KRK39965.1 protein (Lactobacillus bifermentans)

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second shell of interactors

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Edges:

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Known Interactions

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experimentally determined

Predicted Interactions

gene neighborhood

gene fusions

gene co-occurrence

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textmining

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protein homology

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Gene Fusion

Cooccurrence

Coexpression

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Score

KRK39965.1

Hypothetical protein. (149 aa)

Predicted Functional Partners:

KRK32646.1

0.809

KRK34612.1

0.749

KRK33429.1

0.694

metG

0.641

KRK40193.1

0.603

KRK33427.1

0.603

KRK39963.1

0.603

pgi

0.583

KRK32613.1

0.565

KRK33428.1

0.553

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
KRK32613.1	KRK32646.1	FC07_GL002043	FC07_GL002078	Mannose-6-phosphate isomerase; Belongs to the mannose-6-phosphate isomerase type 1 family.	Phosphotransferase system, mannose fructose-specific component IIA.	0.925
KRK32613.1	KRK39965.1	FC07_GL002043	FC07_GL001819	Mannose-6-phosphate isomerase; Belongs to the mannose-6-phosphate isomerase type 1 family.	Hypothetical protein.	0.565
KRK32613.1	pgi	FC07_GL002043	FC07_GL002768	Mannose-6-phosphate isomerase; Belongs to the mannose-6-phosphate isomerase type 1 family.	Glucose-6-phosphate isomerase; Belongs to the GPI family.	0.933
KRK32646.1	KRK32613.1	FC07_GL002078	FC07_GL002043	Phosphotransferase system, mannose fructose-specific component IIA.	Mannose-6-phosphate isomerase; Belongs to the mannose-6-phosphate isomerase type 1 family.	0.925
KRK32646.1	KRK39965.1	FC07_GL002078	FC07_GL001819	Phosphotransferase system, mannose fructose-specific component IIA.	Hypothetical protein.	0.809
KRK32646.1	pgi	FC07_GL002078	FC07_GL002768	Phosphotransferase system, mannose fructose-specific component IIA.	Glucose-6-phosphate isomerase; Belongs to the GPI family.	0.427
KRK33427.1	KRK33428.1	FC07_GL001188	FC07_GL001189	UDP-galactose phosphate transferase.	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	0.981
KRK33427.1	KRK33429.1	FC07_GL001188	FC07_GL001190	UDP-galactose phosphate transferase.	Hypothetical protein.	0.983
KRK33427.1	KRK39965.1	FC07_GL001188	FC07_GL001819	UDP-galactose phosphate transferase.	Hypothetical protein.	0.603
KRK33428.1	KRK33427.1	FC07_GL001189	FC07_GL001188	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	UDP-galactose phosphate transferase.	0.981
KRK33428.1	KRK33429.1	FC07_GL001189	FC07_GL001190	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	Hypothetical protein.	0.988
KRK33428.1	KRK39963.1	FC07_GL001189	FC07_GL001861	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	Galactosyltransferase.	0.783
KRK33428.1	KRK39965.1	FC07_GL001189	FC07_GL001819	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	Hypothetical protein.	0.553
KRK33428.1	KRK40193.1	FC07_GL001189	FC07_GL001052	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	Undecaprenyl-phosphate galactose phosphotransferase.	0.650
KRK33429.1	KRK33427.1	FC07_GL001190	FC07_GL001188	Hypothetical protein.	UDP-galactose phosphate transferase.	0.983
KRK33429.1	KRK33428.1	FC07_GL001190	FC07_GL001189	Hypothetical protein.	CapD protein, required for the biosynthesis of type 1 capsular polysaccharide.	0.988
KRK33429.1	KRK39963.1	FC07_GL001190	FC07_GL001861	Hypothetical protein.	Galactosyltransferase.	0.974
KRK33429.1	KRK39965.1	FC07_GL001190	FC07_GL001819	Hypothetical protein.	Hypothetical protein.	0.694
KRK33429.1	KRK40193.1	FC07_GL001190	FC07_GL001052	Hypothetical protein.	Undecaprenyl-phosphate galactose phosphotransferase.	0.975
KRK33429.1	metG	FC07_GL001190	FC07_GL001198	Hypothetical protein.	methionyl-tRNA synthetase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation; Belongs to the class-I aminoacyl-tRNA synthetase family. MetG type 2B subfamily.	0.563

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Network Stats

number of nodes:

11

number of edges:

15

average node degree:

2.73

avg. local clustering coefficient:

0.798

expected number of edges:

10

PPI enrichment p-value:

0.0993

your network does not have significantly more
interactions than expected (what does that mean?)

