LIP_0136 protein (Limnochorda pilosa) - STRING interaction network

Nodes:

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second shell of interactors

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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

LIP_0136

Glutaredoxin. (51 aa)

Predicted Functional Partners:

LIP_0135

0.899

LIP_1370

0.755

LIP_3502

0.755

LIP_0137

0.746

LIP_0134

0.550

LIP_1372

0.478

adk

0.425

Your Current Organism:

Limnochorda pilosa

NCBI taxonomy Id: 1555112
Other names: DSM 28787, L. pilosa, Limnochorda pilosa Watanabe et al. 2015, NBRC 110152, bacterium HC45, strain HC45

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
LIP_0134	LIP_0135	LIP_0134	LIP_0135	Hypothetical protein.	Glutaredoxin.	0.741
LIP_0134	LIP_0136	LIP_0134	LIP_0136	Hypothetical protein.	Glutaredoxin.	0.550
LIP_0134	LIP_0137	LIP_0134	LIP_0137	Hypothetical protein.	Asparaginase.	0.533
LIP_0135	LIP_0134	LIP_0135	LIP_0134	Glutaredoxin.	Hypothetical protein.	0.741
LIP_0135	LIP_0136	LIP_0135	LIP_0136	Glutaredoxin.	Glutaredoxin.	0.899
LIP_0135	LIP_0137	LIP_0135	LIP_0137	Glutaredoxin.	Asparaginase.	0.553
LIP_0135	LIP_1370	LIP_0135	LIP_1370	Glutaredoxin.	Thioredoxin peroxidase.	0.755
LIP_0135	LIP_1372	LIP_0135	LIP_1372	Glutaredoxin.	GTPase.	0.419
LIP_0135	LIP_3502	LIP_0135	LIP_3502	Glutaredoxin.	Peroxiredoxin; Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides.	0.755
LIP_0136	LIP_0134	LIP_0136	LIP_0134	Glutaredoxin.	Hypothetical protein.	0.550
LIP_0136	LIP_0135	LIP_0136	LIP_0135	Glutaredoxin.	Glutaredoxin.	0.899
LIP_0136	LIP_0137	LIP_0136	LIP_0137	Glutaredoxin.	Asparaginase.	0.746
LIP_0136	LIP_1370	LIP_0136	LIP_1370	Glutaredoxin.	Thioredoxin peroxidase.	0.755
LIP_0136	LIP_1372	LIP_0136	LIP_1372	Glutaredoxin.	GTPase.	0.478
LIP_0136	LIP_3502	LIP_0136	LIP_3502	Glutaredoxin.	Peroxiredoxin; Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides.	0.755
LIP_0136	adk	LIP_0136	LIP_0138	Glutaredoxin.	Adenylate kinase; Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism; Belongs to the adenylate kinase family.	0.425
LIP_0137	LIP_0134	LIP_0137	LIP_0134	Asparaginase.	Hypothetical protein.	0.533
LIP_0137	LIP_0135	LIP_0137	LIP_0135	Asparaginase.	Glutaredoxin.	0.553
LIP_0137	LIP_0136	LIP_0137	LIP_0136	Asparaginase.	Glutaredoxin.	0.746
LIP_0137	adk	LIP_0137	LIP_0138	Asparaginase.	Adenylate kinase; Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism; Belongs to the adenylate kinase family.	0.438

page 1 of 2

Network Stats

number of nodes:

10

number of edges:

16

average node degree:

3.2

avg. local clustering coefficient:

0.919

expected number of edges:

9

PPI enrichment p-value:

0.0286

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:0042147

Retrograde transport, endosome to Golgi

4 of 87

1.96

1.48

0.0014

GO:0072673

Lamellipodium morphogenesis

2 of 7

2.75

0.85

0.0326

GO:0034498

Early endosome to Golgi transport

2 of 9

2.64

0.8

0.0399

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005158

Insulin receptor binding

3 of 23

2.41

1.62

0.0012

GO:1990460

Leptin receptor binding

2 of 4

2.99

1.18

0.0086

GO:1990459

Transferrin receptor binding

2 of 11

2.55

0.94

0.0222

GO:0034452

Dynactin binding

2 of 12

2.52

0.94

0.0222

GO:0035091

Phosphatidylinositol binding

4 of 270

1.47

0.9

0.0118

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030905

Retromer, tubulation complex

4 of 4

3.29

4.72

4.78e-09

GO:0097422

Tubular endosome

2 of 5

2.9

1.48

0.0025

GO:0031901

Early endosome membrane

4 of 180

1.64

1.4

0.0010

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:11485546

(2001) A large family of endosome-localized proteins related to sorting nexin 1.

4 of 6

3.12

2.53

3.54e-05

PMID:24866125

(2014) Rapid mapping of interactions between Human SNX-BAR proteins measured in vitro by AlphaScreen and single-molecule spectroscopy.

4 of 9

2.94

2.49

4.01e-05

PMID:24735875

(2014) Going forward with retromer.

4 of 9

2.94

2.49

4.01e-05

PMID:18472259

(2008) Retromer.

4 of 9

2.94

2.49

4.01e-05

PMID:31576058

(2019) Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins.

5 of 38

2.41

2.42

3.54e-05

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:14014

Retromer, tubulation complex

4 of 5

3.2

4.37

1.92e-08

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

hsa04144

Endocytosis

4 of 241

1.51

1.24

0.0016

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0030905

Retromer, tubulation complex

4 of 4

3.29

4.69

5.38e-09

GOCC:0097422

Tubular endosome

2 of 5

2.9

1.39

0.0037

GOCC:0010008

Endosome membrane

4 of 330

1.38

0.91

0.0090

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0446

Lipid-binding

4 of 251

1.5

1.11

0.0036

KW-0967

Endosome

4 of 568

1.14

0.59

0.0431

KW-0653

Protein transport

4 of 617

1.11

0.57

0.0431

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF09325

Vps5 C terminal like

4 of 5

3.2

4.53

9.72e-09

PF03700

Sorting nexin, N-terminal domain

2 of 2

3.29

1.6

0.0016

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR015404

Sorting nexin/Vps5-like, C-terminal

4 of 5

3.2

4.26

3.02e-08

IPR001683

Phox homology

4 of 46

2.23

2.41

2.73e-05

IPR036871

PX domain superfamily

4 of 51

2.19

2.38

2.73e-05

IPR027267

AH/BAR domain superfamily

4 of 77

2.01

2.03

9.80e-05

IPR005329

Sorting nexin, N-terminal

2 of 2

3.29

1.55

0.0020

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00312

PhoX homologous domain, present in p47phox and p40phox.

3 of 42

2.15

1.59

0.0011

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