotated protein.	Unannotated protein.	0.946
GCA_001559865_01025	GCA_001559865_02305	Unannotated protein.	Unannotated protein.	0.907

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

36

average node degree:

6.55

avg. local clustering coefficient:

0.876

expected number of edges:

11

PPI enrichment p-value:

1.44e-09

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:0046395

Carboxylic acid catabolic process

6 of 155

1.71

2.25

3.69e-06

GO:0044282

Small molecule catabolic process

7 of 235

1.6

2.24

1.00e-06

GO:0009063

Cellular amino acid catabolic process

4 of 77

1.84

1.69

0.00029

GO:0006520

Cellular amino acid metabolic process

5 of 205

1.51

1.45

0.00029

GO:0019752

Carboxylic acid metabolic process

7 of 555

1.22

1.28

7.10e-05

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016405

CoA-ligase activity

3 of 15

2.42

1.69

0.00070

GO:0016878

Acid-thiol ligase activity

3 of 22

2.26

1.59

0.00098

GO:0050218

propionate-CoA ligase activity

2 of 2

3.12

1.54

0.0017

GO:0003987

acetate-CoA ligase activity

2 of 2

3.12

1.54

0.0017

GO:0016491

Oxidoreductase activity

6 of 600

1.12

0.92

0.0017

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005739

Mitochondrion

10 of 1137

1.07

1.31

1.27e-07

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:18031

Valine, leucine and isoleucine degradation, and Peroxisomal lipid metabolism

8 of 80

2.12

5.23

6.40e-13

CL:18143

Aldehyde dehydrogenase family, and Branched-chain amino acid catabolism

5 of 15

2.65

4.71

1.01e-09

CL:18145

Degradation of GABA, and Phytol metabolic process

3 of 5

2.9

2.75

9.32e-06

CL:18032

Fatty acid beta-oxidation, and Biotin transport and metabolism

3 of 55

1.86

1.19

0.0043

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00280

Valine, leucine and isoleucine degradation

7 of 53

2.24

5.4

1.55e-12

map00640

Propanoate metabolism

4 of 35

2.18

2.87

1.63e-06

map00410

beta-Alanine metabolism

3 of 31

2.11

1.93

0.00016

map00380

Tryptophan metabolism

3 of 44

1.96

1.73

0.00033

map00250

Alanine, aspartate and glutamate metabolism

3 of 43

1.97

1.73

0.00033

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-71384

Ethanol oxidation

2 of 5

2.73

1.13

0.0089

MAP-1430728

Metabolism

10 of 1828

0.86

0.85

1.56e-05

MAP-71291

Metabolism of amino acids and derivatives

4 of 252

1.32

0.79

0.0152

MAP-211945

Phase I - Functionalization of compounds

3 of 105

1.58

0.78

0.0257

MAP-70895

Branched-chain amino acid catabolism

2 of 20

2.12

0.76

0.0390

(more ...)

Tissue Expression (TISSUES)

tissue

description

count in network

strength

signal

false discovery rate

BTO:0000759

Liver

5 of 504

1.12

0.6

0.0336

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005739

Mitochondrion

9 of 637

1.27

1.79

5.05e-08

GOCC:0005737

Cytoplasm

10 of 4348

0.48

0.32

0.0360

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0560

Oxidoreductase

4 of 157

1.53

1.25

0.0014

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF13193

AMP-binding enzyme C-terminal domain

3 of 10

2.6

2.05

0.00016

PF00501

AMP-binding enzyme

3 of 21

2.28

1.72

0.00056

PF16177

Acetyl-coenzyme A synthetase N-terminus

2 of 2

3.12

1.52

0.0018

PF00202

Aminotransferase class-III

2 of 5

2.73

1.28

0.0048

PF00171

Aldehyde dehydrogenase family

2 of 16

2.22

0.84

0.0276

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR025110

AMP-binding enzyme, C-terminal domain

3 of 11

2.56

1.78

0.00053

IPR045851

AMP-binding enzyme, C-terminal domain superfamily

3 of 12

2.52

1.77

0.00053

IPR042099

ANL, N-terminal domain

3 of 13

2.49

1.77

0.00053

IPR020845

AMP-binding, conserved site

3 of 12

2.52

1.77

0.00053

IPR000873

AMP-dependent synthetase/ligase domain

3 of 13

2.49

1.77

0.00053

(more ...)

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