APT56603.1 protein (Roseomonas gilardii) - STRING interaction network

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

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second shell of interactors

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proteins of unknown 3D structure

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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

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Score

APT56603.1

Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (686 aa)

Predicted Functional Partners:

APT57745.1

0.775

APT58059.1

0.629

APT60048.1

0.546

APT57109.1

0.538

APT58555.1

0.524

APT56957.1

0.517

APT59562.1

0.513

APT59346.1

0.501

APT58750.1

0.489

APT56677.1

0.487

Your Current Organism:

Roseomonas gilardii

NCBI taxonomy Id: 257708
Other names: ATCC 49956, CCUG 33005, CIP 104026, R. gilardii, strain 5424

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
APT56603.1	APT56677.1	RGI145_05265	RGI145_05695	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.487
APT56603.1	APT56957.1	RGI145_05265	RGI145_07460	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.517
APT56603.1	APT57109.1	RGI145_05265	RGI145_08390	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Sigma-54-dependent Fis family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.538
APT56603.1	APT57745.1	RGI145_05265	RGI145_12120	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.775
APT56603.1	APT58059.1	RGI145_05265	RGI145_13970	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.629
APT56603.1	APT58555.1	RGI145_05265	RGI145_17005	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Response regulator receiver protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.524
APT56603.1	APT58750.1	RGI145_05265	RGI145_18200	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.489
APT56603.1	APT59346.1	RGI145_05265	RGI145_14015	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hybrid sensor histidine kinase/response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
APT56603.1	APT59562.1	RGI145_05265	RGI145_19645	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Sigma-54-dependent Fis family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.513
APT56603.1	APT60048.1	RGI145_05265	RGI145_19725	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hybrid sensor histidine kinase/response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.546
APT56677.1	APT56603.1	RGI145_05695	RGI145_05265	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.487
APT56677.1	APT56957.1	RGI145_05695	RGI145_07460	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.729
APT56677.1	APT58555.1	RGI145_05695	RGI145_17005	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Response regulator receiver protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.566
APT56677.1	APT59346.1	RGI145_05695	RGI145_14015	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hybrid sensor histidine kinase/response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.749
APT56677.1	APT60048.1	RGI145_05695	RGI145_19725	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hybrid sensor histidine kinase/response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.647
APT56957.1	APT56603.1	RGI145_07460	RGI145_05265	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.517
APT56957.1	APT56677.1	RGI145_07460	RGI145_05695	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.729
APT56957.1	APT57109.1	RGI145_07460	RGI145_08390	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sigma-54-dependent Fis family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.511
APT56957.1	APT57745.1	RGI145_07460	RGI145_12120	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.909
APT56957.1	APT58059.1	RGI145_07460	RGI145_13970	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.738

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Network Stats

number of nodes:

11

number of edges:

53

average node degree:

9.64

avg. local clustering coefficient:

0.962

expected number of edges:

10

PPI enrichment p-value:

< 1.0e-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:0090087

Regulation of peptide transport

2 of 3

2.88

1.27

0.0051

GO:0050714

Positive regulation of protein secretion

2 of 2

3.06

1.27

0.0051

GO:0046952

Ketone body catabolic process

2 of 2

3.06

1.27

0.0051

GO:0019521

D-gluconate metabolic process

2 of 4

2.76

1.26

0.0051

GO:0032787

Monocarboxylic acid metabolic process

6 of 317

1.33

1.25

0.00041

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030729

acetoacetate-CoA ligase activity

2 of 2

3.06

1.2

0.0068

GO:0008260

3-oxoacid CoA-transferase activity

2 of 2

3.06

1.2

0.0068

GO:0004616

Phosphogluconate dehydrogenase (decarboxylating) activity

2 of 2

3.06

1.2

0.0068

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:12431

Valine, leucine and isoleucine degradation, and Beta oxidation of butanoyl-CoA to acetyl-CoA

4 of 32

2.15

2.24

3.76e-05

CL:14589

Pentose phosphate pathway, and Glycolytic process

4 of 44

2.02

2.15

4.12e-05

CL:14667

D-gluconate metabolic process, and Glucosamine/galactosamine-6-phosphate isomerase

2 of 5

2.66

1.5

0.0018

CL:12482

Coenzyme A transferase, and Thiolase, acyl-enzyme intermediate active site

2 of 5

2.66

1.5

0.0018

CL:14641

Pentose phosphate pathway

2 of 13

2.24

1.13

0.0078

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00650

Butanoate metabolism

4 of 35

2.12

2.65

3.99e-06

map00030

Pentose phosphate pathway

4 of 39

2.07

2.62

3.99e-06

map00280

Valine, leucine and isoleucine degradation

4 of 87

1.72

1.93

3.87e-05

map00072

Synthesis and degradation of ketone bodies

2 of 11

2.32

1.52

0.0014

map01200

Carbon metabolism

4 of 207

1.34

1.2

0.00072

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-74182

Ketone body metabolism

4 of 8

2.76

3.67

1.48e-07

MAP-77108

Utilization of Ketone Bodies

2 of 3

2.88

1.37

0.0033

MAP-77111

Synthesis of Ketone Bodies

2 of 6

2.58

1.21

0.0061

MAP-71336

Pentose phosphate pathway

2 of 22

2.02

0.72

0.0450

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0020015

Glycosome

2 of 2

3.06

1.32

0.0042

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0570

Pentose shunt

2 of 4

2.76

1.43

0.0025

KW-0521

NADP

2 of 29

1.9

0.75

0.0385

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF02502

Ribose/Galactose Isomerase

2 of 2

3.06

1.31

0.0044

PF03446

NAD binding domain of 6-phosphogluconate dehydrogenase

2 of 6

2.58

1.09

0.0103

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR036569

Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily

2 of 2

3.06

1.05

0.0126

IPR014388

3-oxoacid CoA-transferase

2 of 2

3.06

1.05

0.0126

IPR012792

3-oxoacid CoA-transferase, subunit A

2 of 2

3.06

1.05

0.0126

IPR012791

3-oxoacid CoA-transferase, subunit B

2 of 2

3.06

1.05

0.0126

IPR011860

Ribose 5-phosphate isomerase B, Actinobacteria-type

2 of 2

3.06

1.05

0.0126

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM01350

6-phosphogluconate dehydrogenase, C-terminal domain

2 of 2

3.06

1.58

0.0014

SM00882

Coenzyme A transferase

2 of 2

3.06

1.58

0.0014

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