rebO_3 protein (Oxobacter pfennigii) - STRING interaction network

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Known Interactions

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experimentally determined

Predicted Interactions

gene neighborhood

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gene co-occurrence

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Score

rebO_3

Flavin-dependent L-tryptophan oxidase RebO precursor. (574 aa)

Predicted Functional Partners:

puuB

0.753

KPU42185.1

0.719

rapA_1

0.682

KPU42445.1

0.589

dhaT_1

0.577

yndE_4

0.566

crtI_1

0.559

gerBC_3

0.552

KPU44577.1

0.538

KPU43765.1

0.536

Your Current Organism:

Oxobacter pfennigii

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

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
KPU42185.1	rebO_3	OXPF_39640	OXPF_16590	Putative methyltransferase.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.719
KPU42445.1	dhaT_1	OXPF_42300	OXPF_30020	Hypothetical protein.	1,3-propanediol dehydrogenase.	0.734
KPU42445.1	puuB	OXPF_42300	OXPF_26620	Hypothetical protein.	Gamma-glutamylputrescine oxidoreductase.	0.809
KPU42445.1	rebO_3	OXPF_42300	OXPF_16590	Hypothetical protein.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.589
KPU43765.1	crtI_1	OXPF_26250	OXPF_07550	2-oxoacid dehydrogenases acyltransferase (catalytic domain).	Phytoene desaturase (lycopene-forming).	0.848
KPU43765.1	rebO_3	OXPF_26250	OXPF_16590	2-oxoacid dehydrogenases acyltransferase (catalytic domain).	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.536
KPU44577.1	gerBC_3	OXPF_16600	OXPF_16630	Hypothetical protein.	Spore germination protein B3 precursor.	0.680
KPU44577.1	rebO_3	OXPF_16600	OXPF_16590	Hypothetical protein.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.538
KPU44577.1	yndE_4	OXPF_16600	OXPF_16620	Hypothetical protein.	Spore germination protein YndE.	0.680
crtI_1	KPU43765.1	OXPF_07550	OXPF_26250	Phytoene desaturase (lycopene-forming).	2-oxoacid dehydrogenases acyltransferase (catalytic domain).	0.848
crtI_1	puuB	OXPF_07550	OXPF_26620	Phytoene desaturase (lycopene-forming).	Gamma-glutamylputrescine oxidoreductase.	0.463
crtI_1	rebO_3	OXPF_07550	OXPF_16590	Phytoene desaturase (lycopene-forming).	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.559
dhaT_1	KPU42445.1	OXPF_30020	OXPF_42300	1,3-propanediol dehydrogenase.	Hypothetical protein.	0.734
dhaT_1	rebO_3	OXPF_30020	OXPF_16590	1,3-propanediol dehydrogenase.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.577
gerBC_3	KPU44577.1	OXPF_16630	OXPF_16600	Spore germination protein B3 precursor.	Hypothetical protein.	0.680
gerBC_3	rebO_3	OXPF_16630	OXPF_16590	Spore germination protein B3 precursor.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.552
gerBC_3	yndE_4	OXPF_16630	OXPF_16620	Spore germination protein B3 precursor.	Spore germination protein YndE.	0.991
puuB	KPU42445.1	OXPF_26620	OXPF_42300	Gamma-glutamylputrescine oxidoreductase.	Hypothetical protein.	0.809
puuB	crtI_1	OXPF_26620	OXPF_07550	Gamma-glutamylputrescine oxidoreductase.	Phytoene desaturase (lycopene-forming).	0.463
puuB	rebO_3	OXPF_26620	OXPF_16590	Gamma-glutamylputrescine oxidoreductase.	Flavin-dependent L-tryptophan oxidase RebO precursor.	0.753

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

44

average node degree:

8

avg. local clustering coefficient:

0.843

expected number of edges:

15

PPI enrichment p-value:

