JG29_10080 protein (Lactobacillus mellis) - STRING interaction network

Nodes:

Network nodes represent proteins

splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

Node Color

colored nodes:
query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
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

JG29_10080

Uncharacterized protein. (73 aa)

Predicted Functional Partners:

rnjA

0.876

rpoE

0.818

rpoZ

0.798

rpoB

0.776

rpoC

0.776

rpoA

0.776

spxA

0.758

sigA

0.723

JG29_06100

0.707

JG29_02790

0.701

Your Current Organism:

Lactobacillus mellis

NCBI taxonomy Id: 1218508
Other names: CCUG 63289, DSM 26255, L. mellis, Lactobacillus mellis Olofsson et al. 2014, Lactobacillus sp. H1HS38N, Lactobacillus sp. Hon2, Lactobacillus sp. Hon2N, strain Hon2N

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
JG29_02790	JG29_10080	JG29_02790	JG29_10080	Putative DNA helicase.	Uncharacterized protein.	0.701
JG29_02790	rpoA	JG29_02790	JG29_03630	Putative DNA helicase.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.805
JG29_02790	rpoB	JG29_02790	JG29_03270	Putative DNA helicase.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.819
JG29_02790	rpoC	JG29_02790	JG29_03280	Putative DNA helicase.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.800
JG29_02790	rpoE	JG29_02790	JG29_03010	Putative DNA helicase.	Putative DNA-directed RNA polymerase subunit delta; Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling; Belongs to the RpoE family.	0.800
JG29_02790	rpoZ	JG29_02790	JG29_06360	Putative DNA helicase.	DNA-directed RNA polymerase subunit omega; Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.	0.771
JG29_06100	JG29_10080	JG29_06100	JG29_10080	Uncharacterized protein.	Uncharacterized protein.	0.707
JG29_10080	JG29_02790	JG29_10080	JG29_02790	Uncharacterized protein.	Putative DNA helicase.	0.701
JG29_10080	JG29_06100	JG29_10080	JG29_06100	Uncharacterized protein.	Uncharacterized protein.	0.707
JG29_10080	rnjA	JG29_10080	JG29_10090	Uncharacterized protein.	Ribonuclease J 1; An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay.	0.876
JG29_10080	rpoA	JG29_10080	JG29_03630	Uncharacterized protein.	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.776
JG29_10080	rpoB	JG29_10080	JG29_03270	Uncharacterized protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.776
JG29_10080	rpoC	JG29_10080	JG29_03280	Uncharacterized protein.	DNA-directed RNA polymerase subunit beta; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	0.776
JG29_10080	rpoE	JG29_10080	JG29_03010	Uncharacterized protein.	Putative DNA-directed RNA polymerase subunit delta; Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling; Belongs to the RpoE family.	0.818
JG29_10080	rpoZ	JG29_10080	JG29_06360	Uncharacterized protein.	DNA-directed RNA polymerase subunit omega; Promotes RNA polymerase assembly. Latches the N- and C- terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.	0.798
JG29_10080	sigA	JG29_10080	JG29_07320	Uncharacterized protein.	RNA polymerase sigma factor; Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.	0.723
JG29_10080	spxA	JG29_10080	JG29_12200	Uncharacterized protein.	Regulatory protein spx; Belongs to the ArsC family.	0.758
rnjA	JG29_10080	JG29_10090	JG29_10080	Ribonuclease J 1; An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay.	Uncharacterized protein.	0.876
rpoA	JG29_02790	JG29_03630	JG29_02790	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Putative DNA helicase.	0.805
rpoA	JG29_10080	JG29_03630	JG29_10080	DNA-directed RNA polymerase subunit alpha; DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.	Uncharacterized protein.	0.776

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

50

average node degree:

9.09

avg. local clustering coefficient:

0.949

expected number of edges:

23

PPI enrichment p-value:

5.72e-07

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:0006366

Transcription by RNA polymerase II

9 of 91

1.9

4.59

3.78e-13

GO:0001172

Transcription, RNA-templated

3 of 6

2.61

2.5

2.20e-05

GO:0006383

Transcription by RNA polymerase III

3 of 21

2.06

1.71

0.00045

GO:0006360

Transcription by RNA polymerase I

3 of 22

2.04

1.68

0.00049

GO:0045948

Positive regulation of translational initiation

2 of 3

2.73

1.51

0.0018

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003899

DNA-directed 5-3 RNA polymerase activity

5 of 25

2.21

3.28

2.16e-07

GO:0031369

Translation initiation factor binding

2 of 10

2.21

1.04

0.0118

GO:0003677

DNA binding

7 of 602

0.97

0.86

0.00045

GO:0003676

Nucleic acid binding

9 of 1218

0.78

0.68

0.00023

GO:1901363

Heterocyclic compound binding

10 of 2361

0.53

0.41

0.0029

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005665

RNA polymerase II, core complex

9 of 13

2.75

9.83

2.35e-20

GO:0005654

Nucleoplasm

11 of 218

1.61

3.81

7.10e-16

GO:0005736

RNA polymerase I complex

3 of 11

2.34

2.42

2.34e-05

GO:0005666

RNA polymerase III complex

3 of 15

2.21

4.96e-05

GO:0032044

DSIF complex

2 of 2

2.91

1.93

0.00031

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1772

RNA polymerase II, core complex

9 of 11

2.82

10.07

1.54e-20

CL:1776

RNA polymerase II, core complex

6 of 6

2.91

6.89

9.94e-14

CL:1686

DNA-directed RNA polymerase complex, and Regulation of DNA-templated transcription, elongation

11 of 126

1.85

5.37

3.79e-18

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03020

RNA polymerase

9 of 45

2.21

6.85

4.61e-17

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-113418

Formation of the Early Elongation Complex

11 of 32

2.44

10.14

7.67e-24

MAP-6796648

TP53 Regulates Transcription of DNA Repair Genes

11 of 40

2.35

9.43

3.17e-23

MAP-75955

RNA Polymerase II Transcription Elongation

11 of 43

2.32

9.22

4.25e-23

MAP-77075

RNA Pol II CTD phosphorylation and interaction with CE

10 of 30

2.43

9.19

2.51e-21

MAP-72086

mRNA Capping

10 of 32

2.4

9.05

2.90e-21

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

8 of 85

1.88

4.11

1.61e-11

GOCC:0005665

RNA polymerase II, core complex

4 of 5

2.81

3.99

3.79e-08

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

5 of 58

1.84

2.6

1.08e-06

GOCC:0005736

RNA polymerase I complex

2 of 5

2.51

1.43

0.0023

GOCC:0005654

Nucleoplasm

5 of 236

1.23

1.11

0.00060

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0804

Transcription

4 of 109

1.47

1.18

0.0018

KW-0240

DNA-directed RNA polymerase

2 of 14

2.06

0.91

0.0192

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (12%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About