EPD33883.1 protein (Propionimicrobium lymphophilum)

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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

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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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[Homology]

Score

EPD33883.1

Hypothetical protein. (209 aa)

Predicted Functional Partners:

EPD32077.1

0.693

EPD32305.1

0.693

EPD33882.1

0.555

EPD33881.1

0.554

EPD32640.1

0.462

EPD33938.1

0.450

menC

0.429

EPD33880.1

0.417

nnrE

0.410

EPD33463.1

0.408

Your Current Organism:

Propionimicrobium lymphophilum

NCBI taxonomy Id: 883161
Other names: P. lymphophilum ACS-093-V-SCH5, Propionimicrobium lymphophilum ACS-093-V-SCH5

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
EPD32077.1	EPD32305.1	HMPREF9306_01641	HMPREF9306_01874	Hypothetical protein.	Hypothetical protein.	0.773
EPD32077.1	EPD32640.1	HMPREF9306_01641	HMPREF9306_01339	Hypothetical protein.	Hypothetical protein.	0.499
EPD32077.1	EPD33883.1	HMPREF9306_01641	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.693
EPD32077.1	EPD33938.1	HMPREF9306_01641	HMPREF9306_00163	Hypothetical protein.	Hypothetical protein.	0.742
EPD32077.1	menC	HMPREF9306_01641	HMPREF9306_02017	Hypothetical protein.	Hypothetical protein; Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB).	0.468
EPD32305.1	EPD32077.1	HMPREF9306_01874	HMPREF9306_01641	Hypothetical protein.	Hypothetical protein.	0.773
EPD32305.1	EPD32640.1	HMPREF9306_01874	HMPREF9306_01339	Hypothetical protein.	Hypothetical protein.	0.499
EPD32305.1	EPD33883.1	HMPREF9306_01874	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.693
EPD32305.1	EPD33938.1	HMPREF9306_01874	HMPREF9306_00163	Hypothetical protein.	Hypothetical protein.	0.742
EPD32305.1	menC	HMPREF9306_01874	HMPREF9306_02017	Hypothetical protein.	Hypothetical protein; Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB).	0.468
EPD32640.1	EPD32077.1	HMPREF9306_01339	HMPREF9306_01641	Hypothetical protein.	Hypothetical protein.	0.499
EPD32640.1	EPD32305.1	HMPREF9306_01339	HMPREF9306_01874	Hypothetical protein.	Hypothetical protein.	0.499
EPD32640.1	EPD33883.1	HMPREF9306_01339	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.462
EPD33463.1	EPD33883.1	HMPREF9306_01003	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.408
EPD33880.1	EPD33881.1	HMPREF9306_00297	HMPREF9306_00298	Hypothetical protein.	Hypothetical protein.	0.619
EPD33880.1	EPD33882.1	HMPREF9306_00297	HMPREF9306_00299	Hypothetical protein.	Hypothetical protein.	0.619
EPD33880.1	EPD33883.1	HMPREF9306_00297	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.417
EPD33881.1	EPD33880.1	HMPREF9306_00298	HMPREF9306_00297	Hypothetical protein.	Hypothetical protein.	0.619
EPD33881.1	EPD33882.1	HMPREF9306_00298	HMPREF9306_00299	Hypothetical protein.	Hypothetical protein.	0.984
EPD33881.1	EPD33883.1	HMPREF9306_00298	HMPREF9306_00300	Hypothetical protein.	Hypothetical protein.	0.554

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

27

average node degree:

4.91

avg. local clustering coefficient:

0.895

expected number of edges:

11

PPI enrichment p-value:

1.9e-05

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:0006412

Translation

10 of 100

1.34

2.22

1.96e-10

GO:0009059

Macromolecule biosynthetic process

11 of 164

1.17

1.72

1.96e-10

GO:0010467

Gene expression

11 of 187

1.11

1.57

1.96e-10

GO:0044271

Cellular nitrogen compound biosynthetic process

11 of 244

1.0

1.26

1.51e-09

GO:0044238

Primary metabolic process

11 of 736

0.52

0.45

0.00011

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003735

Structural constituent of ribosome

10 of 55

1.6

3.41

7.00e-13

GO:0019843

rRNA binding

8 of 41

1.64

3.03

5.68e-10

GO:0003723

RNA binding

9 of 99

1.3

1.97

4.42e-09

GO:0070180

Large ribosomal subunit rRNA binding

2 of 2

2.34

1.08

0.0103

GO:0000049

tRNA binding

3 of 24

1.44

0.83

0.0156

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005840

Ribosome

10 of 57

1.59

3.45

1.16e-13

GO:0044391

Ribosomal subunit

4 of 14

1.8

2.22

9.87e-06

GO:0015934

Large ribosomal subunit

3 of 8

1.92

1.89

0.00012

GO:0032991

Protein-containing complex

5 of 143

0.89

0.69

0.0026

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:27330141

(2016) Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity.

7 of 26

1.78

2.96

3.35e-08

PMID:28977619

(2017) The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression.

8 of 51

1.54

2.45

3.35e-08

PMID:22043294

(2011) Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes.

4 of 8

2.04

1.98

0.00011

PMID:20019804

(2009) Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis.

6 of 65

1.31

1.32

0.00015

PMID:30779773

(2019) Multiplexing polysome profiling experiments to study translation in Escherichia coli.

3 of 7

1.98

1.24

0.0040

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:95

rRNA-binding

8 of 31

1.76

3.73

1.37e-11

CL:86

Ribosome, and Translational elongation

11 of 69

1.55

3.38

1.30e-14

CL:89

Ribosome

10 of 59

1.57

3.36

2.01e-13

CL:91

Ribosome

9 of 50

1.6

3.28

4.05e-12

CL:147

Large ribosomal subunit rRNA binding, and Translation regulation

4 of 5

2.25

3.03

9.25e-07

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

llm03010

Ribosome

10 of 55

1.6

3.53

9.24e-14

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0015934

Large ribosomal subunit

5 of 10

2.04

3.23

1.01e-07

GOCC:0005840

Ribosome

8 of 45

1.59

2.87

9.60e-10

GOCC:0022625

Cytosolic large ribosomal subunit

3 of 6

2.04

1.94

0.00013

GOCC:0043229

Intracellular organelle

10 of 224

0.99

1.19

5.88e-08

GOCC:0032991

Protein-containing complex

6 of 331

0.6

0.38

0.0297

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0689

Ribosomal protein

10 of 56

1.6

3.45

2.01e-13

KW-0699

rRNA-binding

8 of 39

1.66

3.24

9.68e-11

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