5.57e-10

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:0042351

De novo GDP-L-fucose biosynthetic process

4 of 5

3.5

4.94

1.19e-09

GO:0009226

Nucleotide-sugar biosynthetic process

5 of 44

2.65

4.68

1.19e-09

GO:1901137

Carbohydrate derivative biosynthetic process

7 of 518

1.73

3.04

6.86e-09

GO:0018130

Heterocycle biosynthetic process

7 of 983

1.45

2.04

4.44e-07

GO:0030656

Regulation of vitamin metabolic process

2 of 6

3.12

1.86

0.00044

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0050577

GDP-L-fucose synthase activity

3 of 3

3.6

3.66

2.56e-07

GO:0016853

Isomerase activity

6 of 321

1.87

2.92

1.62e-07

GO:0047918

GDP-mannose 3,5-epimerase activity

2 of 2

3.6

2.0

0.00025

GO:0003824

Catalytic activity

11 of 12906

0.53

0.43

0.00081

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:37836106

(2023) Genome and Transcriptome Analyses of Genes Involved in Ascorbate Biosynthesis in Pepper Indicate Key Genes Related to Fruit Development, Stresses, and Phytohormone Exposures.

2 of 5

3.2

0.9

0.0243

PMID:34179502

(2021) In silico analysis of glycosyltransferase 2 family genes in duckweed (Spirodela polyrhiza) and its role in salt stress tolerance.

2 of 3

3.42

0.9

0.0243

PMID:33328457

(2020) A CCAAT-binding factor, SlNFYA10, negatively regulates ascorbate accumulation by modulating the D-mannoseL-galactose pathway in tomato.

2 of 5

3.2

0.9

0.0243

PMID:32252624

(2020) Genome-wide analysis of Myo-inositol oxygenase gene family in tomato reveals their involvement in ascorbic acid accumulation.

2 of 5

3.2

0.9

0.0243

PMID:25023870

(2014) Annotation of gene function in citrus using gene expression information and co-expression networks.

2 of 3

3.42

0.9

0.0243

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:33170

De novo GDP-L-fucose biosynthetic process, and MobA-like NTP transferase domain

7 of 12

3.36

9.71

1.45e-18

CL:33172

MobA-like NTP transferase domain, and GDP-mannose 3,5-epimerase

3 of 7

3.23

3.26

1.25e-06

CL:33716

Dolichol-phosphate-mannose synthase complex, and alpha-1,3-mannosyltransferase activity

2 of 5

3.2

1.69

0.00091

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00520

Amino sugar and nucleotide sugar metabolism

9 of 297

2.08

6.09

3.02e-16

map00051

Fructose and mannose metabolism

6 of 137

2.24

4.86

3.89e-11

map00510

N-Glycan biosynthesis

2 of 76

2.02

1.14

0.0066

map00053

Ascorbate and aldarate metabolism

2 of 99

1.9

1.06

0.0088

map01100

Metabolic pathways

11 of 6275

0.84

0.92

2.79e-08

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-446219

Synthesis of substrates in N-glycan biosythesis

9 of 58

2.79

10.51

1.20e-21

MAP-446193

Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein

9 of 87

2.61

9.52

1.82e-20

MAP-446203

Asparagine N-linked glycosylation

9 of 344

2.02

5.61

1.96e-15

MAP-6787639

GDP-fucose biosynthesis

4 of 6

3.42

5.53

9.31e-11

MAP-597592

Post-translational protein modification

9 of 1407

1.4

2.38

3.26e-10

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005829

Cytosol

5 of 1060

1.27

0.93

0.0046

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0413

Isomerase

5 of 144

2.14

3.39

7.94e-08

KW-0060

Ascorbate biosynthesis

2 of 3

3.42

2.18

0.00012

KW-0511

Multifunctional enzyme

2 of 22

2.56

1.46

0.0021

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR001509

NAD-dependent epimerase/dehydratase

4 of 54

2.47

2.78

5.35e-06

IPR029044

Nucleotide-diphospho-sugar transferases

4 of 152

2.02

1.99

9.85e-05

IPR033890

GDP-mannose 3,5-epimerase

2 of 2

3.6

1.84

0.00050

IPR028614

GDP-L-fucose synthase/GDP-L-colitose synthase

2 of 2

3.6

1.84

0.00050

IPR036291

NAD(P)-binding domain superfamily

5 of 394

1.7

1.81

7.99e-05

(more ...)

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