map protein (Xanthomarina gelatinilytica) - STRING interaction network

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

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[Homology]

Score

map

Methionine aminopeptidase; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). (272 aa)

Predicted Functional Partners:

rplR

0.990

D778_00711

0.990

D778_00703

0.986

D778_00713

0.984

D778_00705

0.982

D778_00702

0.979

D778_00710

0.978

D778_00701

0.977

D778_00698

0.976

D778_00715

0.974

Your Current Organism:

Xanthomarina gelatinilytica

NCBI taxonomy Id: 1137281
Other names: Formosa sp. AK20, JCM 18821, MTCC 11705, X. gelatinilytica, Xanthomarina gelatinilytica Vaidya et al. 2015, strain AK20

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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

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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
D778_00698	D778_00701	D778_00698	D778_00701	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L5p (L11e).	0.999
D778_00698	D778_00702	D778_00698	D778_00702	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L24p (L26e).	0.999
D778_00698	D778_00703	D778_00698	D778_00703	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L14p (L23e).	0.999
D778_00698	D778_00705	D778_00698	D778_00705	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L29p (L35e).	0.999
D778_00698	D778_00710	D778_00698	D778_00710	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L2p (L8e).	0.999
D778_00698	D778_00711	D778_00698	D778_00711	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L23p (L23Ae).	0.999
D778_00698	D778_00713	D778_00698	D778_00713	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L3p (L3e).	0.999
D778_00698	D778_00715	D778_00698	D778_00715	LSU ribosomal protein L6p (L9e).	Translation elongation factor G.	0.999
D778_00698	map	D778_00698	D778_02476	LSU ribosomal protein L6p (L9e).	Methionine aminopeptidase; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val).	0.976
D778_00698	rplR	D778_00698	D778_00697	LSU ribosomal protein L6p (L9e).	LSU ribosomal protein L18p (L5e); This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.	0.999
D778_00701	D778_00698	D778_00701	D778_00698	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L6p (L9e).	0.999
D778_00701	D778_00702	D778_00701	D778_00702	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L24p (L26e).	0.999
D778_00701	D778_00703	D778_00701	D778_00703	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L14p (L23e).	0.999
D778_00701	D778_00705	D778_00701	D778_00705	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L29p (L35e).	0.999
D778_00701	D778_00710	D778_00701	D778_00710	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L2p (L8e).	0.999
D778_00701	D778_00711	D778_00701	D778_00711	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L23p (L23Ae).	0.999
D778_00701	D778_00713	D778_00701	D778_00713	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L3p (L3e).	0.999
D778_00701	D778_00715	D778_00701	D778_00715	LSU ribosomal protein L5p (L11e).	Translation elongation factor G.	0.999
D778_00701	map	D778_00701	D778_02476	LSU ribosomal protein L5p (L11e).	Methionine aminopeptidase; Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val).	0.977
D778_00701	rplR	D778_00701	D778_00697	LSU ribosomal protein L5p (L11e).	LSU ribosomal protein L18p (L5e); This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.	0.999

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Network Stats

number of nodes:

11

number of edges:

29

average node degree:

5.27

avg. local clustering coefficient:

0.751

expected number of edges:

10

PPI enrichment p-value:

1.85e-06

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:0030433

Ubiquitin-dependent ERAD pathway

5 of 41

1.99

2.86

6.76e-07

GO:0016567

Protein ubiquitination

7 of 125

1.66

2.55

1.50e-07

GO:0010033

Response to organic substance

7 of 150

1.58

2.37

1.86e-07

GO:0043161

Proteasome-mediated ubiquitin-dependent protein catabolic process

6 of 144

1.53

2.02

2.64e-06

GO:0051603

Proteolysis involved in protein catabolic process

7 of 235

1.38

1.83

1.20e-06

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0004842

Ubiquitin-protein transferase activity

6 of 90

1.73

2.46

9.21e-07

GO:0061631

Ubiquitin conjugating enzyme activity

3 of 26

1.97

1.38

0.0020

GO:0043130

Ubiquitin binding

3 of 29

1.92

1.36

0.0020

GO:0097027

Ubiquitin-protein transferase activator activity

2 of 5

2.51

1.23

0.0056

GO:0061630

Ubiquitin protein ligase activity

3 of 52

1.67

1.09

0.0056

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000836

Hrd1p ubiquitin ligase complex

3 of 5

2.69

2.31

5.57e-05

GO:0000151

Ubiquitin ligase complex

4 of 70

1.66

1.61

0.00023

GO:0140535

Intracellular protein-containing complex

7 of 371

1.18

1.24

5.57e-05

GO:1990234

Transferase complex

5 of 340

1.08

0.8

0.0045

GO:0005783

Endoplasmic reticulum

5 of 429

0.97

0.66

0.0101

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:7371

Mixed, incl. Ubiquitin-dependent ERAD pathway, and Hedgehog ligand biogenesis

5 of 40

2.0

2.69

1.91e-06

CL:604

Ubiquitin-conjugating enzyme E2

3 of 7

2.54

2.29

5.41e-05

CL:567

Mixed, incl. Ubiquitin-like protein conjugating enzyme activity, and HECT domain

4 of 45

1.86

1.98

5.99e-05

CL:7375

Ubiquitin-dependent ERAD pathway, and Hedgehog ligand biogenesis

3 of 29

1.92

1.48

0.0011

CL:13337

CCR4-NOT core complex, and Ubiquitin-protein transferase regulator activity

2 of 10

2.21

1.06

0.0105

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map04141

Protein processing in endoplasmic reticulum

7 of 168

1.53

2.39

4.77e-08

map04120

Ubiquitin mediated proteolysis

4 of 102

1.5

1.39

0.00045

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000835

ER ubiquitin ligase complex

4 of 12

2.43

2.96

2.18e-06

GOCC:0000151

Ubiquitin ligase complex

5 of 76

1.73

2.17

7.77e-06

GOCC:1990389

CUE1-UBC7 ubiquitin-conjugating enzyme complex

2 of 2

2.91

1.59

0.0013

GOCC:0005789

Endoplasmic reticulum membrane

5 of 137

1.47

1.55

9.85e-05

GOCC:0000836

Hrd1p ubiquitin ligase complex

2 of 10

2.21

1.13

0.0079

(more ...)

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR000608

Ubiquitin-conjugating enzyme E2

3 of 23

2.02

1.06

0.0098

IPR016135

Ubiquitin-conjugating enzyme/RWD-like

3 of 28

1.94

1.04

0.0098

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00184

Ring finger

3 of 55

1.64

0.92

0.0129

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