SMF58395.1 protein (Trinickia caryophylli) - 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:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

SMF58395.1

Thioredoxin reductase. (482 aa)

Predicted Functional Partners:

SMF58398.1

0.994

SMF58401.1

0.988

SMF15697.1

0.985

SMF07378.1

0.980

SMF58991.1

0.979

SMF15719.1

0.956

SMF04761.1

0.934

SMF17558.1

0.916

SMF15711.1

0.910

SMF28892.1

0.906

Your Current Organism:

Trinickia caryophylli

NCBI taxonomy Id: 28094
Other names: ATCC 25418, Burkholderia caryophylli, CCUG 20834, CFBP 2429, CFBP 3818, CIP 105770, DSM 50341, HAMBI 2159, ICMP 512, JCM 10488, JCM 9310, LMG 2155, LMG:2155, NCPPB 2151, Paraburkholderia caryophylli, Phytomonas caryophylli, Pseudomonas caryophylli, Pseudomonas caryophyllii, T. caryophylli

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

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

... protein node degrees:

download

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

... network coordinates:

download

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

... protein sequences:

download

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

... protein annotations:

download

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

... functional annotations:

download

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
SMF04761.1	SMF15711.1	SAMN06295900_102103	SAMN06295900_103239	Glycine/D-amino acid oxidase.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.910
SMF04761.1	SMF28892.1	SAMN06295900_102103	SAMN06295900_10523	Glycine/D-amino acid oxidase.	Sarcosine oxidase subunit delta.	0.799
SMF04761.1	SMF58395.1	SAMN06295900_102103	SAMN06295900_11178	Glycine/D-amino acid oxidase.	Thioredoxin reductase.	0.934
SMF04761.1	SMF58398.1	SAMN06295900_102103	SAMN06295900_11179	Glycine/D-amino acid oxidase.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.838
SMF07378.1	SMF15711.1	SAMN06295900_102298	SAMN06295900_103239	Sarcosine oxidase subunit beta.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.819
SMF07378.1	SMF28892.1	SAMN06295900_102298	SAMN06295900_10523	Sarcosine oxidase subunit beta.	Sarcosine oxidase subunit delta.	0.845
SMF07378.1	SMF58395.1	SAMN06295900_102298	SAMN06295900_11178	Sarcosine oxidase subunit beta.	Thioredoxin reductase.	0.980
SMF07378.1	SMF58398.1	SAMN06295900_102298	SAMN06295900_11179	Sarcosine oxidase subunit beta.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.830
SMF15697.1	SMF15711.1	SAMN06295900_103237	SAMN06295900_103239	Sarcosine oxidase subunit beta.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.960
SMF15697.1	SMF15719.1	SAMN06295900_103237	SAMN06295900_103240	Sarcosine oxidase subunit beta.	Glycine/D-amino acid oxidase.	0.838
SMF15697.1	SMF28892.1	SAMN06295900_103237	SAMN06295900_10523	Sarcosine oxidase subunit beta.	Sarcosine oxidase subunit delta.	0.819
SMF15697.1	SMF58395.1	SAMN06295900_103237	SAMN06295900_11178	Sarcosine oxidase subunit beta.	Thioredoxin reductase.	0.985
SMF15697.1	SMF58398.1	SAMN06295900_103237	SAMN06295900_11179	Sarcosine oxidase subunit beta.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.839
SMF15711.1	SMF04761.1	SAMN06295900_103239	SAMN06295900_102103	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Glycine/D-amino acid oxidase.	0.910
SMF15711.1	SMF07378.1	SAMN06295900_103239	SAMN06295900_102298	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Sarcosine oxidase subunit beta.	0.819
SMF15711.1	SMF15697.1	SAMN06295900_103239	SAMN06295900_103237	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Sarcosine oxidase subunit beta.	0.960
SMF15711.1	SMF15719.1	SAMN06295900_103239	SAMN06295900_103240	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Glycine/D-amino acid oxidase.	0.961
SMF15711.1	SMF17558.1	SAMN06295900_103239	SAMN06295900_103362	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Glycine/D-amino acid oxidase.	0.707
SMF15711.1	SMF58395.1	SAMN06295900_103239	SAMN06295900_11178	2Fe-2S iron-sulfur cluster binding domain-containing protein.	Thioredoxin reductase.	0.910
SMF15711.1	SMF58398.1	SAMN06295900_103239	SAMN06295900_11179	2Fe-2S iron-sulfur cluster binding domain-containing protein.	2Fe-2S iron-sulfur cluster binding domain-containing protein.	0.646

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

32

average node degree:

5.82

avg. local clustering coefficient:

0.828

expected number of edges:

11

PPI enrichment p-value:

3.05e-07

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:0055085

Transmembrane transport

11 of 641

0.85

0.89

7.45e-07

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0015099

Nickel cation transmembrane transporter activity

10 of 36

2.06

6.23

3.69e-17

GO:0015413

ABC-type nickel transporter activity

2 of 2

2.61

1.41

0.0026

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005886

Plasma membrane

11 of 895

0.7

0.67

2.86e-06

GO:0016021

Integral component of membrane

9 of 1090

0.53

0.41

0.0035

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:6402

Nickel cation transmembrane transporter activity, and Peptide transport

10 of 47

1.94

5.58

1.01e-16

CL:6399

Nickel cation transmembrane transporter activity, and Peptide transport

11 of 65

1.84

5.23

1.49e-17

CL:6485

ABC-type nickel transporter activity, and Oligopeptide transport permease C-like, N-terminal domain

5 of 5

2.61

4.76

6.98e-10

CL:6403

Nickel cation transmembrane transporter activity, and Peptide transport

5 of 41

1.7

2.25

3.34e-06

CL:6404

Nickel cation transmembrane transporter activity, and Peptide transport

3 of 30

1.61

1.1

0.0045

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

siw02024

Quorum sensing

5 of 160

1.11

0.87

0.0026

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-1222499

Latent infection - Other responses of Mtb to phagocytosis

9 of 90

1.61

3.41

1.15e-12

MAP-9635486

Infection with Mycobacterium tuberculosis

9 of 151

1.39

2.41

4.87e-11

MAP-5663205

Infectious disease

9 of 154

1.38

2.39

4.87e-11

MAP-1643685

Disease

9 of 158

1.37

2.35

4.87e-11

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

6 of 64

1.58

2.17

1.50e-06

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0813

Transport

9 of 317

1.07

1.27

5.15e-07

KW-1003

Cell membrane

9 of 322

1.06

1.25

5.15e-07

KW-1133

Transmembrane helix

8 of 948

0.54

0.36

0.0195

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF12911

N-terminal TM domain of oligopeptide transport permease C

5 of 11

2.27

3.65

3.98e-08

PF00528

Binding-protein-dependent transport system inner membrane component

8 of 96

1.53

2.57

5.85e-09

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR025966

Oligopeptide transport permease C-like, N-terminal domain

6 of 11

2.35

4.49

7.69e-10

IPR035906

MetI-like superfamily

8 of 97

1.53

2.53

8.11e-09

IPR000515

ABC transporter type 1, transmembrane domain MetI-like

8 of 97

1.53

2.53

8.11e-09

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (26%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About