ADZ07053.1 protein (Lactobacillus amylovorus)

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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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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

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textmining

co-expression

protein homology

Your Input:

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[Homology]

Score

ADZ07053.1

Hypothetical protein. (204 aa)

Predicted Functional Partners:

ADZ08009.1

0.720

ADZ07729.1

0.678

ADZ07492.1

0.580

ADZ08069.1

0.555

ADZ07675.1

0.552

ADZ07134.1

0.517

ADZ07052.1

0.510

ADZ07915.1

0.484

ADZ07387.1

0.482

ADZ07180.1

0.470

Your Current Organism:

Lactobacillus amylovorus

NCBI taxonomy Id: 1604
Other names: ATCC 33620, CCUG 27201, CIP 102989, DSM 16698 [[Lactobacillus sobrius]], DSM 20531, L. amylovorus, LMG 9496, LMG:9496, Lactobacillus acidophilus group A3, Lactobacillus sobrius, Lactobacillus sobrius Konstantinov et al. 2006, NCAIM B.01458, NCCB 100067 [[Lactobacillus sobrius]], NRRL B-4540, strain OTU171-001 [[Lactobacillus sobrius]]

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
ADZ07052.1	ADZ07053.1	LAC30SC_04470	LAC30SC_04475	Hypothetical protein; COG0778 Nitroreductase.	Hypothetical protein.	0.510
ADZ07053.1	ADZ07052.1	LAC30SC_04475	LAC30SC_04470	Hypothetical protein.	Hypothetical protein; COG0778 Nitroreductase.	0.510
ADZ07053.1	ADZ07134.1	LAC30SC_04475	LAC30SC_04915	Hypothetical protein.	Na+-H+ antiporter; COG0025 NhaP-type Na+/H+ and K+/H+ antiporters.	0.517
ADZ07053.1	ADZ07180.1	LAC30SC_04475	LAC30SC_05145	Hypothetical protein.	Hypothetical protein.	0.470
ADZ07053.1	ADZ07387.1	LAC30SC_04475	LAC30SC_06295	Hypothetical protein.	Hypothetical protein.	0.482
ADZ07053.1	ADZ07492.1	LAC30SC_04475	LAC30SC_06870	Hypothetical protein.	Hypothetical protein; COG0583 Transcriptional regulator.	0.580
ADZ07053.1	ADZ07675.1	LAC30SC_04475	LAC30SC_07840	Hypothetical protein.	Hypothetical protein.	0.552
ADZ07053.1	ADZ07729.1	LAC30SC_04475	LAC30SC_08140	Hypothetical protein.	Hypothetical protein.	0.678
ADZ07053.1	ADZ07915.1	LAC30SC_04475	LAC30SC_09080	Hypothetical protein.	Hypothetical protein; COG5549 Predicted Zn-dependent protease.	0.484
ADZ07053.1	ADZ08009.1	LAC30SC_04475	LAC30SC_09550	Hypothetical protein.	Hypothetical protein.	0.720
ADZ07053.1	ADZ08069.1	LAC30SC_04475	LAC30SC_09850	Hypothetical protein.	COG1266 Predicted metal-dependent membrane protease.	0.555
ADZ07134.1	ADZ07053.1	LAC30SC_04915	LAC30SC_04475	Na+-H+ antiporter; COG0025 NhaP-type Na+/H+ and K+/H+ antiporters.	Hypothetical protein.	0.517
ADZ07180.1	ADZ07053.1	LAC30SC_05145	LAC30SC_04475	Hypothetical protein.	Hypothetical protein.	0.470
ADZ07180.1	ADZ07915.1	LAC30SC_05145	LAC30SC_09080	Hypothetical protein.	Hypothetical protein; COG5549 Predicted Zn-dependent protease.	0.410
ADZ07387.1	ADZ07053.1	LAC30SC_06295	LAC30SC_04475	Hypothetical protein.	Hypothetical protein.	0.482
ADZ07387.1	ADZ07492.1	LAC30SC_06295	LAC30SC_06870	Hypothetical protein.	Hypothetical protein; COG0583 Transcriptional regulator.	0.666
ADZ07387.1	ADZ07729.1	LAC30SC_06295	LAC30SC_08140	Hypothetical protein.	Hypothetical protein.	0.657
ADZ07387.1	ADZ08069.1	LAC30SC_06295	LAC30SC_09850	Hypothetical protein.	COG1266 Predicted metal-dependent membrane protease.	0.619
ADZ07492.1	ADZ07053.1	LAC30SC_06870	LAC30SC_04475	Hypothetical protein; COG0583 Transcriptional regulator.	Hypothetical protein.	0.580
ADZ07492.1	ADZ07387.1	LAC30SC_06870	LAC30SC_06295	Hypothetical protein; COG0583 Transcriptional regulator.	Hypothetical protein.	0.666

page 1 of 2

Network Stats

number of nodes:

7

number of edges:

9

average node degree:

2.57

avg. local clustering coefficient:

0.814

expected number of edges:

7

PPI enrichment p-value:

0.228

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?)
disable highlight explain columns

