PcaF protein (Yangia pacifica) - 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

PcaF

3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family. (397 aa)

Predicted Functional Partners:

SFT07154.1

0.987

SFS80475.1

0.985

SFT13448.1

0.984

SFS90833.1

0.983

SFS31157.1

0.981

SFT22549.1

0.981

SFS31148.1

0.980

SFT11331.1

0.939

SFT18169.1

0.939

SFS67612.1

0.931

Your Current Organism:

Yangia pacifica

NCBI taxonomy Id: 311180
Other names: CGMCC 1.3455, DSM 26894, JCM 12573, Y. pacifica, Yangia pacifica Dai et al. 2006, alpha proteobacterium DX5-10, strain DX5-10

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
PcaF	SFS31148.1	SAMN04488050_10161	SAMN04488050_10159	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-oxoadipate CoA-transferase, alpha subunit.	0.980
PcaF	SFS31157.1	SAMN04488050_10161	SAMN04488050_10160	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-oxoadipate CoA-transferase beta subunit.	0.981
PcaF	SFS67612.1	SAMN04488050_10161	SAMN04488050_103354	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	propionyl-CoA carboxylase carboxyltransferase subunit.	0.931
PcaF	SFS80475.1	SAMN04488050_10161	SAMN04488050_10561	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-hydroxyacyl-CoA dehydrogenase.	0.985
PcaF	SFS90833.1	SAMN04488050_10161	SAMN04488050_106228	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase.	0.983
PcaF	SFT07154.1	SAMN04488050_10161	SAMN04488050_109179	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-hydroxyacyl-CoA dehydrogenase; Belongs to the enoyl-CoA hydratase/isomerase family.	0.987
PcaF	SFT11331.1	SAMN04488050_10161	SAMN04488050_110236	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	glutaryl-CoA dehydrogenase.	0.939
PcaF	SFT13448.1	SAMN04488050_10161	SAMN04488050_111126	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-hydroxyacyl-CoA dehydrogenase.	0.984
PcaF	SFT18169.1	SAMN04488050_10161	SAMN04488050_113102	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	acyl-CoA dehydrogenase.	0.939
PcaF	SFT22549.1	SAMN04488050_10161	SAMN04488050_11686	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	3-hydroxyacyl-CoA dehydrogenase.	0.981
SFS31148.1	PcaF	SAMN04488050_10159	SAMN04488050_10161	3-oxoadipate CoA-transferase, alpha subunit.	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	0.980
SFS31148.1	SFS31157.1	SAMN04488050_10159	SAMN04488050_10160	3-oxoadipate CoA-transferase, alpha subunit.	3-oxoadipate CoA-transferase beta subunit.	0.999
SFS31157.1	PcaF	SAMN04488050_10160	SAMN04488050_10161	3-oxoadipate CoA-transferase beta subunit.	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	0.981
SFS31157.1	SFS31148.1	SAMN04488050_10160	SAMN04488050_10159	3-oxoadipate CoA-transferase beta subunit.	3-oxoadipate CoA-transferase, alpha subunit.	0.999
SFS31157.1	SFS80475.1	SAMN04488050_10160	SAMN04488050_10561	3-oxoadipate CoA-transferase beta subunit.	3-hydroxyacyl-CoA dehydrogenase.	0.429
SFS31157.1	SFS90833.1	SAMN04488050_10160	SAMN04488050_106228	3-oxoadipate CoA-transferase beta subunit.	3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase.	0.429
SFS31157.1	SFT07154.1	SAMN04488050_10160	SAMN04488050_109179	3-oxoadipate CoA-transferase beta subunit.	3-hydroxyacyl-CoA dehydrogenase; Belongs to the enoyl-CoA hydratase/isomerase family.	0.429
SFS31157.1	SFT13448.1	SAMN04488050_10160	SAMN04488050_111126	3-oxoadipate CoA-transferase beta subunit.	3-hydroxyacyl-CoA dehydrogenase.	0.429
SFS31157.1	SFT22549.1	SAMN04488050_10160	SAMN04488050_11686	3-oxoadipate CoA-transferase beta subunit.	3-hydroxyacyl-CoA dehydrogenase.	0.429
SFS67612.1	PcaF	SAMN04488050_103354	SAMN04488050_10161	propionyl-CoA carboxylase carboxyltransferase subunit.	3-oxoadipyl-CoA thiolase; Belongs to the thiolase-like superfamily. Thiolase family.	0.931

page 1 of 5

Network Stats

number of nodes:

