ycjS protein (Salinivirga cyanobacteriivorans)

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

ycjS

Putative oxidoreductase YcjS. (325 aa)

Predicted Functional Partners:

rnhA_1

0.816

ALO14819.1

0.688

lysS

0.599

ALO14504.1

0.594

rfbB

0.594

iolC

0.549

bglX_1

0.499

bglX_2

0.466

csxA

0.466

ALO14506.1

0.426

Your Current Organism:

Salinivirga cyanobacteriivorans

NCBI taxonomy Id: 1307839
Other names: DSM 27204, JCM 31231, KCTC 15528, S. cyanobacteriivorans, Salinivirga cyanobacteriivorans Ben Hania et al. 2017, bacterium L21-Spi-D4, strain L21-Spi-D4

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
ALO14504.1	ycjS	L21SP5_00833	L21SP5_00834	Putative carboxyl-terminal-processing protease, deltaproteobacterial.	Putative oxidoreductase YcjS.	0.594
ALO14506.1	ycjS	L21SP5_00835	L21SP5_00834	CAAX amino terminal protease self- immunity.	Putative oxidoreductase YcjS.	0.426
ALO14819.1	iolC	L21SP5_01160	L21SP5_01080	Gluconolactonase.	5-dehydro-2-deoxygluconokinase.	0.630
ALO14819.1	ycjS	L21SP5_01160	L21SP5_00834	Gluconolactonase.	Putative oxidoreductase YcjS.	0.688
bglX_1	bglX_2	L21SP5_02816	L21SP5_02988	Periplasmic beta-glucosidase precursor.	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	0.909
bglX_1	csxA	L21SP5_02816	L21SP5_03521	Periplasmic beta-glucosidase precursor.	Exo-beta-D-glucosaminidase precursor.	0.647
bglX_1	iolC	L21SP5_02816	L21SP5_01080	Periplasmic beta-glucosidase precursor.	5-dehydro-2-deoxygluconokinase.	0.461
bglX_1	ycjS	L21SP5_02816	L21SP5_00834	Periplasmic beta-glucosidase precursor.	Putative oxidoreductase YcjS.	0.499
bglX_2	bglX_1	L21SP5_02988	L21SP5_02816	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	Periplasmic beta-glucosidase precursor.	0.909
bglX_2	csxA	L21SP5_02988	L21SP5_03521	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	Exo-beta-D-glucosaminidase precursor.	0.646
bglX_2	iolC	L21SP5_02988	L21SP5_01080	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	5-dehydro-2-deoxygluconokinase.	0.450
bglX_2	ycjS	L21SP5_02988	L21SP5_00834	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	Putative oxidoreductase YcjS.	0.466
csxA	bglX_1	L21SP5_03521	L21SP5_02816	Exo-beta-D-glucosaminidase precursor.	Periplasmic beta-glucosidase precursor.	0.647
csxA	bglX_2	L21SP5_03521	L21SP5_02988	Exo-beta-D-glucosaminidase precursor.	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	0.646
csxA	ycjS	L21SP5_03521	L21SP5_00834	Exo-beta-D-glucosaminidase precursor.	Putative oxidoreductase YcjS.	0.466
iolC	ALO14819.1	L21SP5_01080	L21SP5_01160	5-dehydro-2-deoxygluconokinase.	Gluconolactonase.	0.630
iolC	bglX_1	L21SP5_01080	L21SP5_02816	5-dehydro-2-deoxygluconokinase.	Periplasmic beta-glucosidase precursor.	0.461
iolC	bglX_2	L21SP5_01080	L21SP5_02988	5-dehydro-2-deoxygluconokinase.	Periplasmic beta-glucosidase precursor; Belongs to the glycosyl hydrolase 3 family.	0.450
iolC	ycjS	L21SP5_01080	L21SP5_00834	5-dehydro-2-deoxygluconokinase.	Putative oxidoreductase YcjS.	0.549
lysS	ycjS	L21SP5_02668	L21SP5_00834	Lysine--tRNA ligase; Belongs to the class-II aminoacyl-tRNA synthetase family.	Putative oxidoreductase YcjS.	0.599

