RD1_2255 protein (Roseobacter denitrificans)

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

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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

RD1_2255

Lipoprotein, putative. (168 aa)

Predicted Functional Partners:

RD1_2256

0.731

RD1_2040

0.723

RD1_0657

0.678

RD1_1889

0.676

RD1_1944

0.653

RD1_3406

0.652

trgA

0.643

RD1_2691

0.636

RD1_3280

0.634

RD1_3975

0.633

Your Current Organism:

Roseobacter denitrificans

NCBI taxonomy Id: 375451
Other names: Erythrobacter sp. OCh114, R. denitrificans OCh 114, Roseobacter denitrificans ATCC 33942, Roseobacter denitrificans DSM 7001, Roseobacter denitrificans OCh 114, Roseobacter denitrificans str. OCh 114, Roseobacter denitrificans strain OCh 114, Roseobacter sp. OCh114

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
RD1_0657	RD1_1889	RD1_0657	RD1_1889	Hypothetical protein.	Conserved hypothetical protein.	0.462
RD1_0657	RD1_2255	RD1_0657	RD1_2255	Hypothetical protein.	Lipoprotein, putative.	0.678
RD1_0657	RD1_2691	RD1_0657	RD1_2691	Hypothetical protein.	Hypothetical protein.	0.439
RD1_0657	RD1_3406	RD1_0657	RD1_3406	Hypothetical protein.	Hypothetical protein.	0.743
RD1_0657	RD1_3975	RD1_0657	RD1_3975	Hypothetical protein.	Conserved hypothetical protein.	0.687
RD1_1889	RD1_0657	RD1_1889	RD1_0657	Conserved hypothetical protein.	Hypothetical protein.	0.462
RD1_1889	RD1_1944	RD1_1889	RD1_1944	Conserved hypothetical protein.	Peptidoglycan binding domain protein, putative.	0.770
RD1_1889	RD1_2040	RD1_1889	RD1_2040	Conserved hypothetical protein.	Hypothetical protein.	0.626
RD1_1889	RD1_2255	RD1_1889	RD1_2255	Conserved hypothetical protein.	Lipoprotein, putative.	0.676
RD1_1889	RD1_2691	RD1_1889	RD1_2691	Conserved hypothetical protein.	Hypothetical protein.	0.772
RD1_1889	RD1_3406	RD1_1889	RD1_3406	Conserved hypothetical protein.	Hypothetical protein.	0.571
RD1_1889	RD1_3975	RD1_1889	RD1_3975	Conserved hypothetical protein.	Conserved hypothetical protein.	0.691
RD1_1889	trgA	RD1_1889	RD1_2297	Conserved hypothetical protein.	Tellurite resistance protein TrgA.	0.450
RD1_1944	RD1_1889	RD1_1944	RD1_1889	Peptidoglycan binding domain protein, putative.	Conserved hypothetical protein.	0.770
RD1_1944	RD1_2040	RD1_1944	RD1_2040	Peptidoglycan binding domain protein, putative.	Hypothetical protein.	0.439
RD1_1944	RD1_2255	RD1_1944	RD1_2255	Peptidoglycan binding domain protein, putative.	Lipoprotein, putative.	0.653
RD1_1944	RD1_2691	RD1_1944	RD1_2691	Peptidoglycan binding domain protein, putative.	Hypothetical protein.	0.711
RD1_1944	RD1_3406	RD1_1944	RD1_3406	Peptidoglycan binding domain protein, putative.	Hypothetical protein.	0.573
RD1_1944	RD1_3975	RD1_1944	RD1_3975	Peptidoglycan binding domain protein, putative.	Conserved hypothetical protein.	0.697
RD1_1944	trgA	RD1_1944	RD1_2297	Peptidoglycan binding domain protein, putative.	Tellurite resistance protein TrgA.	0.529

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

14

PPI enrichment p-value:

1.11e-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:0046653

Tetrahydrofolate metabolic process

8 of 33

2.83

9.02

2.97e-18

GO:0006730

One-carbon metabolic process

8 of 54

2.62

8.18

2.62e-17

GO:0019264

Glycine biosynthetic process from serine

6 of 9

3.27

8.07

1.48e-15

GO:0006565

L-serine catabolic process

6 of 9

3.27

8.07

1.48e-15

GO:0046655

Folic acid metabolic process

6 of 11

3.18

7.92

2.29e-15

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016742

Hydroxymethyl-, formyl- and related transferase activity

7 of 20

2.99

8.45

1.12e-16

GO:0070905

Serine binding

6 of 9

3.27

8.0

1.96e-15

GO:0004372

Glycine hydroxymethyltransferase activity

6 of 9

3.27

8.0

1.96e-15

GO:0030170

Pyridoxal phosphate binding

6 of 98

2.23

4.62

1.47e-10

GO:0016741

Transferase activity, transferring one-carbon groups

8 of 365

1.79

3.8

1.96e-11

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0009570

Chloroplast stroma

4 of 558

1.3

0.81

0.0128

GO:0005739

Mitochondrion

5 of 1344

1.02

0.66

0.0128

GO:0005737

Cytoplasm

11 of 10715

0.46

0.35

0.0070

GO:0043231

Intracellular membrane-bounded organelle

10 of 11116

0.4

0.28

0.0404

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:35599880

(2022) Glycine max Homologs of DOESNT MAKE INFECTIONS 1, 2, and 3 Function to Impair Heterodera glycines Parasitism While Also Regulating Mitogen Activated Protein Kinase Expression.

6 of 14

3.08

7.22

3.98e-14

PMID:34557481

(2021) Interkingdom Comparison of Threonine Metabolism for Stem Cell Maintenance in Plants and Animals.

6 of 15

3.05

7.2

3.98e-14

PMID:24957993

(2013) Amino Acid biosynthesis pathways in diatoms.

6 of 127

2.12

3.97

2.31e-09

PMID:35033026

(2022) Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration.

2 of 10

2.75

1.26

0.0051

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:8212

Mixed, incl. Glycine metabolic process, and De novo IMP biosynthetic process

10 of 67

2.62

10.34

2.17e-22

CL:8266

De novo IMP biosynthetic process, and Serine hydroxymethyltransferase

8 of 22

3.01

10.16

4.59e-20

CL:8213

Serine family amino acid catabolic process, and De novo IMP biosynthetic process

9 of 50

2.7

9.83

1.28e-20

CL:8268

De novo IMP biosynthetic process

3 of 11

2.88

2.74

9.52e-06

CL:8294

One carbon pool by folate

2 of 5

3.05

1.55

0.0016

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

ppp00670

One carbon pool by folate

8 of 22

3.01

10.6

6.04e-21

ppp00460

Cyanoamino acid metabolism

6 of 17

3.0

7.78

2.48e-15

ppp00630

Glyoxylate and dicarboxylate metabolism

7 of 97

2.31

6.09

5.59e-14

ppp00260

Glycine, serine and threonine metabolism

6 of 71

2.37

5.55

2.89e-12

ppp01230

Biosynthesis of amino acids

6 of 258

1.81

3.33

3.01e-09

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-196757

Metabolism of folate and pterines

7 of 37

2.72

7.52

2.05e-15

MAP-196849

Metabolism of water-soluble vitamins and cofactors

7 of 177

2.05

4.47

3.32e-11

MAP-196854

Metabolism of vitamins and cofactors

7 of 201

1.99

4.27

5.28e-11

MAP-73817

Purine ribonucleoside monophosphate biosynthesis

4 of 25

2.65

3.94

3.56e-08

MAP-8956320

Nucleotide biosynthesis

4 of 29

2.59

3.83

5.10e-08

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0554

One-carbon metabolism

6 of 15

3.05

7.61

6.33e-15

KW-0663

Pyridoxal phosphate

6 of 64

2.42

5.45

7.60e-12

KW-0808

Transferase

6 of 941

1.25

1.37

3.37e-05

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00464

Serine hydroxymethyltransferase

4 of 7

3.2

4.5

6.46e-09

PF01212

Beta-eliminating lyase

2 of 12

2.67

1.06

0.0118

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR019798

Serine hydroxymethyltransferase, pyridoxal phosphate binding site

6 of 7

3.38

7.86

4.35e-15

IPR039429

Serine hydroxymethyltransferase-like domain

6 of 8

3.32

7.84

4.35e-15

IPR001085

Serine hydroxymethyltransferase

6 of 8

3.32

7.84

4.35e-15

IPR015422

Pyridoxal phosphate-dependent transferase, small domain

6 of 83

2.31

4.57

3.64e-10

IPR015424

Pyridoxal phosphate-dependent transferase

6 of 92

2.26

4.44

5.27e-10

(more ...)

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