pdg protein (Anaerohalosphaera lusitana) - STRING interaction network

Nodes:

Network nodes represent proteins

splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.

Node Color

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:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

pdg

UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate. (247 aa)

Predicted Functional Partners:

nqrD_1

0.873

AQT69219.1

0.711

xthA

0.669

polA

0.570

mutM

0.568

nqrD_2

0.541

AQT67361.1

0.521

AQT67212.1

0.509

AQT67050.1

0.461

AQT69761.1

0.461

Your Current Organism:

Anaerohalosphaera lusitana

NCBI taxonomy Id: 1936003
Other names: A. lusitana, Anaerohalosphaera lusitana Pradel et al., DSM 103484, JCM 31926, KCTC 15600, Phycisphaerae bacterium ST-NAGAB-D1, strain ST-NAGAB-D1

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
AQT67050.1	pdg	STSP2_00189	STSP2_00356	Exonuclease III.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.461
AQT67050.1	polA	STSP2_00189	STSP2_01137	Exonuclease III.	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.836
AQT67050.1	xthA	STSP2_00189	STSP2_02898	Exonuclease III.	Exodeoxyribonuclease III.	0.900
AQT67212.1	pdg	STSP2_00355	STSP2_00356	Hypothetical protein.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.509
AQT67361.1	nqrD_1	STSP2_00505	STSP2_00506	Na(+)-translocating NADH-quinone reductase subunit C.	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	0.987
AQT67361.1	nqrD_2	STSP2_00505	STSP2_02680	Na(+)-translocating NADH-quinone reductase subunit C.	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	0.441
AQT67361.1	pdg	STSP2_00505	STSP2_00356	Na(+)-translocating NADH-quinone reductase subunit C.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.521
AQT69219.1	pdg	STSP2_02408	STSP2_00356	NAD synthetase.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.711
AQT69761.1	pdg	STSP2_02958	STSP2_00356	Endonuclease/Exonuclease/phosphatase family protein.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.461
AQT69761.1	polA	STSP2_02958	STSP2_01137	Endonuclease/Exonuclease/phosphatase family protein.	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.836
mutM	pdg	STSP2_03337	STSP2_00356	Formamidopyrimidine-DNA glycosylase; Belongs to the FPG family.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.568
mutM	polA	STSP2_03337	STSP2_01137	Formamidopyrimidine-DNA glycosylase; Belongs to the FPG family.	DNA polymerase I; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.989
nqrD_1	AQT67361.1	STSP2_00506	STSP2_00505	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	Na(+)-translocating NADH-quinone reductase subunit C.	0.987
nqrD_1	pdg	STSP2_00506	STSP2_00356	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.873
nqrD_2	AQT67361.1	STSP2_02680	STSP2_00505	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	Na(+)-translocating NADH-quinone reductase subunit C.	0.441
nqrD_2	pdg	STSP2_02680	STSP2_00356	Na(+)-translocating NADH-quinone reductase subunit D; Belongs to the NqrDE/RnfAE family.	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	0.541
pdg	AQT67050.1	STSP2_00356	STSP2_00189	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	Exonuclease III.	0.461
pdg	AQT67212.1	STSP2_00356	STSP2_00355	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	Hypothetical protein.	0.509
pdg	AQT67361.1	STSP2_00356	STSP2_00505	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	Na(+)-translocating NADH-quinone reductase subunit C.	0.521
pdg	AQT69219.1	STSP2_00356	STSP2_02408	UV-endonuclease; DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'- phosphate.	NAD synthetase.	0.711

page 1 of 2

Network Stats

number of nodes:

11

number of edges:

14

average node degree:

2.55

avg. local clustering coefficient:

0.872

expected number of edges:

10

PPI enrichment p-value:

0.157

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

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:795

Mixed, incl. Nucleotide-diphospho-sugar transferases, and S-layer organization

10 of 23

1.72

4.05

5.56e-14

CL:801

Streptomycin biosynthesis, and Methyltransferase type 11

5 of 7

1.94

2.85

4.57e-07

CL:798

Mixed, incl. Streptomycin biosynthesis, and Galactose metabolism

6 of 13

1.75

2.76

1.04e-07

CL:831

Starch and sucrose metabolism, and Glycosyl transferases group 1

4 of 5

1.98

2.38

1.05e-05

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00052

Galactose metabolism

2 of 4

1.78

0.75

0.0362

map00521

Streptomycin biosynthesis

2 of 6

1.6

0.72

0.0362

map00500

Starch and sucrose metabolism

2 of 6

1.6

0.72

0.0362

map01100

Metabolic pathways

10 of 382

0.5

0.39

0.0028

map01110

Biosynthesis of secondary metabolites

6 of 165

0.64

0.39

0.0362

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF12804

MobA-like NTP transferase domain

3 of 5

1.86

1.22

0.0037

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR016040

NAD(P)-binding domain

3 of 4

1.96

1.11

0.0072

IPR005835

Nucleotidyl transferase domain

3 of 4

1.96

1.11

0.0072

IPR029044

Nucleotide-diphospho-sugar transferases

3 of 14

1.41

0.64

0.0446

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (14%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About