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

47

average node degree:

8.55

avg. local clustering coefficient:

0.968

expected number of edges:

10

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:0045039

Protein insertion into mitochondrial inner membrane

3 of 7

3.0

2.53

2.54e-05

GO:0046834

Lipid phosphorylation

2 of 2

3.37

1.79

0.00060

GO:0046512

Sphingosine biosynthetic process

2 of 5

2.97

1.59

0.0013

GO:0006121

Mitochondrial electron transport, succinate to ubiquinone

2 of 6

2.89

1.59

0.0013

GO:0006099

Tricarboxylic acid cycle

2 of 29

2.2

1.05

0.0111

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0140318

Protein transporter activity

3 of 25

2.44

1.87

0.00032

GO:0004402

Histone acetyltransferase activity

2 of 23

2.3

0.85

0.0274

GO:0140110

Transcription regulator activity

4 of 412

1.35

0.78

0.0171

GO:0046872

Metal ion binding

6 of 2233

0.79

0.46

0.0331

GO:0005488

Binding

10 of 7866

0.47

0.32

0.0274

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0042721

TIM22 mitochondrial import inner membrane insertion complex

3 of 4

3.24

3.32

9.53e-07

GO:0098800

Inner mitochondrial membrane protein complex

5 of 120

1.99

2.79

9.53e-07

GO:0042719

Mitochondrial intermembrane space protein transporter complex

2 of 3

3.19

2.13

0.00014

GO:0005749

Mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)

2 of 5

2.97

1.98

0.00026

GO:0032991

Protein-containing complex

6 of 2897

0.68

0.45

0.0164

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:24142

Tim10-like, and TIM22 mitochondrial import inner membrane insertion complex

3 of 7

3.0

2.59

1.96e-05

CL:19911

Fumarate reductase complex

2 of 5

2.97

1.48

0.0021

CL:1544

Mixed, incl. Lectin, and Met-10+ like-protein

2 of 11

2.63

1.31

0.0040

CL:21436

Sphingolipid metabolism

2 of 18

2.41

1.12

0.0088

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00020

Citrate cycle (TCA cycle)

2 of 49

1.98

0.79

0.0330

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-1268020

Mitochondrial protein import

3 of 72

1.99

1.25

0.0037

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0042719

Mitochondrial intermembrane space protein transporter complex

2 of 4

3.06

1.6

0.0013

GOCC:0045281

Succinate dehydrogenase complex

2 of 7

2.82

1.52

0.0017

GOCC:0098798

Mitochondrial protein complex

4 of 184

1.7

1.42

0.00090

GOCC:0005740

Mitochondrial envelope

4 of 367

1.4

1.12

0.0019

GOCC:0098800

Inner mitochondrial membrane protein complex

2 of 75

1.79

0.82

0.0255

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0811

Translocation

2 of 13

2.55

1.41

0.0026

KW-0496

Mitochondrion

3 of 102

1.83

1.28

0.0026

KW-1015

Disulfide bond

2 of 92

1.7

0.7

0.0428

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF02953

Tim10/DDP family zinc finger

2 of 4

3.06

1.41

0.0029

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR034804

Fumarate reductase/succinate dehydrogenase, transmembrane subunit

2 of 3

3.19

1.39

0.0032

IPR001206

Diacylglycerol kinase, catalytic domain

2 of 2

3.37

1.39

0.0032

IPR035427

Tim10-like domain superfamily

2 of 4

3.06

1.38

0.0032

IPR017438

Inorganic polyphosphate/ATP-NAD kinase, N-terminal

2 of 5

2.97

1.38

0.0032

IPR016064

NAD kinase/diacylglycerol kinase-like domain superfamily

2 of 5

2.97

1.38

0.0032

(more ...)

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (20%) [HD]

Permalink

Network

Neighborhood

Databases

Fusion

Textmining

Cooccurrence

Experiments

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About