Biological Process (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0071103

DNA conformation change

6 of 97

2.07

3.53

2.04e-08

GO:0006260

DNA replication

7 of 161

1.92

3.51

4.10e-09

GO:0006265

DNA topological change

3 of 8

2.85

2.59

1.78e-05

GO:0006261

DNA-templated DNA replication

5 of 113

1.92

2.45

5.20e-06

GO:0006268

DNA unwinding involved in DNA replication

3 of 21

2.43

2.03

0.00016

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0140097

Catalytic activity, acting on DNA

8 of 218

1.84

3.82

7.89e-11

GO:0003916

DNA topoisomerase activity

3 of 7

2.91

2.79

7.78e-06

GO:0140640

Catalytic activity, acting on a nucleic acid

9 of 551

1.49

2.62

5.21e-10

GO:0008094

ATP-dependent activity, acting on DNA

5 of 118

1.91

2.52

2.91e-06

GO:0061749

Forked DNA-dependent helicase activity

2 of 2

3.28

1.86

0.00045

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005694

Chromosome

7 of 1032

1.11

1.03

0.00031

GO:0042645

Mitochondrial nucleoid

2 of 39

1.99

0.8

0.0311

GO:0000228

Nuclear chromosome

3 of 182

1.5

0.78

0.0235

GO:0098687

Chromosomal region

3 of 259

1.34

0.67

0.0353

GO:0005654

Nucleoplasm

9 of 2977

0.76

0.65

0.00031

(more ...)

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:37488659

(2023) Human adaptation and diversification in the Microsporum canis complex.

3 of 9

2.8

1.54

0.0016

PMID:9786955

(1998) Cyclin-dependent kinases participate in death of neurons evoked by DNA-damaging agents.

3 of 13

2.64

1.53

0.0016

PMID:37944988

(2023) The proofreading exonuclease of leading-strand DNA polymerase epsilon prevents replication fork collapse at broken template strands.

3 of 12

2.68

1.53

0.0016

PMID:31733064

(2020) pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species.

3 of 13

2.64

1.53

0.0016

PMID:25780573

(2013) Breaking news from spermatids.

3 of 12

2.68

1.53

0.0016

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:784

Mixed, incl. DNA replication, and Fanconi anemia pathway

7 of 197

1.83

3.2

1.12e-08

CL:786

Catalytic activity, acting on DNA, and Fanconi anemia pathway

6 of 183

1.79

2.64

5.16e-07

CL:788

DNA-templated DNA replication, and HDR through Single Strand Annealing (SSA)

4 of 134

1.75

1.5

0.00067

CL:1140

SprT-like, and tyrosyl-DNA phosphodiesterase activity

2 of 6

2.8

1.25

0.0054

CL:797

RecQ family helicase-topoisomerase III complex, and Removal of the Flap Intermediate from the C-strand

2 of 13

2.47

0.96

0.0174

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

ecb03030

DNA replication

3 of 32

2.25

1.9

0.00023

ecb03420

Nucleotide excision repair

2 of 43

1.95

0.74

0.0408

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-5685942

HDR through Homologous Recombination (HRR)

4 of 60

2.1

2.19

4.38e-05

MAP-4615885

SUMOylation of DNA replication proteins

3 of 24

2.38

1.9

0.00027

MAP-174417

Telomere C-strand (Lagging Strand) Synthesis

3 of 33

2.24

1.77

0.00043

MAP-5685938

HDR through Single Strand Annealing (SSA)

3 of 40

2.15

1.69

0.00056

MAP-180786

Extension of Telomeres

3 of 55

2.02

1.54

0.00093

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0009330

DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex

2 of 2

3.28

1.48

0.0022

GOCC:0005657

Replication fork

3 of 39

2.17

1.4

0.0022

GOCC:0042645

Mitochondrial nucleoid

2 of 26

2.17

0.9

0.0214

GOCC:0070013

Intracellular organelle lumen

6 of 1406

0.91

0.56

0.0194

GOCC:0005694

Chromosome

4 of 629

1.08

0.56

0.0419

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0799

Topoisomerase

3 of 6

2.98

2.99

3.54e-06

KW-0238

DNA-binding

4 of 660

1.06

0.57

0.0362

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF08070

DTHCT (NUC029) region

2 of 2

3.28

1.37

0.0034

PF16124

RecQ zinc-binding

2 of 4

2.98

1.31

0.0043

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR044876

HRDC domain superfamily

2 of 3

3.1

1.1

0.0106

IPR034157

DNA topoisomerase 2, TOPRIM domain

2 of 2

3.28

1.1

0.0106

IPR031660

C-terminal associated domain of TOPRIM

2 of 2

3.28

1.1

0.0106

IPR018982

RQC domain

2 of 2

3.28

1.1

0.0106

IPR018522

DNA topoisomerase, type IIA, conserved site

2 of 2

3.28

1.1

0.0106

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00956

This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain PUBMED:16530788.

2 of 2

3.28

1.62

0.0012

SM00434

DNA Topoisomerase IV

2 of 2

3.28

1.62

0.0012

SM00433

TopoisomeraseII

2 of 2

3.28

1.62

0.0012

SM00341

Helicase and RNase D C-terminal

2 of 3

3.1

1.62

0.0012

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