GCA_000283235_00395 protein (Methylocystis parvus)

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

GCA_000283235_00395

Unannotated protein. (460 aa)

Predicted Functional Partners:

GCA_000283235_00394

0.865

GCA_000283235_00396

0.826

GCA_000283235_01829

0.812

GCA_000283235_00592

0.652

GCA_000283235_00061

0.649

Acs

0.646

GCA_000283235_03063

0.637

GCA_000283235_00400

0.618

RplM

0.609

GCA_000283235_00406

0.608

Your Current Organism:

Methylocystis parvus

NCBI taxonomy Id: 1134912
Other names: M. parvus OBBP, Methylocystis parvus OBBP, Methylocystis parvus str. OBBP, Methylocystis parvus strain OBBP

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

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

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

... protein sequences:

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

... protein annotations:

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

... functional annotations:

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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
Acs	GCA_000283235_00395	GCA_000283235_00890	GCA_000283235_00395	Unannotated protein.	Unannotated protein.	0.646
Acs	GCA_000283235_00406	GCA_000283235_00890	GCA_000283235_00406	Unannotated protein.	Unannotated protein.	0.541
Acs	GCA_000283235_00592	GCA_000283235_00890	GCA_000283235_00592	Unannotated protein.	Unannotated protein.	0.959
Acs	GCA_000283235_03063	GCA_000283235_00890	GCA_000283235_03063	Unannotated protein.	Unannotated protein.	0.539
GCA_000283235_00061	GCA_000283235_00395	GCA_000283235_00061	GCA_000283235_00395	Unannotated protein.	Unannotated protein.	0.649
GCA_000283235_00061	GCA_000283235_00406	GCA_000283235_00061	GCA_000283235_00406	Unannotated protein.	Unannotated protein.	0.649
GCA_000283235_00061	GCA_000283235_00592	GCA_000283235_00061	GCA_000283235_00592	Unannotated protein.	Unannotated protein.	0.424
GCA_000283235_00061	GCA_000283235_03063	GCA_000283235_00061	GCA_000283235_03063	Unannotated protein.	Unannotated protein.	0.649
GCA_000283235_00061	RplM	GCA_000283235_00061	GCA_000283235_01567	Unannotated protein.	Unannotated protein.	0.999
GCA_000283235_00394	GCA_000283235_00395	GCA_000283235_00394	GCA_000283235_00395	Unannotated protein.	Unannotated protein.	0.865
GCA_000283235_00394	GCA_000283235_00396	GCA_000283235_00394	GCA_000283235_00396	Unannotated protein.	Unannotated protein.	0.832
GCA_000283235_00395	Acs	GCA_000283235_00395	GCA_000283235_00890	Unannotated protein.	Unannotated protein.	0.646
GCA_000283235_00395	GCA_000283235_00061	GCA_000283235_00395	GCA_000283235_00061	Unannotated protein.	Unannotated protein.	0.649
GCA_000283235_00395	GCA_000283235_00394	GCA_000283235_00395	GCA_000283235_00394	Unannotated protein.	Unannotated protein.	0.865
GCA_000283235_00395	GCA_000283235_00396	GCA_000283235_00395	GCA_000283235_00396	Unannotated protein.	Unannotated protein.	0.826
GCA_000283235_00395	GCA_000283235_00400	GCA_000283235_00395	GCA_000283235_00400	Unannotated protein.	Unannotated protein.	0.618
GCA_000283235_00395	GCA_000283235_00406	GCA_000283235_00395	GCA_000283235_00406	Unannotated protein.	Unannotated protein.	0.608
GCA_000283235_00395	GCA_000283235_00592	GCA_000283235_00395	GCA_000283235_00592	Unannotated protein.	Unannotated protein.	0.652
GCA_000283235_00395	GCA_000283235_01829	GCA_000283235_00395	GCA_000283235_01829	Unannotated protein.	Unannotated protein.	0.812
GCA_000283235_00395	GCA_000283235_03063	GCA_000283235_00395	GCA_000283235_03063	Unannotated protein.	Unannotated protein.	0.637

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

25

PPI enrichment p-value:

7.3e-08

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

11 of 92

1.32

2.29

4.91e-12

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0019843

rRNA binding

10 of 37

1.68

3.81

1.21e-13

GO:0003735

Structural constituent of ribosome

10 of 49

1.56

3.21

7.30e-13

GO:0000049

tRNA binding

5 of 19

1.67

2.13

6.14e-06

GO:0003676

Nucleic acid binding

11 of 225

0.93

1.11

6.14e-09

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0044391

Ribosomal subunit

6 of 12

1.94

3.67

2.03e-09

GO:0005840

Ribosome

10 of 53

1.52

3.08

7.12e-13

GO:0015935

Small ribosomal subunit

3 of 6

1.94

1.87

0.00015

GO:0015934

Large ribosomal subunit

3 of 6

1.94

1.87

0.00015

GO:0005622

Intracellular anatomical structure

11 of 682

0.45

0.39

0.00015

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:64

Ribosome, and Translational elongation

11 of 72

1.43

2.78

1.87e-13

CL:68

Ribosome, and Elongation factor

9 of 61

1.41

2.45

1.49e-10

CL:72

Ribosome

5 of 28

1.5

1.8

1.36e-05

CL:154

rRNA binding, and Elongation factor Tu GTP binding domain

4 of 18

1.59

1.68

9.76e-05

CL:75

Ribosome

4 of 22

1.51

1.5

0.00019

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03010

Ribosome

10 of 52

1.53

3.13

5.28e-13

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0044391

Ribosomal subunit

6 of 15

1.85

3.0

6.83e-08

GOCC:0015934

Large ribosomal subunit

4 of 6

2.07

2.65

3.45e-06

GOCC:0005840

Ribosome

7 of 36

1.53

2.37

6.83e-08

GOCC:0022626

Cytosolic ribosome

4 of 10

1.85

2.23

1.26e-05

GOCC:0043229

Intracellular organelle

10 of 171

1.01

1.22

6.83e-08

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0689

Ribosomal protein

10 of 52

1.53

3.1

8.99e-13

KW-0687

Ribonucleoprotein

10 of 52

1.53

3.1

8.99e-13

KW-0820

tRNA-binding

4 of 10

1.85

2.17

1.77e-05

KW-0699

rRNA-binding

6 of 31

1.53

2.15

7.32e-07

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