argX protein (Methanofastidiosum methylthiophilus)

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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Gene Fusion

Cooccurrence

Coexpression

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[Homology]

Score

argX

Glutamate--LysW ligase ArgX. (293 aa)

Predicted Functional Partners:

AMQ22_01191

0.808

AMQ22_00745

0.781

APG08_00486

0.719

APG08_00319

0.684

lpdA

0.670

APG08_00082

0.669

aksF

0.652

gatB

0.643

APG08_01198

0.631

gltA

0.619

Your Current Organism:

Methanofastidiosum methylthiophilus

NCBI taxonomy Id: 1705564
Other names: Arc I group archaeon ADurb1013_Bin02101, Arc I group archaeon ADurb1113_Bin01801, Arc I group archaeon ADurb1213_Bin02801, Arc I group archaeon B03fssc0709_Meth_Bin005, Arc I group archaeon B15fssc0709_Meth_Bin003, Arc I group archaeon BMIXfssc0709_Meth_Bin006, Arc I group archaeon U1lsi0528_Bin055, Arc I group archaeon U1lsi0528_Bin089, C. Methanofastidiosum methylthiophilus, Ca. Methanofastidiosum methylthiophilus, Candidatus Methanofastidiosum methylthiophilus, WSA2 group archaeon U1lsi0528_Bin055, WSA2 group archaeon U1lsi0528_Bin089

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
AMQ22_00745	aksF	APG08_00559	APG08_00563	Uncharacterized protein.	Homoisocitrate dehydrogenase.	0.828
AMQ22_00745	argX	APG08_00559	APG08_01196	Uncharacterized protein.	Glutamate--LysW ligase ArgX.	0.781
AMQ22_01191	APG08_01198	APG08_01197	APG08_01198	RLAN domain-containing protein.	annotation not available	0.631
AMQ22_01191	argX	APG08_01197	APG08_01196	RLAN domain-containing protein.	Glutamate--LysW ligase ArgX.	0.808
APG08_00082	argX	APG08_00082	APG08_01196	annotation not available	Glutamate--LysW ligase ArgX.	0.669
APG08_00319	argX	APG08_00319	APG08_01196	annotation not available	Glutamate--LysW ligase ArgX.	0.684
APG08_00319	lpdA	APG08_00319	APG08_01242	annotation not available	Dihydrolipoyl dehydrogenase.	0.874
APG08_00486	argX	APG08_00486	APG08_01196	annotation not available	Glutamate--LysW ligase ArgX.	0.719
APG08_01198	AMQ22_01191	APG08_01198	APG08_01197	annotation not available	RLAN domain-containing protein.	0.631
APG08_01198	argX	APG08_01198	APG08_01196	annotation not available	Glutamate--LysW ligase ArgX.	0.631
aksF	AMQ22_00745	APG08_00563	APG08_00559	Homoisocitrate dehydrogenase.	Uncharacterized protein.	0.828
aksF	argX	APG08_00563	APG08_01196	Homoisocitrate dehydrogenase.	Glutamate--LysW ligase ArgX.	0.652
aksF	gltA	APG08_00563	APG08_00593	Homoisocitrate dehydrogenase.	Citrate synthase.	0.844
aksF	lpdA	APG08_00563	APG08_01242	Homoisocitrate dehydrogenase.	Dihydrolipoyl dehydrogenase.	0.839
argX	AMQ22_00745	APG08_01196	APG08_00559	Glutamate--LysW ligase ArgX.	Uncharacterized protein.	0.781
argX	AMQ22_01191	APG08_01196	APG08_01197	Glutamate--LysW ligase ArgX.	RLAN domain-containing protein.	0.808
argX	APG08_00082	APG08_01196	APG08_00082	Glutamate--LysW ligase ArgX.	annotation not available	0.669
argX	APG08_00319	APG08_01196	APG08_00319	Glutamate--LysW ligase ArgX.	annotation not available	0.684
argX	APG08_00486	APG08_01196	APG08_00486	Glutamate--LysW ligase ArgX.	annotation not available	0.719
argX	APG08_01198	APG08_01196	APG08_01198	Glutamate--LysW ligase ArgX.	annotation not available	0.631

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

14

PPI enrichment p-value:

1.11e-16

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:0000398

mRNA splicing, via spliceosome

11 of 238

2.06

6.78

2.42e-19

GO:1903241

U2-type prespliceosome assembly

2 of 3

3.22

1.81

0.00055

GO:0000245

Spliceosomal complex assembly

3 of 46

2.21

1.8

0.00035

GO:0022618

Ribonucleoprotein complex assembly

4 of 162

1.79

1.72

0.00020

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:1990935

Splicing factor binding

3 of 3

3.39

3.25

1.35e-06

GO:0003723

RNA binding

10 of 1350

1.26

1.89

2.67e-09

GO:0030620

U2 snRNA binding

2 of 7

2.85

1.44

0.0025

GO:0003676

Nucleic acid binding

11 of 4200

0.81

0.83

1.35e-06

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0071011

Precatalytic spliceosome

11 of 51

2.73

12.67

4.16e-27

GO:0005686

U2 snRNP

9 of 18

3.09

12.32

3.56e-24

GO:0071005

U2-type precatalytic spliceosome

10 of 46

2.73

11.51

2.64e-24

GO:0097525

Spliceosomal snRNP complex

10 of 54

2.66

11.1

6.75e-24

GO:0005684

U2-type spliceosomal complex

11 of 90

2.48

10.7

6.50e-25

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:26589

U2 snRNP

10 of 12

3.32

14.56

6.18e-28

CL:26586

Spliceosomal snRNP complex, and Nuclear cap binding complex

11 of 37

2.87

13.55

6.18e-28

CL:26590

Splicing factor binding, and PSP, proline-rich

6 of 6

3.39

8.48

3.13e-16

CL:26601

U2-type prespliceosome assembly, and U2 small nuclear ribonucleoprotein A

4 of 6

3.22

4.9

1.17e-09

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03040

Spliceosome

11 of 279

1.99

6.58

3.21e-20

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-72165

mRNA Splicing - Minor Pathway

7 of 57

2.48

6.49

5.09e-14

MAP-72172

mRNA Splicing

11 of 303

1.95

6.1

6.60e-19

MAP-72203

Processing of Capped Intron-Containing Pre-mRNA

11 of 407

1.83

5.2

8.02e-18

MAP-8953854

Metabolism of RNA

11 of 993

1.44

2.86

6.66e-14

MAP-72163

mRNA Splicing - Major Pathway

4 of 281

1.55

1.28

0.0012

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:1990904

Ribonucleoprotein complex

11 of 470

1.76

4.71

7.19e-17

GOCC:0097525

Spliceosomal snRNP complex

5 of 38

2.51

4.4

2.76e-09

GOCC:0005686

U2 snRNP

3 of 5

3.17

3.42

6.13e-07

GOCC:0005681

Spliceosomal complex

5 of 117

2.03

3.1

1.95e-07

GOCC:0005689

U12-type spliceosomal complex

2 of 9

2.74

1.6

0.0012

(more ...)

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