GCA_001696485_06222 protein (Planobispora rosea)

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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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

Experiments

Databases

Textmining

[Homology]

Score

GCA_001696485_06222

Unannotated protein. (414 aa)

Predicted Functional Partners:

GCA_001696485_06226

0.864

GCA_001696485_06220

0.825

GCA_001696485_06221

0.773

GCA_001696485_06219

0.751

GCA_001696485_04739

0.717

GCA_001696485_04742

0.677

GCA_001696485_06225

0.622

GCA_001696485_00576

0.591

GCA_001696485_00577

0.591

GCA_001696485_02324

0.591

Your Current Organism:

Planobispora rosea

NCBI taxonomy Id: 35762
Other names: ATCC 23866, DSM 43051, IFO 15558, JCM 3166, NBRC 15558, NRRL B-8121, P. rosea

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Browse interactions in tabular form:

node1	node2	node1 annotation	node2 annotation	score
GCA_001696485_00576	GCA_001696485_00577	Unannotated protein.	Unannotated protein.	0.994
GCA_001696485_00576	GCA_001696485_04739	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_00576	GCA_001696485_04742	Unannotated protein.	Unannotated protein.	0.996
GCA_001696485_00576	GCA_001696485_06222	Unannotated protein.	Unannotated protein.	0.591
GCA_001696485_00577	GCA_001696485_00576	Unannotated protein.	Unannotated protein.	0.994
GCA_001696485_00577	GCA_001696485_04739	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_00577	GCA_001696485_04742	Unannotated protein.	Unannotated protein.	0.996
GCA_001696485_00577	GCA_001696485_06222	Unannotated protein.	Unannotated protein.	0.591
GCA_001696485_02324	GCA_001696485_04739	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_02324	GCA_001696485_04742	Unannotated protein.	Unannotated protein.	0.996
GCA_001696485_02324	GCA_001696485_06222	Unannotated protein.	Unannotated protein.	0.591
GCA_001696485_04739	GCA_001696485_00576	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_04739	GCA_001696485_00577	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_04739	GCA_001696485_02324	Unannotated protein.	Unannotated protein.	0.990
GCA_001696485_04739	GCA_001696485_04742	Unannotated protein.	Unannotated protein.	0.999
GCA_001696485_04739	GCA_001696485_06219	Unannotated protein.	Unannotated protein.	0.996
GCA_001696485_04739	GCA_001696485_06220	Unannotated protein.	Unannotated protein.	0.818
GCA_001696485_04739	GCA_001696485_06221	Unannotated protein.	Unannotated protein.	0.458
GCA_001696485_04739	GCA_001696485_06222	Unannotated protein.	Unannotated protein.	0.717
GCA_001696485_04739	GCA_001696485_06225	Unannotated protein.	Unannotated protein.	0.704

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

53

average node degree:

9.64

avg. local clustering coefficient:

0.968

expected number of edges:

14

PPI enrichment p-value:

3e-15

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:0006096

Glycolytic process

7 of 13

2.03

4.16

2.35e-10

GO:0006006

Glucose metabolic process

6 of 11

2.04

3.86

1.85e-09

GO:0006091

Generation of precursor metabolites and energy

9 of 43

1.62

3.18

5.45e-11

GO:0006094

Gluconeogenesis

4 of 7

2.06

2.66

3.00e-06

GO:0005975

Carbohydrate metabolic process

10 of 97

1.31

2.12

2.35e-10

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016861

Intramolecular oxidoreductase activity, interconverting aldoses and ketoses

4 of 8

2.0

8.58e-05

GO:0004807

Triose-phosphate isomerase activity

2 of 2

2.3

0.9

0.0218

GO:0004347

glucose-6-phosphate isomerase activity

2 of 2

2.3

0.9

0.0218

GO:0016744

Transketolase or transaldolase activity

2 of 5

1.9

0.73

0.0414

GO:0003824

Catalytic activity

11 of 1120

0.29

0.23

0.0464

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005737

Cytoplasm

11 of 822

0.43

0.35

0.0019

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:29932393

(2018) Using glycolysis enzyme sequences to inform Lactobacillus phylogeny.

6 of 7

2.23

4.19

1.76e-09

PMID:37660047

(2023) The regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7.

7 of 24

1.77

3.22

2.98e-09

PMID:30134518

(2018) Dietary Nutrients, Proteomes, and Adhesion of Probiotic Lactobacilli to Mucin and Host Epithelial Cells.

5 of 12

1.92

2.75

7.68e-07

PMID:31964939

(2020) Proteomic analysis reveals potential factors associated with enhanced EPS production in Streptococcus thermophilus ASCC 1275.

6 of 35

1.54

2.12

1.09e-06

PMID:29740087

(2018) The lactose operon from Lactobacillus casei is involved in the transport and metabolism of the human milk oligosaccharide core-2 N-acetyllactosamine.

3 of 10

1.78

1.32

0.0019

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1468

Glycolytic process, and Aldehyde-lyase activity

10 of 15

2.13

6.59

2.33e-17

CL:1469

Glycolysis

8 of 10

2.2

5.8

6.26e-14

CL:1471

Gluconeogenesis, and Phosphotransferase activity, carboxyl group as acceptor

5 of 5

2.3

3.96

9.23e-09

CL:1462

Mixed, incl. Microbial metabolism in diverse environments, and Import across plasma membrane

11 of 117

1.27

2.16

1.32e-12

CL:1488

Aldehyde-lyase activity, and Streptomycin biosynthesis

2 of 5

1.9

0.94

0.0153

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

lfe01200

Carbon metabolism

11 of 49

1.65

4.08

2.19e-16

lfe00010

Glycolysis / Gluconeogenesis

8 of 24

1.82

4.08

3.88e-12

lfe01120

Microbial metabolism in diverse environments

11 of 93

1.37

2.6

7.14e-14

lfe00030

Pentose phosphate pathway

5 of 20

1.7

2.44

7.40e-07

lfe01230

Biosynthesis of amino acids

8 of 76

1.32

1.99

9.06e-09

(more ...)

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-168249

Innate Immune System

2 of 16

1.4

0.62

0.0494

MAP-168256

Immune System

2 of 20

1.3

0.6

0.0494

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005737

Cytoplasm

10 of 697

0.46

0.33

0.0172

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0324

Glycolysis

6 of 9

2.13

3.97

2.33e-09

KW-0312

Gluconeogenesis

3 of 5

2.08

1.73

0.00042

KW-0670

Pyruvate

2 of 6

1.82

0.82

0.0257

KW-0963

Cytoplasm

6 of 215

0.75

0.49

0.0155

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00342

Phosphoglucose isomerase

2 of 2

2.3

0.74

0.0447

PF00121

Triosephosphate isomerase

2 of 2

2.3

0.74

0.0447

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