APZ43363.1 protein (Acidihalobacter ferrooxidans)

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

APZ43363.1

Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (395 aa)

Predicted Functional Partners:

APZ43362.1

0.962

APZ44650.1

0.949

APZ43361.1

0.914

APZ43365.1

0.860

APZ43368.1

0.837

APZ43366.1

0.835

APZ43367.1

0.834

APZ43370.1

0.834

APZ43371.1

0.833

APZ44651.1

0.827

Your Current Organism:

Acidihalobacter ferrooxidans

NCBI taxonomy Id: 1765967
Other names: A. ferrooxidans

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
APZ43361.1	APZ43362.1	BW247_09875	BW247_09885	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.923
APZ43361.1	APZ43363.1	BW247_09875	BW247_09890	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.914
APZ43361.1	APZ43365.1	BW247_09875	BW247_09900	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sulfur reduction protein DsrE; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.852
APZ43361.1	APZ43366.1	BW247_09875	BW247_09905	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Glycine cleavage system protein H; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.816
APZ43361.1	APZ43367.1	BW247_09875	BW247_09910	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Disulfide reductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.812
APZ43361.1	APZ43368.1	BW247_09875	BW247_09915	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit C; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.819
APZ43361.1	APZ43370.1	BW247_09875	BW247_09925	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Pyridine nucleotide-disulfide oxidoreductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.824
APZ43361.1	APZ43371.1	BW247_09875	BW247_09930	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit B; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.815
APZ43361.1	APZ44650.1	BW247_09875	BW247_09880	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Geranylgeranyl reductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.897
APZ43361.1	APZ44651.1	BW247_09875	BW247_09935	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit C; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.813
APZ43362.1	APZ43361.1	BW247_09885	BW247_09875	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.923
APZ43362.1	APZ43363.1	BW247_09885	BW247_09890	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Radical SAM protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.962
APZ43362.1	APZ43365.1	BW247_09885	BW247_09900	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sulfur reduction protein DsrE; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.871
APZ43362.1	APZ43366.1	BW247_09885	BW247_09905	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Glycine cleavage system protein H; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.996
APZ43362.1	APZ43367.1	BW247_09885	BW247_09910	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Disulfide reductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.817
APZ43362.1	APZ43368.1	BW247_09885	BW247_09915	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit C; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.848
APZ43362.1	APZ43370.1	BW247_09885	BW247_09925	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Pyridine nucleotide-disulfide oxidoreductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.859
APZ43362.1	APZ43371.1	BW247_09885	BW247_09930	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit B; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.843
APZ43362.1	APZ44650.1	BW247_09885	BW247_09880	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Geranylgeranyl reductase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.940
APZ43362.1	APZ44651.1	BW247_09885	BW247_09935	Lipoate--protein ligase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Heterodisulfide reductase subunit C; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.840

page 1 of 6

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

13

PPI enrichment p-value:

< 1.0e-16

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:0000467

Exonucleolytic trimming to generate mature 3-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

11 of 14

2.68

11.66

4.48e-25

GO:0071038

Nuclear polyadenylation-dependent tRNA catabolic process

11 of 16

2.62

11.42

4.48e-25

GO:0016075

rRNA catabolic process

11 of 25

2.43

10.12

5.49e-24

GO:0071035

Nuclear polyadenylation-dependent rRNA catabolic process

9 of 15

2.56

9.01

1.41e-19

GO:0034427

Nuclear-transcribed mRNA catabolic process, exonucleolytic, 3-5

8 of 13

2.58

8.0

4.15e-17

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003723

RNA binding

11 of 460

1.17

1.7

2.37e-10

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000176

Nuclear exosome (RNase complex)

11 of 12

2.75

12.38

3.33e-26

GO:0000177

Cytoplasmic exosome (RNase complex)

10 of 12

2.71

11.0

2.68e-23

GO:0005730

Nucleolus

11 of 227

1.47

3.06

1.36e-14

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:3967

Exonucleolytic trimming to generate mature 3-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

11 of 13

2.71

12.08

8.47e-26

CL:3971

Nuclear exosome (RNase complex)

8 of 8

2.79

8.76

7.38e-18

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03018

RNA degradation

11 of 89

1.88

5.68

6.12e-19

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-450513

Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA

10 of 13

2.67

10.51

2.10e-22

MAP-450385

Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA

10 of 15

2.61

10.24

3.00e-22

MAP-429958

mRNA decay by 3 to 5 exoribonuclease

10 of 19

2.51

9.62

1.22e-21

MAP-450531

Regulation of mRNA stability by proteins that bind AU-rich elements

10 of 26

2.37

8.71

1.16e-20

MAP-429914

Deadenylation-dependent mRNA decay

10 of 40

2.18

7.37

3.76e-19

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000178

Exosome (RNase complex)

11 of 14

2.68

11.89

1.22e-25

GOCC:0000176

Nuclear exosome (RNase complex)

7 of 7

2.79

7.55

2.66e-15

GOCC:0000177

Cytoplasmic exosome (RNase complex)

6 of 8

2.66

5.99

2.35e-12

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0269

Exonuclease

2 of 6

2.31

0.98

0.0153

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF01138

3 exoribonuclease family, domain 1

6 of 6

2.79

6.1

2.47e-12

PF15985

KH domain

2 of 2

2.79

1.25

0.0055

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR027408

PNPase/RNase PH domain superfamily

6 of 6

2.79

5.86

7.48e-12

IPR001247

Exoribonuclease, phosphorolytic domain 1

6 of 6

2.79

5.86

7.48e-12

IPR020568

Ribosomal protein S5 domain 2-type fold

6 of 29

2.1

3.84

4.32e-09

IPR036345

Exoribonuclease, PH domain 2 superfamily

3 of 3

2.79

2.42

3.69e-05

IPR012340

Nucleic acid-binding, OB-fold

4 of 52

1.67

1.46

0.00062

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00316

Ribosomal protein S1-like RNA-binding domain

2 of 5

2.39

1.03

0.0130

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (28%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About