ldh protein (Spiroplasma citri) - STRING interaction network

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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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

Cooccurrence

Coexpression

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[Homology]

Score

ldh

L-lactate dehydrogenase; Catalyzes the conversion of lactate to pyruvate. (318 aa)

Predicted Functional Partners:

pyk

0.984

pdhB

0.963

pdhA

0.951

ldhA

0.950

gpi

0.920

fbaA2

0.897

gapN

0.888

tkt-2

0.856

tkt

0.856

APE74543.1

0.842

Your Current Organism:

Spiroplasma citri

NCBI taxonomy Id: 2133
Other names: ATCC 27556, NCPPB 2647, S. citri

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
APE74543.1	gapN	SCITRI_00647	SCITRI_00516	Threonine dehydratase.	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	0.405
APE74543.1	ldh	SCITRI_00647	SCITRI_001285	Threonine dehydratase.	L-lactate dehydrogenase; Catalyzes the conversion of lactate to pyruvate.	0.842
fbaA2	gapN	SCITRI_001904	SCITRI_00516	Fructose-bisphosphate aldolase.	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	0.948
fbaA2	gpi	SCITRI_001904	SCITRI_00316	Fructose-bisphosphate aldolase.	Glucose-6-phosphate isomerase.	0.983
fbaA2	ldh	SCITRI_001904	SCITRI_001285	Fructose-bisphosphate aldolase.	L-lactate dehydrogenase; Catalyzes the conversion of lactate to pyruvate.	0.897
fbaA2	pdhA	SCITRI_001904	SCITRI_00409	Fructose-bisphosphate aldolase.	Pyruvate dehydrogenase E1 component subunit alpha; The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).	0.869
fbaA2	pdhB	SCITRI_001904	SCITRI_00410	Fructose-bisphosphate aldolase.	Pyruvate dehydrogenase E1 component subunit beta.	0.888
fbaA2	pyk	SCITRI_001904	SCITRI_001127	Fructose-bisphosphate aldolase.	Pyruvate kinase; Belongs to the pyruvate kinase family.	0.955
fbaA2	tkt	SCITRI_001904	SCITRI_00867	Fructose-bisphosphate aldolase.	Transketolase; Belongs to the transketolase family.	0.932
fbaA2	tkt-2	SCITRI_001904	SCITRI_00599	Fructose-bisphosphate aldolase.	Putative transketolase; Belongs to the transketolase family.	0.932
gapN	APE74543.1	SCITRI_00516	SCITRI_00647	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Threonine dehydratase.	0.405
gapN	fbaA2	SCITRI_00516	SCITRI_001904	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Fructose-bisphosphate aldolase.	0.948
gapN	gpi	SCITRI_00516	SCITRI_00316	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Glucose-6-phosphate isomerase.	0.927
gapN	ldh	SCITRI_00516	SCITRI_001285	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	L-lactate dehydrogenase; Catalyzes the conversion of lactate to pyruvate.	0.888
gapN	pdhA	SCITRI_00516	SCITRI_00409	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Pyruvate dehydrogenase E1 component subunit alpha; The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).	0.869
gapN	pdhB	SCITRI_00516	SCITRI_00410	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Pyruvate dehydrogenase E1 component subunit beta.	0.892
gapN	pyk	SCITRI_00516	SCITRI_001127	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Pyruvate kinase; Belongs to the pyruvate kinase family.	0.921
gapN	tkt	SCITRI_00516	SCITRI_00867	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Transketolase; Belongs to the transketolase family.	0.855
gapN	tkt-2	SCITRI_00516	SCITRI_00599	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Belongs to the aldehyde dehydrogenase family.	Putative transketolase; Belongs to the transketolase family.	0.855
gpi	fbaA2	SCITRI_00316	SCITRI_001904	Glucose-6-phosphate isomerase.	Fructose-bisphosphate aldolase.	0.983

page 1 of 5

Network Stats

number of nodes:

11

number of edges:

35

average node degree:

6.36

avg. local clustering coefficient:

0.852

expected number of edges:

24

PPI enrichment p-value:

0.0189

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:0006260

DNA replication

4 of 38

1.26

0.89

0.0056

GO:0090304

Nucleic acid metabolic process

10 of 248

0.84

0.82

1.68e-05

GO:0006259

DNA metabolic process

6 of 128

0.9

0.67

0.0044

GO:0009059

Macromolecule biosynthetic process

6 of 166

0.79

0.53

0.0123

GO:0044260

Cellular macromolecule metabolic process

8 of 295

0.67

0.49

0.0044

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0140640

Catalytic activity, acting on a nucleic acid

9 of 154

1.0

1.08

4.70e-06

GO:0016779

Nucleotidyltransferase activity

4 of 31

1.34

1.06

0.0023

GO:0003677

DNA binding

9 of 185

0.92

0.94

1.13e-05

GO:0003697

Single-stranded DNA binding

2 of 4

1.93

0.85

0.0238

GO:0140097

Catalytic activity, acting on DNA

5 of 73

1.07

0.83

0.0027

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0061695

Transferase complex, transferring phosphorus-containing groups

3 of 10

1.71

1.19

0.0034

GO:0000428

DNA-directed RNA polymerase complex

2 of 5

1.84

0.96

0.0133

GO:0140535

Intracellular protein-containing complex

3 of 20

1.41

0.95

0.0068

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:556

Mixed, incl. DNA replication, and Nucleotide excision repair

5 of 29

1.47

1.44

0.00024

CL:551

Mixed, incl. Catalytic activity, acting on DNA, and DNA replication

6 of 68

1.18

1.13

0.00024

CL:323

tRNA aminoacylation

3 of 15

1.53

0.95

0.0094

CL:558

Mixed, incl. Nucleotide excision repair, and Mre11 nuclease, N-terminal metallophosphatase domain

3 of 18

1.46

0.87

0.0126

CL:215

RNA polymerase

2 of 5

1.84

0.77

0.0328

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03030

DNA replication

4 of 22

1.49

1.3

0.00083

map03440

Homologous recombination

4 of 31

1.34

1.12

0.0014

map03020

RNA polymerase

2 of 4

1.93

0.96

0.0146

map03430

Mismatch repair

3 of 27

1.28

0.78

0.0146

map03410

Base excision repair

2 of 10

1.53

0.7

0.0377

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0548

Nucleotidyltransferase

4 of 21

1.51

1.27

0.0011

KW-0235

DNA replication

3 of 14

1.56

1.02

0.0065

KW-0240

DNA-directed RNA polymerase

2 of 5

1.84

0.92

0.0163

KW-0239

DNA-directed DNA polymerase

2 of 5

1.84

0.92

0.0163

KW-0234

DNA repair

3 of 23

1.35

0.82

0.0136

(more ...)

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