RvY_19330-1 protein (Ramazzottius varieornatus)

Nodes:

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

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second shell of interactors

Node Content

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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

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[Homology]

Score

RvY_19330-1

SSD domain-containing protein. (1044 aa)

Predicted Functional Partners:

RvY_19332-1

0.991

RvY_15338-1

0.927

RvY_15461-1

0.909

RvY_15469-1

0.909

RvY_01080-1

0.896

RvY_01332-1

0.860

RvY_01404

0.755

RvY_01404-1

0.755

RvY_15195-1

0.742

RvY_14823-1

0.737

Your Current Organism:

Ramazzottius varieornatus

NCBI taxonomy Id: 947166
Other names: R. varieornatus

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
RvY_01080-1	RvY_14823-1	A0A1D1UIM9	A0A1D1VUE8	Uncharacterized protein.	GDNF domain-containing protein.	0.819
RvY_01080-1	RvY_15338-1	A0A1D1UIM9	A0A1D1VW61	Uncharacterized protein.	Uncharacterized protein.	0.833
RvY_01080-1	RvY_15461-1	A0A1D1UIM9	A0A1D1VV00	Uncharacterized protein.	Uncharacterized protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.849
RvY_01080-1	RvY_15469-1	A0A1D1UIM9	A0A1D1VWL4	Uncharacterized protein.	G_PROTEIN_RECEP_F2_4 domain-containing protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.849
RvY_01080-1	RvY_19330-1	A0A1D1UIM9	A0A1D1WC81	Uncharacterized protein.	SSD domain-containing protein.	0.896
RvY_01080-1	RvY_19332-1	A0A1D1UIM9	A0A1D1W922	Uncharacterized protein.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.996
RvY_01332-1	RvY_01404	A0A1D1UM12	A0A1D1UNB0	E3 ubiquitin-protein ligase.	Uncharacterized protein.	0.486
RvY_01332-1	RvY_01404-1	A0A1D1UM12	A0A1D1URF6	E3 ubiquitin-protein ligase.	Uncharacterized protein.	0.486
RvY_01332-1	RvY_15195-1	A0A1D1UM12	A0A1D1VXI2	E3 ubiquitin-protein ligase.	E3 ubiquitin-protein ligase.	0.790
RvY_01332-1	RvY_15338-1	A0A1D1UM12	A0A1D1VW61	E3 ubiquitin-protein ligase.	Uncharacterized protein.	0.797
RvY_01332-1	RvY_15461-1	A0A1D1UM12	A0A1D1VV00	E3 ubiquitin-protein ligase.	Uncharacterized protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.401
RvY_01332-1	RvY_15469-1	A0A1D1UM12	A0A1D1VWL4	E3 ubiquitin-protein ligase.	G_PROTEIN_RECEP_F2_4 domain-containing protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.401
RvY_01332-1	RvY_19330-1	A0A1D1UM12	A0A1D1WC81	E3 ubiquitin-protein ligase.	SSD domain-containing protein.	0.860
RvY_01404	RvY_01332-1	A0A1D1UNB0	A0A1D1UM12	Uncharacterized protein.	E3 ubiquitin-protein ligase.	0.486
RvY_01404	RvY_15195-1	A0A1D1UNB0	A0A1D1VXI2	Uncharacterized protein.	E3 ubiquitin-protein ligase.	0.690
RvY_01404	RvY_15461-1	A0A1D1UNB0	A0A1D1VV00	Uncharacterized protein.	Uncharacterized protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.772
RvY_01404	RvY_15469-1	A0A1D1UNB0	A0A1D1VWL4	Uncharacterized protein.	G_PROTEIN_RECEP_F2_4 domain-containing protein; Belongs to the G-protein coupled receptor Fz/Smo family.	0.772
RvY_01404	RvY_19330-1	A0A1D1UNB0	A0A1D1WC81	Uncharacterized protein.	SSD domain-containing protein.	0.755
RvY_01404	RvY_19332-1	A0A1D1UNB0	A0A1D1W922	Uncharacterized protein.	Hedgehog protein; Intercellular signal essential for a variety of patterning events during development.	0.654
RvY_01404-1	RvY_01332-1	A0A1D1URF6	A0A1D1UM12	Uncharacterized protein.	E3 ubiquitin-protein ligase.	0.486