11

number of edges:

40

average node degree:

7.27

avg. local clustering coefficient:

0.875

expected number of edges:

11

PPI enrichment p-value:

4.94e-12

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:0009252

Peptidoglycan biosynthetic process

8 of 38

1.96

4.42

8.65e-12

GO:0071555

Cell wall organization

4 of 26

1.83

2.07

2.98e-05

GO:0008360

Regulation of cell shape

4 of 26

1.83

2.07

2.98e-05

GO:0051301

Cell division

3 of 44

1.47

0.99

0.0063

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0008955

Peptidoglycan glycosyltransferase activity

5 of 7

2.49

4.05

1.40e-08

GO:0008658

Penicillin binding

4 of 6

2.46

3.21

7.03e-07

GO:0009002

Serine-type D-Ala-D-Ala carboxypeptidase activity

3 of 5

2.42

2.34

3.71e-05

GO:0016757

Glycosyltransferase activity

6 of 61

1.63

2.33

7.03e-07

GO:0004180

Carboxypeptidase activity

4 of 19

1.96

2.32

1.32e-05

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1359

Mixed, incl. Peptidoglycan biosynthesis, and Cell division

11 of 46

2.02

6.54

2.68e-19

CL:1363

Mixed, incl. Peptidoglycan biosynthesis, and Cell division site

9 of 33

2.07

5.85

1.83e-15

CL:1416

Peptidoglycan glycosyltransferase activity, and Peptidoglycan muralytic activity

4 of 5

2.54

3.48

2.33e-07

CL:1365

Mixed, incl. Cell shape, and Cell division site

5 of 23

1.98

3.01

2.35e-07

CL:1398

Mixed, incl. Cell cycle protein, and Cell morphogenesis

2 of 5

2.24

1.07

0.0102

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00550

Peptidoglycan biosynthesis

6 of 33

1.9

3.33

1.15e-08

map01501

beta-Lactam resistance

4 of 121

1.16

0.79

0.0083

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0032153

Cell division site

3 of 9

2.16

1.68

0.00059

GOCC:0005618

Cell wall

3 of 21

1.79

1.26

0.0027

GOCC:0071944

Cell periphery

7 of 713

0.63

0.39

0.0319

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0961

Cell wall biogenesis/degradation

3 of 16

1.91

1.38

0.0018

KW-0133

Cell shape

3 of 16

1.91

1.38

0.0018

KW-0997

Cell inner membrane

3 of 42

1.49

0.94

0.0087

KW-0573

Peptidoglycan synthesis

2 of 15

1.76

0.87

0.0198

KW-0328

Glycosyltransferase

2 of 22

1.6

0.73

0.0348

(more ...)

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00905

Penicillin binding protein transpeptidase domain

4 of 6

2.46

2.98

2.11e-06

PF03717

Penicillin-binding Protein dimerisation domain

2 of 2

2.64

1.11

0.0097

PF01098

Cell cycle protein

2 of 2

2.64

1.11

0.0097

PF00912

Transglycosylase

2 of 4

2.34

1.04

0.0120

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR001460

Penicillin-binding protein, transpeptidase

4 of 6

2.46

2.92

2.73e-06

IPR012338

Beta-lactamase/transpeptidase-like

5 of 18

2.08

2.84

1.26e-06

IPR036138

Penicillin-binding protein, dimerisation domain superfamily

2 of 2

2.64

0.98

0.0167

IPR005311

Penicillin-binding protein, dimerisation domain

2 of 2

2.64

0.98

0.0167

IPR001182

Probable peptidoglycan glycosyltransferase FtsW/RodA

2 of 2

2.64

0.98

0.0167

(more ...)

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