KRK40313.1 protein (Lactobacillus bifermentans)

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

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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

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Textmining

[Homology]

Score

KRK40313.1

Histidine protein kinase. (342 aa)

Predicted Functional Partners:

KRK40312.1

0.983

KRK40876.1

0.943

KRK40507.1

0.918

KRK39472.1

0.911

KRK40314.1

0.886

KRK40316.1

0.772

KRK40309.1

0.684

KRK40310.1

0.681

KRK40311.1

0.681

KRK40303.1

0.672

Your Current Organism:

Lactobacillus bifermentans

NCBI taxonomy Id: 1423726
Other names: L. bifermentans DSM 20003, Lactobacillus bifermentans DSM 20003

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
KRK39472.1	KRK40313.1	FC07_GL002441	FC07_GL001028	Chemotaxis protein CheY.	Histidine protein kinase.	0.911
KRK40303.1	KRK40312.1	FC07_GL001018	FC07_GL001027	Hypothetical protein.	Response regulator.	0.537
KRK40303.1	KRK40313.1	FC07_GL001018	FC07_GL001028	Hypothetical protein.	Histidine protein kinase.	0.672
KRK40303.1	KRK40314.1	FC07_GL001018	FC07_GL001029	Hypothetical protein.	Hypothetical protein.	0.761
KRK40303.1	KRK40316.1	FC07_GL001018	FC07_GL001031	Hypothetical protein.	Hypothetical protein.	0.879
KRK40309.1	KRK40310.1	FC07_GL001024	FC07_GL001025	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	Hypothetical protein.	0.773
KRK40309.1	KRK40311.1	FC07_GL001024	FC07_GL001026	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	Hypothetical protein.	0.773
KRK40309.1	KRK40312.1	FC07_GL001024	FC07_GL001027	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	Response regulator.	0.741
KRK40309.1	KRK40313.1	FC07_GL001024	FC07_GL001028	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	Histidine protein kinase.	0.684
KRK40309.1	KRK40314.1	FC07_GL001024	FC07_GL001029	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	Hypothetical protein.	0.539
KRK40310.1	KRK40309.1	FC07_GL001025	FC07_GL001024	Hypothetical protein.	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	0.773
KRK40310.1	KRK40311.1	FC07_GL001025	FC07_GL001026	Hypothetical protein.	Hypothetical protein.	0.803
KRK40310.1	KRK40312.1	FC07_GL001025	FC07_GL001027	Hypothetical protein.	Response regulator.	0.741
KRK40310.1	KRK40313.1	FC07_GL001025	FC07_GL001028	Hypothetical protein.	Histidine protein kinase.	0.681
KRK40310.1	KRK40314.1	FC07_GL001025	FC07_GL001029	Hypothetical protein.	Hypothetical protein.	0.539
KRK40311.1	KRK40309.1	FC07_GL001026	FC07_GL001024	Hypothetical protein.	Trans-hexaprenyltranstransferase, component II; Belongs to the FPP/GGPP synthase family.	0.773
KRK40311.1	KRK40310.1	FC07_GL001026	FC07_GL001025	Hypothetical protein.	Hypothetical protein.	0.803
KRK40311.1	KRK40312.1	FC07_GL001026	FC07_GL001027	Hypothetical protein.	Response regulator.	0.742
KRK40311.1	KRK40313.1	FC07_GL001026	FC07_GL001028	Hypothetical protein.	Histidine protein kinase.	0.681
KRK40311.1	KRK40314.1	FC07_GL001026	FC07_GL001029	Hypothetical protein.	Hypothetical protein.	0.539

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

38

average node degree:

6.91

avg. local clustering coefficient:

0.946

expected number of edges:

17

PPI enrichment p-value:

1.45e-05

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:0006351

Transcription, DNA-templated

3 of 17

1.72

0.93

0.0135

GO:0010467

Gene expression

7 of 206

1.0

0.82

0.0016

GO:0009059

Macromolecule biosynthetic process

7 of 209

1.0

0.81

0.0016

GO:0044271

Cellular nitrogen compound biosynthetic process

7 of 362

0.76

0.5

0.0135

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003899

DNA-directed 5-3 RNA polymerase activity

3 of 6

2.17

1.61

0.00084

GO:0019843

rRNA binding

4 of 41

1.46

1.2

0.0014

GO:0003735

Structural constituent of ribosome

4 of 57

1.32

0.97

0.0039

GO:0003676

Nucleic acid binding

9 of 361

0.87

0.81

9.00e-05

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000428

DNA-directed RNA polymerase complex

3 of 7

2.1

1.73

0.00042

GO:0015935

Small ribosomal subunit

2 of 6

1.99

1.19

0.0051

GO:0005840

Ribosome

4 of 60

1.29

1.06

0.0017

GO:0032991

Protein-containing complex

5 of 200

0.87

0.63

0.0051

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:34702846

(2021) MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes.

2 of 25

1.37

0.63

0.0450

PMID:37041201

(2023) Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms.

2 of 34

1.24

0.6

0.0450

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:217

RNA polymerase

3 of 5

2.25

2.06

0.00011

CL:5015

Mixed, incl. ArsC family, and Cold-shock protein, DNA-binding

3 of 6

2.17

1.97

0.00015

CL:80

Ribosome, and Translation regulator activity

7 of 74

1.45

1.96

1.05e-06

CL:131

Mixed, incl. Small ribosomal subunit, and K Homology domain, type 2

3 of 9

1.99

1.72

0.00036

CL:92

Ribosome

4 of 54

1.34

1.12

0.0014

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

otm03020

RNA polymerase

3 of 4

2.35

2.09

0.00011

otm03010

Ribosome

4 of 54

1.34

1.11

0.0015

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0022626

Cytosolic ribosome

3 of 22

1.61

0.85

0.0179

GOCC:0044391

Ribosomal subunit

3 of 26

1.53

0.83

0.0179

GOCC:0022627

Cytosolic small ribosomal subunit

2 of 10

1.77

0.8

0.0272

GOCC:0000428

DNA-directed RNA polymerase complex

3 of 42

1.32

0.71

0.0266

GOCC:0032991

Protein-containing complex

6 of 450

0.6

0.35

0.0461

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

3 of 5

2.25

1.83

0.00033

KW-0689

Ribosomal protein

4 of 56

1.32

1.0

0.0032

KW-0699

rRNA-binding

3 of 38

1.37

0.83

0.0136

KW-0548

Nucleotidyltransferase

3 of 37

1.38

0.83

0.0136

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR012340

Nucleic acid-binding, OB-fold

4 of 30

1.6

1.12

0.0040

IPR002059

Cold-shock protein, DNA-binding

2 of 2

2.47

0.77

0.0403

IPR011129

Cold shock domain

2 of 3

2.29

0.74

0.0446

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00357

Cold shock protein domain

2 of 3

2.29

1.06

0.0109

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