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

33

average node degree:

6

avg. local clustering coefficient:

0.699

expected number of edges:

15

PPI enrichment p-value:

2.41e-05

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:0006364

rRNA processing

10 of 188

1.79

4.4

2.31e-14

GO:0000154

rRNA modification

4 of 19

2.38

3.23

5.19e-07

GO:0009451

RNA modification

5 of 98

1.77

2.39

2.32e-06

GO:0031167

rRNA methylation

3 of 14

2.39

2.27

5.06e-05

GO:1990258

Histone glutamine methylation

2 of 3

2.88

1.68

0.00091

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003723

RNA binding

10 of 563

1.31

2.09

4.41e-10

GO:0003676

Nucleic acid binding

11 of 1166

1.04

1.33

2.69e-09

GO:0030515

snoRNA binding

2 of 20

2.06

0.83

0.0282

GO:0008168

Methyltransferase activity

3 of 117

1.47

0.74

0.0271

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0031428

Box C/D RNP complex

4 of 7

2.82

4.24

1.29e-08

GO:0005730

Nucleolus

10 of 225

1.71

4.04

3.30e-14

GO:0032040

Small-subunit processome

4 of 37

2.09

2.77

1.95e-06

GO:0030684

Preribosome

5 of 83

1.84

2.71

4.93e-07

GO:0005634

Nucleus

11 of 2309

0.74

5.31e-07

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:33075080

(2020) Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin.

2 of 6

2.58

1.76

0.00057

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:7710

Ribosome biogenesis

11 of 147

1.93

5.93

1.37e-18

CL:7712

Ribosome biogenesis

9 of 136

1.88

4.74

4.04e-14

CL:7713

Preribosome, and Ribosome biogenesis

8 of 129

1.85

4.13

5.98e-12

CL:7720

Small-subunit processome, and Maturation of SSU-rRNA

5 of 46

2.1

3.35

7.46e-08

CL:7787

Box C/D RNP complex

3 of 5

2.84

2.94

3.88e-06

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03008

Ribosome biogenesis in eukaryotes

6 of 101

1.83

3.14

1.96e-08

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-8868773

rRNA processing in the nucleus and cytosol

5 of 143

1.6

1.72

7.88e-05

MAP-72312

rRNA processing

5 of 146

1.6

1.71

7.88e-05

MAP-6791226

Major pathway of rRNA processing in the nucleolus and cytosol

4 of 139

1.52

1.24

0.0014

MAP-8953854

Metabolism of RNA

6 of 665

1.02

0.82

0.0018

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005732

Small nucleolar ribonucleoprotein complex

5 of 17

2.53

4.47

2.12e-09

GOCC:0031428

Box C/D snoRNP complex

4 of 6

2.88

4.15

2.05e-08

GOCC:0005730

Nucleolus

7 of 101

1.9

3.69

8.22e-10

GOCC:1990904

Ribonucleoprotein complex

6 of 343

1.3

1.49

1.89e-05

GOCC:0043232

Intracellular non-membrane-bounded organelle

8 of 910

1.0

1.04

1.89e-05

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0698

rRNA processing

2 of 18

2.11

0.84

0.0273

KW-0694

RNA-binding

3 of 150

1.36

0.71

0.0280

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF08156

NOP5NT (NUC127) domain

2 of 2

3.06

1.34

0.0038

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR045056

Nucleolar protein Nop56/Nop58

2 of 2

3.06

1.08

0.0112

IPR042239

Nop, C-terminal domain

2 of 3

2.88

1.08

0.0112

IPR036070

Nop domain superfamily

2 of 3

2.88

1.08

0.0112

IPR012976

NOSIC

2 of 3

2.88

1.08

0.0112

IPR012974

Nucleolar protein 58/56, N-terminal

2 of 2

3.06

1.08

0.0112

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM01206

Fibrillarin

2 of 2

3.06

1.58

0.0014

SM00931

NOSIC (NUC001) domain

2 of 3

2.88

1.57

0.0014

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