GCA_001592145_03282 protein (Xylanimicrobium pachnodae)

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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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

GCA_001592145_03282

Unannotated protein. (579 aa)

Predicted Functional Partners:

GCA_001592145_03281

0.967

GCA_001592145_00463

0.866

GCA_001592145_03283

0.828

GCA_001592145_03280

0.818

GCA_001592145_02732

0.812

GCA_001592145_02651

0.773

GCA_001592145_02044

0.747

GCA_001592145_00395

0.739

GCA_001592145_03284

0.709

GCA_001592145_03285

0.709

Your Current Organism:

Xylanimicrobium pachnodae

NCBI taxonomy Id: 1305855
Other names: X. pachnodae JCM 13526 = NBRC 107786, Xylanimicrobium pachnodae JCM 13526, Xylanimicrobium pachnodae JCM 13526 = NBRC 107786, Xylanimicrobium pachnodae NBRC 107786, Xylanimicrobium pachnodae NBRC 107786 = JCM 13526

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Browse interactions in tabular form:

node1	node2	node1 annotation	node2 annotation	score
GCA_001592145_00395	GCA_001592145_00463	Unannotated protein.	Unannotated protein.	0.997
GCA_001592145_00395	GCA_001592145_02044	Unannotated protein.	Unannotated protein.	0.400
GCA_001592145_00395	GCA_001592145_02651	Unannotated protein.	Unannotated protein.	0.422
GCA_001592145_00395	GCA_001592145_03282	Unannotated protein.	Unannotated protein.	0.739
GCA_001592145_00463	GCA_001592145_00395	Unannotated protein.	Unannotated protein.	0.997
GCA_001592145_00463	GCA_001592145_02044	Unannotated protein.	Unannotated protein.	0.741
GCA_001592145_00463	GCA_001592145_02651	Unannotated protein.	Unannotated protein.	0.601
GCA_001592145_00463	GCA_001592145_02732	Unannotated protein.	Unannotated protein.	0.988
GCA_001592145_00463	GCA_001592145_03282	Unannotated protein.	Unannotated protein.	0.866
GCA_001592145_02044	GCA_001592145_00395	Unannotated protein.	Unannotated protein.	0.400
GCA_001592145_02044	GCA_001592145_00463	Unannotated protein.	Unannotated protein.	0.741
GCA_001592145_02044	GCA_001592145_02651	Unannotated protein.	Unannotated protein.	0.915
GCA_001592145_02044	GCA_001592145_03282	Unannotated protein.	Unannotated protein.	0.747
GCA_001592145_02651	GCA_001592145_00395	Unannotated protein.	Unannotated protein.	0.422
GCA_001592145_02651	GCA_001592145_00463	Unannotated protein.	Unannotated protein.	0.601
GCA_001592145_02651	GCA_001592145_02044	Unannotated protein.	Unannotated protein.	0.915
GCA_001592145_02651	GCA_001592145_03282	Unannotated protein.	Unannotated protein.	0.773
GCA_001592145_02732	GCA_001592145_00463	Unannotated protein.	Unannotated protein.	0.988
GCA_001592145_02732	GCA_001592145_03282	Unannotated protein.	Unannotated protein.	0.812
GCA_001592145_03280	GCA_001592145_03281	Unannotated protein.	Unannotated protein.	0.943

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

11

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:0051050

Positive regulation of transport

3 of 17

1.95

1.09

0.0078

GO:0006468

Protein phosphorylation

5 of 111

1.35

0.96

0.0052

GO:1902660

Negative regulation of glucose mediated signaling pathway

2 of 4

2.4

0.93

0.0200

GO:0000212

Meiotic spindle organization

2 of 5

2.3

0.91

0.0209

GO:0071988

Protein localization to spindle pole body

2 of 7

2.16

0.87

0.0239

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0004707

MAP kinase activity

3 of 3

2.7

2.08

0.00015

GO:0005509

Calcium ion binding

4 of 39

1.71

1.59

0.00033

GO:0004674

Protein serine/threonine kinase activity

5 of 88

1.46

1.43

0.00023

GO:0106310

Protein serine kinase activity

4 of 70

1.46

1.17

0.0017

GO:0043167

Ion binding

11 of 1403

0.6

0.51

0.00019

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016459

Myosin complex

3 of 7

2.33

1.87

0.00030

GO:0005816

Spindle pole body

5 of 96

1.42

1.36

0.00030

GO:0016460

Myosin II complex

2 of 3

2.53

1.35

0.0034

GO:0044732

Mitotic spindle pole body

4 of 75

1.43

1.13

0.0020

GO:0005856

Cytoskeleton

7 of 283

1.09

1.03

0.00024

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:656

Myosin II complex, and Myosin I complex

3 of 6

2.4

1.78

0.00046

CL:917

Stress-activated MAPK cascade, and Activation of the AP-1 family of transcription factors

3 of 14

2.03

1.4

0.0019

CL:933

Activation of the AP-1 family of transcription factors, and Transcription factor, MADS-box

2 of 6

2.22

1.04

0.0119

CL:2383

Calmodulin-dependent protein kinase activity, and Synaptonemal structure

2 of 6

2.22

1.04

0.0119

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map04070

Phosphatidylinositol signaling system

3 of 29

1.72

1.17

0.0039

map04011

MAPK signaling pathway - yeast

3 of 79

1.28

0.66

0.0327

map04111

Cell cycle - yeast

3 of 99

1.18

0.6

0.0413

Reactome Pathways

pathway

description

count in network

strength

signal

false discovery rate

MAP-198753

ERK/MAPK targets

3 of 8

2.28

1.79

0.00041

MAP-450282

MAPK targets/ Nuclear events mediated by MAP kinases

3 of 10

2.18

1.73

0.00048

MAP-881907

Gastrin-CREB signalling pathway via PKC and MAPK

2 of 2

2.7

1.73

0.00069

MAP-198725

Nuclear Events (kinase and transcription factor activation)

3 of 11

2.14

1.72

0.00048

MAP-187037

Signaling by NTRK1 (TRKA)

3 of 12

2.1

1.7

0.00048

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0016459

Myosin complex

3 of 9

2.22

1.56

0.0011

GOCC:0016460

Myosin II complex

2 of 2

2.7

1.11

0.0096

GOCC:0071341

Medial cortical node

2 of 7

2.16

0.93

0.0182

GOCC:0005816

Spindle pole body

3 of 45

1.53

0.84

0.0171

GOCC:0032153

Cell division site

4 of 109

1.27

0.81

0.0108

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0106

Calcium

5 of 24

2.02

3.04

2.68e-07

KW-0723

Serine/threonine-protein kinase

4 of 29

1.84

2.05

3.63e-05

KW-0418

Kinase

6 of 171

1.25

1.36

3.63e-05

KW-0547

Nucleotide-binding

5 of 327

0.89

0.59

0.0111

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR018247

EF-Hand 1, calcium-binding site

5 of 17

2.17

3.06

5.59e-07

IPR002048

EF-hand domain

5 of 19

2.12

3.02

5.59e-07

IPR011992

EF-hand domain pair

5 of 21

2.08

2.98

5.59e-07

IPR008271

Serine/threonine-protein kinase, active site

5 of 60

1.62

1.82

4.22e-05

IPR000719

Protein kinase domain

5 of 77

1.51

1.58

0.00011

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00054

EF-hand, calcium binding motif

5 of 10

2.4

4.09

7.78e-09

SM00220

Serine/Threonine protein kinases, catalytic domain

3 of 34

1.65

1.08

0.0054

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