nploc4 protein (Betta splendens) - 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.

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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:

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Gene Fusion

Cooccurrence

Coexpression

Experiments

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[Homology]

Score

nploc4

NPL4 homolog, ubiquitin recognition factor. (623 aa)

Predicted Functional Partners:

ubxn7

0.999

fancm

0.999

ufd1

0.992

derl1

0.985

FANCA

0.982

fancf

0.982

ENSBSLP00000004319

0.982

fancg

0.982

fancl

0.982

fancc

0.982

Your Current Organism:

Betta splendens

NCBI taxonomy Id: 158456
Other names: B. splendens, Siamese fighting fish

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
ENSBSLP00000004319	FANCA	ENSBSLP00000004319	ENSBSLP00000001498	FA core complex associated protein 24.	FA complementation group A.	0.998
ENSBSLP00000004319	fancc	ENSBSLP00000004319	ENSBSLP00000035559	FA core complex associated protein 24.	FA complementation group C.	0.965
ENSBSLP00000004319	fancf	ENSBSLP00000004319	ENSBSLP00000003563	FA core complex associated protein 24.	FA complementation group F.	0.965
ENSBSLP00000004319	fancg	ENSBSLP00000004319	ENSBSLP00000017976	FA core complex associated protein 24.	FA complementation group G.	0.998
ENSBSLP00000004319	fancl	ENSBSLP00000004319	ENSBSLP00000026692	FA core complex associated protein 24.	FA complementation group L.	0.998
ENSBSLP00000004319	fancm	ENSBSLP00000004319	ENSBSLP00000038782	FA core complex associated protein 24.	FA complementation group M.	0.999
ENSBSLP00000004319	nploc4	ENSBSLP00000004319	ENSBSLP00000048828	FA core complex associated protein 24.	NPL4 homolog, ubiquitin recognition factor.	0.982
FANCA	ENSBSLP00000004319	ENSBSLP00000001498	ENSBSLP00000004319	FA complementation group A.	FA core complex associated protein 24.	0.998
FANCA	fancc	ENSBSLP00000001498	ENSBSLP00000035559	FA complementation group A.	FA complementation group C.	0.999
FANCA	fancf	ENSBSLP00000001498	ENSBSLP00000003563	FA complementation group A.	FA complementation group F.	0.999
FANCA	fancg	ENSBSLP00000001498	ENSBSLP00000017976	FA complementation group A.	FA complementation group G.	0.999
FANCA	fancl	ENSBSLP00000001498	ENSBSLP00000026692	FA complementation group A.	FA complementation group L.	0.999
FANCA	fancm	ENSBSLP00000001498	ENSBSLP00000038782	FA complementation group A.	FA complementation group M.	0.999
FANCA	nploc4	ENSBSLP00000001498	ENSBSLP00000048828	FA complementation group A.	NPL4 homolog, ubiquitin recognition factor.	0.982
derl1	nploc4	ENSBSLP00000030069	ENSBSLP00000048828	Derlin 1.	NPL4 homolog, ubiquitin recognition factor.	0.985
derl1	ufd1	ENSBSLP00000030069	ENSBSLP00000022876	Derlin 1.	Ubiquitin recognition factor in ER associated degradation 1.	0.993
fancc	ENSBSLP00000004319	ENSBSLP00000035559	ENSBSLP00000004319	FA complementation group C.	FA core complex associated protein 24.	0.965
fancc	FANCA	ENSBSLP00000035559	ENSBSLP00000001498	FA complementation group C.	FA complementation group A.	0.999
fancc	fancf	ENSBSLP00000035559	ENSBSLP00000003563	FA complementation group C.	FA complementation group F.	0.999
fancc	fancg	ENSBSLP00000035559	ENSBSLP00000017976	FA complementation group C.	FA complementation group G.	0.999

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

28

PPI enrichment p-value:

1.32e-06

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:0006351

Transcription, DNA-templated

7 of 25

2.0

3.95

5.53e-10

GO:0006352

DNA-templated transcription, initiation

3 of 15

1.85

1.41

0.0014

GO:0019438

Aromatic compound biosynthetic process

8 of 270

1.02

1.06

1.90e-05

GO:0018130

Heterocycle biosynthetic process

8 of 294

0.98

0.99

3.13e-05

GO:1901362

Organic cyclic compound biosynthetic process

8 of 305

0.97

0.96

3.63e-05

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0003899

DNA-directed 5-3 RNA polymerase activity

4 of 6

2.37

2.73

5.59e-06

GO:0016987

Sigma factor activity

3 of 15

1.85

1.33

0.0021

GO:0003677

DNA binding

7 of 307

0.91

0.75

0.0010

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000428

DNA-directed RNA polymerase complex

4 of 9

2.2

2.71

3.94e-06

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:37075846

(2023) Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics.

4 of 6

2.37

2.55

1.31e-05

PMID:38741736

(2024) Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus.

3 of 3

2.55

2.0

0.00020

PMID:30200857

(2018) Transcriptional Responses to ppGpp and DksA.

4 of 14

2.0

1.99

9.46e-05

PMID:34254822

(2021) Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa.

3 of 5

2.33

1.84

0.00034

PMID:24516534

(2014) Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72.

4 of 23

1.79

1.67

0.00027

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:215

RNA polymerase, and Transcription termination

3 of 5

2.33

1.63

0.00087

CL:92

Ribosome, and RNA polymerase

4 of 67

1.32

0.8

0.0141

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

rsp03020

RNA polymerase

4 of 4

2.55

3.46

2.66e-07

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

7 of 66

1.57

2.47

6.05e-08

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

4 of 9

2.2

2.63

5.88e-06

KW-0731

Sigma factor

3 of 15

1.85

1.51

0.00081

KW-0804

Transcription

7 of 150

1.22

1.43

5.88e-06

KW-0548

Nucleotidyltransferase

4 of 45

1.5

1.36

0.00055

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF04545

Sigma-70, region 4

3 of 7

2.18

1.52

0.0013

PF04542

Sigma-70 region 2

3 of 11

1.98

1.39

0.0019

PF00140

Sigma-70 factor, region 1.2

2 of 2

2.55

1.12

0.0091

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR000943

RNA polymerase sigma-70

3 of 4

2.42

1.62

0.00096

IPR007630

RNA polymerase sigma-70 region 4

3 of 7

2.18

1.47

0.0016

IPR014284

RNA polymerase sigma-70 like domain

3 of 11

1.98

1.28

0.0033

IPR013325

RNA polymerase sigma factor, region 2

3 of 11

1.98

1.28

0.0033

IPR007627

RNA polymerase sigma-70 region 2

3 of 11

1.98

1.28

0.0033

(more ...)

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