vieA protein (Rhodopseudomonas palustris CGA009)

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:

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Cooccurrence

Coexpression

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[Homology]

Score

vieA

Putative cylclic diguanylate phosphodiesterase (EAL). (404 aa)

Predicted Functional Partners:

RPA0767

0.926

RPA3616

0.854

RPA3832

0.846

RPA0286

0.838

RPA4565

0.834

RPA1818

0.833

RPA3076

0.832

RPA1657

0.831

RPA2769

0.828

RPA3022

0.828

Your Current Organism:

Rhodopseudomonas palustris CGA009

NCBI taxonomy Id: 258594
Other names: R. palustris CGA009, Rhodopseudomonas palustris str. CGA009, Rhodopseudomonas palustris strain CGA009

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

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
RPA0286	RPA0767	RPA0286	RPA0767	Putative diguanylate cyclase (GGDEF) with HAMP domain.	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.466
RPA0286	RPA1818	RPA0286	RPA1818	Putative diguanylate cyclase (GGDEF) with HAMP domain.	Putative diguanylate cyclase (GGDEF).	0.519
RPA0286	RPA3616	RPA0286	RPA3616	Putative diguanylate cyclase (GGDEF) with HAMP domain.	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.479
RPA0286	RPA3832	RPA0286	RPA3832	Putative diguanylate cyclase (GGDEF) with HAMP domain.	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.660
RPA0286	vieA	RPA0286	RPA4516	Putative diguanylate cyclase (GGDEF) with HAMP domain.	Putative cylclic diguanylate phosphodiesterase (EAL).	0.838
RPA0767	RPA0286	RPA0767	RPA0286	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	Putative diguanylate cyclase (GGDEF) with HAMP domain.	0.466
RPA0767	RPA1818	RPA0767	RPA1818	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	Putative diguanylate cyclase (GGDEF).	0.518
RPA0767	RPA3616	RPA0767	RPA3616	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.475
RPA0767	RPA3832	RPA0767	RPA3832	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.621
RPA0767	vieA	RPA0767	RPA4516	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	Putative cylclic diguanylate phosphodiesterase (EAL).	0.926
RPA1657	RPA3616	RPA1657	RPA3616	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.400
RPA1657	RPA3832	RPA1657	RPA3832	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.456
RPA1657	vieA	RPA1657	RPA4516	Putative diguanylate cyclase (GGDEF).	Putative cylclic diguanylate phosphodiesterase (EAL).	0.831
RPA1818	RPA0286	RPA1818	RPA0286	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with HAMP domain.	0.519
RPA1818	RPA0767	RPA1818	RPA0767	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.518
RPA1818	RPA3022	RPA1818	RPA3022	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF).	0.449
RPA1818	RPA3076	RPA1818	RPA3076	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF).	0.448
RPA1818	RPA3616	RPA1818	RPA3616	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.524
RPA1818	RPA3832	RPA1818	RPA3832	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF) with PAS/PAC domain.	0.451
RPA1818	RPA4565	RPA1818	RPA4565	Putative diguanylate cyclase (GGDEF).	Putative diguanylate cyclase (GGDEF).	0.444

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

25

average node degree:

4.55

avg. local clustering coefficient:

0.879

expected number of edges:

12

PPI enrichment p-value:

0.000746

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 354

1.79

4.36

4.84e-14

GO:0002183

Cytoplasmic translational initiation

3 of 27

2.39

2.12

0.00010

GO:0006446

Regulation of translational initiation

3 of 52

2.1

1.67

0.00057

GO:0075522

IRES-dependent viral translational initiation

2 of 5

2.94

1.61

0.0012

GO:0001732

Formation of cytoplasmic translation initiation complex

2 of 19

2.36

1.09

0.0097

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003743

Translation initiation factor activity

7 of 53

2.46

6.09

3.62e-13

GO:0043022

Ribosome binding

3 of 72

1.96

1.33

0.0025

GO:0031369

Translation initiation factor binding

2 of 20

2.34

1.02

0.0130

GO:0003735

Structural constituent of ribosome

3 of 176

1.57

0.85

0.0170

GO:0003723

RNA binding

6 of 1158

1.05

0.83

0.0025

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005850

Eukaryotic translation initiation factor 2 complex

3 of 3

3.34

3.19

1.75e-06

GO:0033290

Eukaryotic 48S preinitiation complex

3 of 16

2.61

2.45

2.82e-05

GO:0005840

Ribosome

5 of 203

1.73

2.11

1.25e-05

GO:0015935

Small ribosomal subunit

3 of 49

2.13

1.8

0.00032

GO:0071541

Eukaryotic translation initiation factor 3 complex, eIF3m

2 of 6

2.86

1.67

0.00094

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:18379

Eukaryotic 43S preinitiation complex, and Eukaryotic translation initiation factor 2 complex

4 of 23

2.58

3.09

1.53e-06

CL:18383

Eukaryotic translation initiation factor 3 complex

3 of 11

2.78

2.85

5.49e-06

CL:18365

Translational initiation, and Negative regulation of translational initiation

5 of 86

2.1

2.82

1.53e-06

CL:17695

Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)

5 of 102

2.03

2.76

1.53e-06

CL:17712

Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)

3 of 43

2.18

1.89

0.00022

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03013

RNA transport

7 of 283

1.73

3.17

2.11e-09

map03010

Ribosome

3 of 198

1.52

0.95

0.0088

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-72695

Formation of the ternary complex, and subsequently, the 43S complex

7 of 64

2.38

5.95

3.31e-13

MAP-72649

Translation initiation complex formation

7 of 70

2.34

5.87

3.31e-13

MAP-72662

Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S

7 of 74

2.32

5.81

3.38e-13

MAP-72702

Ribosomal scanning and start codon recognition

7 of 77

2.3

5.76

3.77e-13

MAP-72706

GTP hydrolysis and joining of the 60S ribosomal subunit

8 of 129

2.13

5.4

2.41e-13

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005850

Eukaryotic translation initiation factor 2 complex

3 of 8

2.91

2.6

1.80e-05

GOCC:0005852

Eukaryotic translation initiation factor 3 complex

2 of 15

2.47

0.93

0.0198

GOCC:0022627

Cytosolic small ribosomal subunit

2 of 24

2.26

0.88

0.0236

GOCC:0005840

Ribosome

3 of 150

1.64

0.84

0.0205

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0396

Initiation factor

6 of 55

2.38

5.1

3.48e-11

KW-0689

Ribosomal protein

3 of 165

1.6

1.03

0.0065

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF08662

Eukaryotic translation initiation factor eIF2A

3 of 3

3.34

3.03

3.31e-06

PF03144

Elongation factor Tu domain 2

2 of 15

2.47

0.83

0.0301

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