Pnap_0373 protein (Polaromonas naphthalenivorans)

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

Pnap_0373

KEGG: sde:Sde_2347 hypothetical protein. (151 aa)

Predicted Functional Partners:

Pnap_2581

0.537

Pnap_1743

0.442

Pnap_3633

0.442

Pnap_2765

0.436

Pnap_4083

0.425

trmB

0.417

Pnap_2947

0.410

Your Current Organism:

Polaromonas naphthalenivorans

NCBI taxonomy Id: 365044
Other names: P. naphthalenivorans CJ2, Polaromonas naphthalenivorans CJ2, Polaromonas naphthalenivorans str. CJ2, Polaromonas naphthalenivorans strain CJ2

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
Pnap_0373	Pnap_1743	Pnap_0373	Pnap_1743	KEGG: sde:Sde_2347 hypothetical protein.	Transposase; KEGG: eba:p2A365 transposase, fragment.	0.442
Pnap_0373	Pnap_2581	Pnap_0373	Pnap_2581	KEGG: sde:Sde_2347 hypothetical protein.	Ornithine-acyl[acyl carrier protein] N-acyltransferase; KEGG: pol:Bpro_2243 hypothetical protein.	0.537
Pnap_0373	Pnap_2765	Pnap_0373	Pnap_2765	KEGG: sde:Sde_2347 hypothetical protein.	PFAM: Silent information regulator protein Sir2; KEGG: dar:Daro_0006 silent information regulator protein Sir2.	0.436
Pnap_0373	Pnap_2947	Pnap_0373	Pnap_2947	KEGG: sde:Sde_2347 hypothetical protein.	3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; KEGG: pol:Bpro_1625 aldehyde dehydrogenase.	0.410
Pnap_0373	Pnap_3633	Pnap_0373	Pnap_3633	KEGG: sde:Sde_2347 hypothetical protein.	Transposase; KEGG: eba:p2A365 transposase, fragment.	0.442
Pnap_0373	Pnap_4083	Pnap_0373	Pnap_4083	KEGG: sde:Sde_2347 hypothetical protein.	PFAM: peptidase M20; peptidase dimerisation domain protein; KEGG: pol:Bpro_4868 peptidase M20.	0.425
Pnap_0373	trmB	Pnap_0373	Pnap_2936	KEGG: sde:Sde_2347 hypothetical protein.	tRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA.	0.417
Pnap_1743	Pnap_0373	Pnap_1743	Pnap_0373	Transposase; KEGG: eba:p2A365 transposase, fragment.	KEGG: sde:Sde_2347 hypothetical protein.	0.442
Pnap_2581	Pnap_0373	Pnap_2581	Pnap_0373	Ornithine-acyl[acyl carrier protein] N-acyltransferase; KEGG: pol:Bpro_2243 hypothetical protein.	KEGG: sde:Sde_2347 hypothetical protein.	0.537
Pnap_2765	Pnap_0373	Pnap_2765	Pnap_0373	PFAM: Silent information regulator protein Sir2; KEGG: dar:Daro_0006 silent information regulator protein Sir2.	KEGG: sde:Sde_2347 hypothetical protein.	0.436
Pnap_2947	Pnap_0373	Pnap_2947	Pnap_0373	3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; PFAM: aldehyde dehydrogenase; KEGG: pol:Bpro_1625 aldehyde dehydrogenase.	KEGG: sde:Sde_2347 hypothetical protein.	0.410
Pnap_3633	Pnap_0373	Pnap_3633	Pnap_0373	Transposase; KEGG: eba:p2A365 transposase, fragment.	KEGG: sde:Sde_2347 hypothetical protein.	0.442
Pnap_4083	Pnap_0373	Pnap_4083	Pnap_0373	PFAM: peptidase M20; peptidase dimerisation domain protein; KEGG: pol:Bpro_4868 peptidase M20.	KEGG: sde:Sde_2347 hypothetical protein.	0.425
trmB	Pnap_0373	Pnap_2936	Pnap_0373	tRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA.	KEGG: sde:Sde_2347 hypothetical protein.	0.417

Network Stats

number of nodes:

11

number of edges:

38

average node degree:

6.91

avg. local clustering coefficient:

0.887

expected number of edges:

10

PPI enrichment p-value:

4.36e-11

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:0070897

Transcription preinitiation complex assembly

6 of 21

2.77

6.0

3.71e-12

GO:0006352

DNA-templated transcription, initiation

7 of 73

2.3

5.37

3.71e-12

GO:0006351

Transcription, DNA-templated

9 of 285

1.82

4.06

3.71e-12

GO:0051123

RNA polymerase II preinitiation complex assembly

4 of 12

2.84

4.02

3.56e-08

GO:0006366

Transcription by RNA polymerase II

5 of 169

1.79

2.32

4.58e-06

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0140296

General transcription initiation factor binding

4 of 34

2.39

2.74

5.68e-06

GO:0017025

TBP-class protein binding

3 of 16

2.59

2.24

7.14e-05

GO:0016251

RNA polymerase II general transcription initiation factor activity

3 of 22

2.45

2.08

0.00013

GO:0008134

Transcription factor binding

6 of 358

1.54

1.91

9.04e-06

GO:0061629

RNA polymerase II-specific DNA-binding transcription factor binding

4 of 188

1.65

1.43

0.00068

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0055029

Nuclear DNA-directed RNA polymerase complex

7 of 97

2.18

4.9

1.34e-11

GO:0005669

Transcription factor TFIID complex

5 of 27

2.59

4.83

4.47e-10

GO:0005667

Transcription regulator complex

8 of 371

1.65

3.14

2.63e-10

GO:0000126

Transcription factor TFIIIB complex

2 of 4

3.02

1.98

0.00026

GO:0097550

Transcription preinitiation complex

2 of 9

2.66

1.66

0.00091

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:10520

RNA Polymerase II Pre-transcription Events, and RNA Polymerase III Transcription Initiation

9 of 159

2.07

5.58

1.36e-14

CL:10650

Basal transcription factors, and Transcription factor TFIID complex

5 of 37

2.45

4.1

9.35e-09

CL:10753

RNA polymerase III complex, and RNA polymerase I complex

4 of 29

2.46

3.2

7.35e-07

CL:10657

RNA polymerase II preinitiation complex assembly, and CENP-S protein

3 of 12

2.72

2.6

1.56e-05

CL:10755

RNA polymerase III complex

3 of 21

2.47

2.25

5.95e-05

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

pret03022

Basal transcription factors

3 of 29

2.33

2.19

6.77e-05

pret03020

RNA polymerase

2 of 25

2.22

1.18

0.0061

pret04623

Cytosolic DNA-sensing pathway

2 of 34

2.09

1.13

0.0073

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-6807505

RNA polymerase II transcribes snRNA genes

7 of 104

2.15

4.72

2.83e-11

MAP-76071

RNA Polymerase III Transcription Initiation From Type 3 Promoter

5 of 29

2.55

4.58

1.36e-09

MAP-76046

RNA Polymerase III Transcription Initiation

5 of 42

2.39

4.15

5.61e-09

MAP-74158

RNA Polymerase III Transcription

5 of 48

2.34

4.02

8.38e-09

MAP-76042

RNA Polymerase II Transcription Initiation And Promoter Clearance

5 of 53

2.29

3.92

1.11e-08

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

4 of 95

1.94

1.85

0.00016

GOCC:0097550

Transcription preinitiation complex

2 of 6

2.84

1.51

0.0018

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

3 of 85

1.87

1.35

0.0019

GOCC:1990234

Transferase complex

6 of 794

1.2

1.12

0.00037

GOCC:0005654

Nucleoplasm

4 of 572

1.16

0.69

0.0194

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

2 of 13

2.5

1.16

0.0074

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR013150

Transcription factor TFIIB, cyclin-like domain

2 of 4

3.02

0.92

0.0224

IPR013137

Zinc finger, TFIIB-type

2 of 4

3.02

0.92

0.0224

IPR000812

Transcription factor TFIIB

2 of 4

3.02

0.92

0.0224

IPR009072

Histone-fold

3 of 70

1.95

0.87

0.0224

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (30%) [HD]

Permalink

Network

Neighborhood

Experiments

Cooccurrence

Databases

Fusion

Textmining

Coexpression

© STRING Consortium 2025

Credits

Access

Info

About