Functional enrichments in your networkNote: some enrichments may be expected here (why?)
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Biological Process (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0045944

Positive regulation of transcription by RNA polymerase II

8 of 1033

1.16

1.26

2.31e-05

GO:0045893

Positive regulation of transcription, DNA-templated

9 of 1437

1.07

1.13

2.31e-05

GO:0010669

Epithelial structure maintenance

2 of 19

2.29

0.85

0.0268

GO:0006357

Regulation of transcription by RNA polymerase II

9 of 2163

0.89

0.84

8.47e-05

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0030274

LIM domain binding

2 of 6

2.8

1.24

0.0057

GO:0140297

DNA-binding transcription factor binding

5 of 411

1.36

0.99

0.0043

GO:0003697

Single-stranded DNA binding

3 of 112

1.7

0.92

0.0143

GO:0061629

RNA polymerase II-specific DNA-binding transcription factor binding

4 of 299

1.4

0.9

0.0088

GO:0043425

bHLH transcription factor binding

2 of 25

2.18

0.78

0.0358

(more ...)

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:33656268

(2021) Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.

5 of 14

2.83

3.83

7.78e-08

PMID:20348955

(2010) SSBP2 is an in vivo tumor suppressor and regulator of LDB1 stability.

5 of 15

2.8

3.83

7.78e-08

PMID:19799863

(2009) Eto2MTG16 and MTGR1 are heteromeric corepressors of the TAL1SCL transcription factor in murine erythroid progenitors.

5 of 16

2.77

3.82

7.78e-08

PMID:25238756

(2014) Requirement for ssbp2 in hematopoietic stem cell maintenance and stress response.

5 of 17

2.74

3.81

7.78e-08

PMID:31819055

(2019) ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.

5 of 26

2.56

3.5

2.27e-07

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:19515

Mixed, incl. RUNX1 regulates transcription of genes involved in differentiation of HSCs, and Transforming protein C-ets

6 of 25

2.65

5.61

1.39e-11

CL:19246

Mixed, incl. Homeobox, and Cell fate commitment

7 of 172

1.88

3.6

1.16e-09

CL:19552

Mixed, incl. Gonad morphogenesis, and LIM interaction domain

3 of 5

3.05

2.93

4.60e-06

CL:19521

Mixed, incl. LIM interaction domain, and Eosinophil differentiation

3 of 5

3.05

2.93

4.60e-06

CL:9390

Integrator complex, and SOSS complex

2 of 23

2.21

0.77

0.0374

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-8939236

RUNX1 regulates transcription of genes involved in differentiation of HSCs

5 of 79

2.07

2.92

7.68e-07

MAP-8878171

Transcriptional regulation by RUNX1

5 of 229

1.61

1.75

6.72e-05

MAP-73857

RNA Polymerase II Transcription

7 of 1566

0.92

0.73

0.0021

MAP-74160

Gene expression (Transcription)

7 of 1860

0.85

0.62

0.0050

MAP-212436

Generic Transcription Pathway

6 of 1399

0.9

0.6

0.0116

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0440

LIM domain

3 of 57

1.99

1.43

0.0016

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF04503

Single-stranded DNA binding protein, SSDP

2 of 3

3.1

1.36

0.0035

PF01803

LIM-domain binding protein

2 of 2

3.27

1.36

0.0035

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR041363

LIM interaction domain

2 of 2

3.27

1.1

0.0107

IPR029005

LIM-domain binding protein/SEUSS

2 of 2

3.27

1.1

0.0107

IPR008116

Sequence-specific single-strand DNA-binding protein

2 of 3

3.1

1.09

0.0107

IPR001781

Zinc finger, LIM-type

3 of 58

1.99

1.03

0.0107

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00132

Zinc-binding domain present in Lin-11, Isl-1, Mec-3.

3 of 59

1.98

1.28

0.0033

SM00667

Lissencephaly type-1-like homology motif

2 of 23

2.21

0.82

0.0305

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