AMN45620.1 protein (Steroidobacter denitrificans)

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Known Interactions

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Predicted Interactions

gene neighborhood

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Score

AMN45620.1

Nitrogen metabolism signal transduction histidine kinase NtrY. (741 aa)

Predicted Functional Partners:

AMN45621.1

0.955

AMN45619.1

0.952

AMN46598.1

0.781

fliE

0.777

AMN45618.1

0.727

AMN46612.1

0.722

AMN47352.1

0.717

AMN47974.1

0.589

AMN47977.1

0.579

AMN47982.1

0.574

Your Current Organism:

Steroidobacter denitrificans

NCBI taxonomy Id: 465721
Other names: DSM 18526, JCM 14622, S. denitrificans, Steroidobacter denitrificans Fahrbach et al. 2008, gamma proteobacterium FS-2007, strain FS

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
AMN45618.1	AMN45619.1	ACG33_00560	ACG33_00565	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	Hypothetical protein.	0.727
AMN45618.1	AMN45620.1	ACG33_00560	ACG33_00570	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	Nitrogen metabolism signal transduction histidine kinase NtrY.	0.727
AMN45618.1	AMN45621.1	ACG33_00560	ACG33_00575	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	Nitrogen assimilation regulatory protein NtrX.	0.680
AMN45618.1	AMN47974.1	ACG33_00560	ACG33_12875	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	Hypothetical protein.	0.436
AMN45619.1	AMN45618.1	ACG33_00565	ACG33_00560	Hypothetical protein.	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	0.727
AMN45619.1	AMN45620.1	ACG33_00565	ACG33_00570	Hypothetical protein.	Nitrogen metabolism signal transduction histidine kinase NtrY.	0.952
AMN45619.1	AMN45621.1	ACG33_00565	ACG33_00575	Hypothetical protein.	Nitrogen assimilation regulatory protein NtrX.	0.839
AMN45619.1	AMN47352.1	ACG33_00565	ACG33_09635	Hypothetical protein.	Hypothetical protein; Belongs to the skp family.	0.675
AMN45620.1	AMN45618.1	ACG33_00570	ACG33_00560	Nitrogen metabolism signal transduction histidine kinase NtrY.	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	0.727
AMN45620.1	AMN45619.1	ACG33_00570	ACG33_00565	Nitrogen metabolism signal transduction histidine kinase NtrY.	Hypothetical protein.	0.952
AMN45620.1	AMN45621.1	ACG33_00570	ACG33_00575	Nitrogen metabolism signal transduction histidine kinase NtrY.	Nitrogen assimilation regulatory protein NtrX.	0.955
AMN45620.1	AMN46598.1	ACG33_00570	ACG33_05695	Nitrogen metabolism signal transduction histidine kinase NtrY.	Flagellar M-ring protein FliF; The M ring may be actively involved in energy transduction. Belongs to the FliF family.	0.781
AMN45620.1	AMN46612.1	ACG33_00570	ACG33_05770	Nitrogen metabolism signal transduction histidine kinase NtrY.	Flagellar biosynthesis protein FlhF.	0.722
AMN45620.1	AMN47352.1	ACG33_00570	ACG33_09635	Nitrogen metabolism signal transduction histidine kinase NtrY.	Hypothetical protein; Belongs to the skp family.	0.717
AMN45620.1	AMN47974.1	ACG33_00570	ACG33_12875	Nitrogen metabolism signal transduction histidine kinase NtrY.	Hypothetical protein.	0.589
AMN45620.1	AMN47977.1	ACG33_00570	ACG33_12890	Nitrogen metabolism signal transduction histidine kinase NtrY.	Hypothetical protein.	0.579
AMN45620.1	AMN47982.1	ACG33_00570	ACG33_12915	Nitrogen metabolism signal transduction histidine kinase NtrY.	Hypothetical protein.	0.574
AMN45620.1	fliE	ACG33_00570	ACG33_05690	Nitrogen metabolism signal transduction histidine kinase NtrY.	Flagellar hook-basal body complex protein FliE.	0.777
AMN45621.1	AMN45618.1	ACG33_00575	ACG33_00560	Nitrogen assimilation regulatory protein NtrX.	16S rRNA methyltransferase B; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA.	0.680
AMN45621.1	AMN45619.1	ACG33_00575	ACG33_00565	Nitrogen assimilation regulatory protein NtrX.	Hypothetical protein.	0.839

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

51

average node degree:

9.27

avg. local clustering coefficient:

0.935

expected number of edges:

15

PPI enrichment p-value:

2.42e-13

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:0030522

Intracellular receptor signaling pathway

7 of 98

2.03

4.08

4.00e-10

GO:0032870

Cellular response to hormone stimulus

10 of 298

1.7

3.81

5.12e-13

GO:0009755

Hormone-mediated signaling pathway

6 of 81

2.05

3.58

1.26e-08

GO:0048384

Retinoic acid receptor signaling pathway

4 of 15

2.6

3.46

2.99e-07

GO:0033993

Response to lipid

7 of 375

1.45

2.01

5.83e-07

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0004879

Nuclear receptor activity

6 of 47

2.28

4.34

1.09e-09

GO:0016922

Nuclear receptor binding

6 of 114

1.9

3.18

3.55e-08

GO:0030374

Nuclear receptor coactivator activity

4 of 43

2.15

2.57

6.89e-06

GO:0061629

RNA polymerase II-specific DNA-binding transcription factor binding

7 of 283

1.57

2.45

7.24e-08

GO:0008134

Transcription factor binding

8 of 448

1.43

2.18

3.55e-08

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005667

Transcription regulator complex

6 of 405

1.35

1.37

0.00015

GO:0005654

Nucleoplasm

8 of 2921

0.61

0.36

0.0485

GO:0005634

Nucleus

11 of 6158

0.43

0.32

0.0148

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:20801112

(2010) Growth differentiation factor 11 signaling controls retinoic acid activity for axial vertebral development.

