ALS99837.1 protein (Lacimicrobium alkaliphilum)

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

ALS99837.1

Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (128 aa)

Predicted Functional Partners:

ALS99838.1

0.791

ALS99836.1

0.773

ALS99835.1

0.613

ALS99839.1

0.501

Your Current Organism:

Lacimicrobium alkaliphilum

NCBI taxonomy Id: 1526571
Other names: Alteromonadaceae bacterium X13M-12, CGMCC 1.12923, KCTC 42674, L. alkaliphilum, Lacimicrobium alkaliphilum Zhong et al. 2016, strain X13M-12

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... functional annotations:

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
ALS99835.1	ALS99836.1	AT746_17240	AT746_17245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.945
ALS99835.1	ALS99837.1	AT746_17240	AT746_17250	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.613
ALS99835.1	ALS99838.1	AT746_17240	AT746_17255	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.770
ALS99836.1	ALS99835.1	AT746_17245	AT746_17240	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.945
ALS99836.1	ALS99837.1	AT746_17245	AT746_17250	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.773
ALS99836.1	ALS99838.1	AT746_17245	AT746_17255	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.828
ALS99836.1	ALS99839.1	AT746_17245	AT746_17260	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
ALS99837.1	ALS99835.1	AT746_17250	AT746_17240	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.613
ALS99837.1	ALS99836.1	AT746_17250	AT746_17245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.773
ALS99837.1	ALS99838.1	AT746_17250	AT746_17255	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.791
ALS99837.1	ALS99839.1	AT746_17250	AT746_17260	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
ALS99838.1	ALS99835.1	AT746_17255	AT746_17240	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.770
ALS99838.1	ALS99836.1	AT746_17255	AT746_17245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.828
ALS99838.1	ALS99837.1	AT746_17255	AT746_17250	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.791
ALS99838.1	ALS99839.1	AT746_17255	AT746_17260	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
ALS99839.1	ALS99836.1	AT746_17260	AT746_17245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Two-component system response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
ALS99839.1	ALS99837.1	AT746_17260	AT746_17250	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501
ALS99839.1	ALS99838.1	AT746_17260	AT746_17255	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.501

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

23

PPI enrichment p-value:

6.55e-09

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

9 of 259

1.88

4.47

5.53e-13

GO:0006366

Transcription by RNA polymerase II

5 of 82

2.12

3.28

1.37e-07

GO:0031990

mRNA export from nucleus in response to heat stress

2 of 2

3.34

2.04

0.00021

GO:0006367

Transcription initiation from RNA polymerase II promoter

3 of 37

2.25

2.01

0.00014

GO:0034402

Recruitment of 3-end processing factors to RNA polymerase II holoenzyme complex

2 of 3

3.16

1.93

0.00033

(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

7 of 37

2.62

6.82

2.93e-14

GO:0031369

Translation initiation factor binding

2 of 16

2.44

1.15

0.0077

GO:0003677

DNA binding

6 of 2294

0.76

0.42

0.0448

GO:1901363

Heterocyclic compound binding

10 of 7560

0.46

0.33

0.0180

GO:0097159

Organic cyclic compound binding

10 of 7587

0.46

0.33

0.0180

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005665

RNA polymerase II, core complex

8 of 18

2.99

10.15

4.24e-20

GO:0055029

Nuclear DNA-directed RNA polymerase complex

10 of 106

2.31

8.26

4.24e-20

GO:0005736

RNA polymerase I complex

4 of 14

2.79

4.44

5.02e-09

GO:0005666

RNA polymerase III complex

4 of 23

2.58

3.98

2.46e-08

GO:0005730

Nucleolus

5 of 329

1.52

1.88

9.04e-06

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:9014

RNA polymerase II, core complex, and Transcription elongation factor, TFIIS

9 of 20

2.99

11.17

3.60e-22

CL:9021

RNA polymerase II, core complex

7 of 10

3.18

9.4

3.36e-18

CL:8998

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

11 of 151

2.2

8.08

2.23e-21

CL:9026

RNA polymerase II, core complex

5 of 5

3.34

6.68

6.42e-13

CL:9230

RNA Polymerase III Transcription, and RNA Polymerase I Transcription Initiation

2 of 34

2.11

0.75

0.0406

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

nnu03020

RNA polymerase

10 of 36

2.78

12.06

3.41e-25

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-9018519

Estrogen-dependent gene expression

9 of 49

2.6

9.37

3.39e-20

MAP-77075

RNA Pol II CTD phosphorylation and interaction with CE

9 of 50

2.59

9.35

3.39e-20

MAP-72086

mRNA Capping

9 of 52

2.58

9.3

3.39e-20

MAP-6807505

RNA polymerase II transcribes snRNA genes

10 of 78

2.45

9.27

2.40e-21

MAP-113418

Formation of the Early Elongation Complex

9 of 55

2.55

9.21

3.51e-20

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0055029

Nuclear DNA-directed RNA polymerase complex

10 of 92

2.37

8.66

1.79e-20

GOCC:0005665

RNA polymerase II, core complex

4 of 7

3.1

4.81

1.50e-09

GOCC:0005736

RNA polymerase I complex

4 of 11

2.9

4.46

5.43e-09

GOCC:0000419

RNA polymerase V complex

3 of 10

2.82

3.11

1.82e-06

GOCC:0031981

Nuclear lumen

8 of 838

1.32

1.89

5.15e-08

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0240

DNA-directed RNA polymerase

10 of 47

2.67

11.08

8.31e-24

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF03871

RNA polymerase Rpb5, N-terminal domain

2 of 2

3.34

1.46

0.0024

PF01191

RNA polymerase Rpb5, C-terminal domain

2 of 2

3.34

1.46

0.0024

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR045222

DNA-directed RNA polymerase II subunit Rpb4-like

3 of 3

3.34

2.79

9.05e-06

IPR038324

Rpb4/RPC9 superfamily

3 of 4

3.21

2.79

9.05e-06

IPR006590

RNA polymerase Rpb4/RPC9, core

3 of 4

3.21

2.79

9.05e-06

IPR005574

RNA polymerase subunit Rpb4/RPC9

3 of 4

3.21

2.79

9.05e-06

IPR010997

HRDC-like superfamily

3 of 8

2.91

2.64

1.49e-05

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00657

DNA-directed RNA-polymerase II subunit

3 of 4

3.21

3.24

1.34e-06

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