LRC_08970 protein (Lactobacillus ruminis) - 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

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:

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[Homology]

Score

LRC_08970

S9 family serine peptidase. (253 aa)

Predicted Functional Partners:

LRC_08980

0.752

LRC_08990

0.737

LRC_09000

0.665

LRC_18780

0.659

LRC_18820

0.659

LRC_12630

0.636

LRC_18250

0.636

LRC_07650

0.524

LRC_11950

0.517

cvpA

0.502

Your Current Organism:

Lactobacillus ruminis

NCBI taxonomy Id: 1069534
Other names: L. ruminis ATCC 27782, Lactobacillus ruminis ATCC 27782, Lactobacillus ruminis str. ATCC 27782, Lactobacillus ruminis strain ATCC 27782

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
LRC_07650	LRC_08970	LRC_07650	LRC_08970	Putative competence protein/transcription factor.	S9 family serine peptidase.	0.524
LRC_07650	LRC_11950	LRC_07650	LRC_11950	Putative competence protein/transcription factor.	RibT protein.	0.628
LRC_07650	cvpA	LRC_07650	LRC_13950	Putative competence protein/transcription factor.	Colicin V production protein.	0.536
LRC_08970	LRC_07650	LRC_08970	LRC_07650	S9 family serine peptidase.	Putative competence protein/transcription factor.	0.524
LRC_08970	LRC_08980	LRC_08970	LRC_08980	S9 family serine peptidase.	Conserved hypothetical protein.	0.752
LRC_08970	LRC_08990	LRC_08970	LRC_08990	S9 family serine peptidase.	Conserved hypothetical membrane-spanning protein.	0.737
LRC_08970	LRC_09000	LRC_08970	LRC_09000	S9 family serine peptidase.	23S rRNA m(5)C methyltransferase.	0.665
LRC_08970	LRC_11950	LRC_08970	LRC_11950	S9 family serine peptidase.	RibT protein.	0.517
LRC_08970	LRC_12630	LRC_08970	LRC_12630	S9 family serine peptidase.	Conserved hypothetical protein.	0.636
LRC_08970	LRC_18250	LRC_08970	LRC_18250	S9 family serine peptidase.	GPH family glycoside-pentoside-hexuronide:cation symporter.	0.636
LRC_08970	LRC_18780	LRC_08970	LRC_18780	S9 family serine peptidase.	PTS system, sucrose-specific IIABC component.	0.659
LRC_08970	LRC_18820	LRC_08970	LRC_18820	S9 family serine peptidase.	PTS system, glucose-specific IIABC component.	0.659
LRC_08970	cvpA	LRC_08970	LRC_13950	S9 family serine peptidase.	Colicin V production protein.	0.502
LRC_08980	LRC_08970	LRC_08980	LRC_08970	Conserved hypothetical protein.	S9 family serine peptidase.	0.752
LRC_08980	LRC_08990	LRC_08980	LRC_08990	Conserved hypothetical protein.	Conserved hypothetical membrane-spanning protein.	0.718
LRC_08980	LRC_09000	LRC_08980	LRC_09000	Conserved hypothetical protein.	23S rRNA m(5)C methyltransferase.	0.760
LRC_08990	LRC_08970	LRC_08990	LRC_08970	Conserved hypothetical membrane-spanning protein.	S9 family serine peptidase.	0.737
LRC_08990	LRC_08980	LRC_08990	LRC_08980	Conserved hypothetical membrane-spanning protein.	Conserved hypothetical protein.	0.718
LRC_08990	LRC_09000	LRC_08990	LRC_09000	Conserved hypothetical membrane-spanning protein.	23S rRNA m(5)C methyltransferase.	0.744
LRC_09000	LRC_08970	LRC_09000	LRC_08970	23S rRNA m(5)C methyltransferase.	S9 family serine peptidase.	0.665

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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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