3 of 18

2.4

1.66

0.00079

PMID:33677245

(2021) Concentrations and endocrine disruptive potential of phthalates in marine mammals from the Norwegian Arctic.

2 of 2

3.18

1.38

0.0033

PMID:32212695

(2020) Environmental Pollutants Modulate Transcriptional Activity of Nuclear Receptors of Whales In Vitro.

2 of 2

3.18

1.38

0.0033

PMID:30681325

(2019) Perfluorinated Alkyl Acids in Hawaiian Cetaceans and Potential Biomarkers of Effect: Peroxisome Proliferator-Activated Receptor Alpha and Cytochrome P450 4A.

2 of 2

3.18

1.38

0.0033

PMID:34081971

(2021) Early-life associations between per- and polyfluoroalkyl substances and serum lipids in a longitudinal birth cohort.

2 of 4

2.88

1.37

0.0033

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:4634

NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux, and Ligand binding domain of hormone receptors

7 of 22

2.68

6.92

2.83e-14

CL:4398

Mixed, incl. Nuclear Receptor transcription pathway, and MAP kinase activation

9 of 191

1.85

4.42

3.06e-13

CL:4635

NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux, and Thyroid hormone binding

4 of 17

2.55

3.38

3.90e-07

CL:4668

Retinoic acid receptor signaling pathway, and Retinol binding

3 of 5

2.96

2.84

6.49e-06

CL:4638

NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis, and Nuclear receptor coactivator

2 of 5

2.78

1.33

0.0039

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map04919

Thyroid hormone signaling pathway

7 of 135

1.89

3.78

3.30e-10

map05200

Pathways in cancer

6 of 516

1.24

1.31

6.74e-05

map03320

PPAR signaling pathway

3 of 94

1.68

1.17

0.0036

map01522

Endocrine resistance

3 of 102

1.65

1.15

0.0036

map04915

Estrogen signaling pathway

3 of 125

1.56

1.06

0.0050

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-383280

Nuclear Receptor transcription pathway

8 of 57

2.32

6.42

1.00e-14

MAP-9006931

Signaling by Nuclear Receptors

8 of 248

1.69

3.21

3.93e-10

MAP-5362517

Signaling by Retinoic Acid

3 of 43

2.02

1.58

0.00079

MAP-9018519

Estrogen-dependent gene expression

4 of 124

1.69

1.55

0.00037

MAP-400206

Regulation of lipid metabolism by PPARalpha

3 of 52

1.94

1.47

0.0012

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005634

Nucleus

11 of 3065

0.73

0.68

1.62e-05

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0010

Activator

5 of 42

2.25

4.04

4.58e-09

KW-0805

Transcription regulation

9 of 251

1.73

3.88

9.17e-13

KW-0539

Nucleus

10 of 796

1.28

2.05

8.41e-11

KW-0675

Receptor

9 of 761

1.25

1.84

4.16e-09

KW-0238

DNA-binding

5 of 512

1.17

1.04

0.00065

(more ...)

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF16665

Unstructured region on nuclear receptor coactivator protein

3 of 3

3.18

2.79

9.00e-06

PF08832

Steroid receptor coactivator

3 of 3

3.18

2.79

9.00e-06

PF08815

Nuclear receptor coactivator

3 of 3

3.18

2.79

9.00e-06

PF16279

Domain of unknown function (DUF4927)

2 of 2

3.18

1.62

0.0012

PF14598

PAS domain

2 of 2

3.18

1.62

0.0012

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR037077

Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily

2 of 2

3.18

1.12

0.0096

IPR017426

Nuclear receptor coactivator

2 of 2

3.18

1.12

0.0096

IPR014935

Nuclear receptor coactivator, receptor-binding domain

2 of 2

3.18

1.12

0.0096

IPR014920

Nuclear receptor coactivator, Ncoa-type, interlocking

2 of 2

3.18

1.12

0.0096

IPR010011

Nuclear receptor coactivator, DUF1518

2 of 2

3.18

1.12

0.0096

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00430

Ligand binding domain of hormone receptors

6 of 45

2.3

4.65

2.22e-10

SM00399

c4 zinc finger in nuclear hormone receptors

5 of 41

2.26

3.75

2.33e-08

SM01151

This domain, which is usually found tandemly repeated, is found various receptor co-activating proteins.

3 of 3

3.18

3.28

1.12e-06

SM00091

PAS domain

3 of 28

2.21

1.93

0.00019

SM00353

Helix loop helix domain

3 of 90

1.7

1.15

0.0042

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