MA16_Dca012858 protein (Dendrobium catenatum)

Nodes:

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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

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second shell of interactors

Node Content

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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

MA16_Dca012858

Uncharacterized protein. (629 aa)

Predicted Functional Partners:

MA16_Dca005167

0.522

MA16_Dca011861

0.522

MA16_Dca018408

0.521

MA16_Dca004666

0.518

PUB72-2

0.518

NOP5-2-2

0.509

RACK1B-3

0.497

MA16_Dca004821

0.493

MA16_Dca007927

0.484

MA16_Dca021189

0.478

Your Current Organism:

Dendrobium catenatum

NCBI taxonomy Id: 906689
Other names: D. catenatum

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
MA16_Dca004666	MA16_Dca004821	A0A2I0VNS3	A0A2I0WG26	Sas10 domain-containing protein.	Coatomer subunit beta'-1.	0.991
MA16_Dca004666	MA16_Dca005167	A0A2I0VNS3	A0A2I0VLF3	Sas10 domain-containing protein.	U3 small nucleolar RNA-associated protein 11; Involved in nucleolar processing of pre-18S ribosomal RNA.	0.999
MA16_Dca004666	MA16_Dca007927	A0A2I0VNS3	A0A2I0XJA5	Sas10 domain-containing protein.	Katanin p80 WD40 repeat-containing subunit B1 like.	0.993
MA16_Dca004666	MA16_Dca011861	A0A2I0VNS3	A0A2I0WEC5	Sas10 domain-containing protein.	PINc domain-containing protein.	0.997
MA16_Dca004666	MA16_Dca012858	A0A2I0VNS3	A0A2I0VXS6	Sas10 domain-containing protein.	Uncharacterized protein.	0.518
MA16_Dca004666	MA16_Dca018408	A0A2I0VNS3	A0A2I0WHL8	Sas10 domain-containing protein.	KRR1 small subunit processome component; Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.	0.999
MA16_Dca004666	NOP5-2-2	A0A2I0VNS3	A0A2I0VR07	Sas10 domain-containing protein.	Putative nucleolar protein 5-2.	0.983
MA16_Dca004666	PUB72-2	A0A2I0VNS3	A0A2I0WFQ3	Sas10 domain-containing protein.	U-box domain-containing protein 72.	0.999
MA16_Dca004666	RACK1B-3	A0A2I0VNS3	A0A2I0XCX1	Sas10 domain-containing protein.	Guanine nucleotide-binding protein subunit beta-like protein B.	0.995
MA16_Dca004821	MA16_Dca004666	A0A2I0WG26	A0A2I0VNS3	Coatomer subunit beta'-1.	Sas10 domain-containing protein.	0.991
MA16_Dca004821	MA16_Dca005167	A0A2I0WG26	A0A2I0VLF3	Coatomer subunit beta'-1.	U3 small nucleolar RNA-associated protein 11; Involved in nucleolar processing of pre-18S ribosomal RNA.	0.994
MA16_Dca004821	MA16_Dca007927	A0A2I0WG26	A0A2I0XJA5	Coatomer subunit beta'-1.	Katanin p80 WD40 repeat-containing subunit B1 like.	0.999
MA16_Dca004821	MA16_Dca011861	A0A2I0WG26	A0A2I0WEC5	Coatomer subunit beta'-1.	PINc domain-containing protein.	0.991
MA16_Dca004821	MA16_Dca012858	A0A2I0WG26	A0A2I0VXS6	Coatomer subunit beta'-1.	Uncharacterized protein.	0.493
MA16_Dca004821	MA16_Dca018408	A0A2I0WG26	A0A2I0WHL8	Coatomer subunit beta'-1.	KRR1 small subunit processome component; Required for 40S ribosome biogenesis. Involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.	0.992
MA16_Dca004821	NOP5-2-2	A0A2I0WG26	A0A2I0VR07	Coatomer subunit beta'-1.	Putative nucleolar protein 5-2.	0.997
MA16_Dca004821	PUB72-2	A0A2I0WG26	A0A2I0WFQ3	Coatomer subunit beta'-1.	U-box domain-containing protein 72.	0.997
MA16_Dca004821	RACK1B-3	A0A2I0WG26	A0A2I0XCX1	Coatomer subunit beta'-1.	Guanine nucleotide-binding protein subunit beta-like protein B.	0.999
MA16_Dca005167	MA16_Dca004666	A0A2I0VLF3	A0A2I0VNS3	U3 small nucleolar RNA-associated protein 11; Involved in nucleolar processing of pre-18S ribosomal RNA.	Sas10 domain-containing protein.	0.999
MA16_Dca005167	MA16_Dca004821	A0A2I0VLF3	A0A2I0WG26	U3 small nucleolar RNA-associated protein 11; Involved in nucleolar processing of pre-18S ribosomal RNA.	Coatomer subunit beta'-1.	0.994

page 1 of 5

Network Stats

number of nodes:

11

number of edges:

21

average node degree:

3.82

avg. local clustering coefficient:

0.931

expected number of edges:

10

PPI enrichment p-value:

0.00172

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:0018871

1-aminocyclopropane-1-carboxylate metabolic process

3 of 3

3.42

3.55

3.89e-07

GO:0007231

Osmosensory signaling pathway

3 of 3

3.42

3.55

3.89e-07

GO:0009693

Ethylene biosynthetic process

4 of 18

2.77

3.48

3.39e-07

GO:0045596

Negative regulation of cell differentiation

3 of 6

3.12

3.28

1.09e-06

GO:0009652

Thigmotropism

3 of 7

3.05

3.21

1.44e-06

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0019842

Vitamin binding

6 of 112

2.15

3.94

3.59e-09

GO:0030170

Pyridoxal phosphate binding

5 of 77

2.23

3.51

7.21e-08

GO:0051019

Mitogen-activated protein kinase binding

3 of 5

3.2

3.28

1.13e-06

GO:0016846

Carbon-sulfur lyase activity

3 of 17

2.67

2.56

1.83e-05

GO:0008483

Transaminase activity

3 of 56

2.15

1.74

0.00043

(more ...)

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:25366742

(2014) Isolation of 1-aminocyclopropane-1-carboxylate synthase gene from Oncidium Gower Ramsey.

5 of 5

3.42

6.68

7.21e-13

PMID:34067834

(2021) An Overview of Metabolic Activity, Beneficial and Pathogenic Aspects of Burkholderia Spp.

5 of 7

3.28

6.46

1.51e-12

PMID:33388891

(2021) Genes and genome editing tools for breeding desirable phenotypes in ornamentals.

6 of 24

2.82

6.4

7.00e-13

PMID:35548315

(2022) The Multifaceted Roles of MYC2 in Plants: Toward Transcriptional Reprogramming and Stress Tolerance by Jasmonate Signaling.

6 of 50

2.5

5.52

9.53e-12

PMID:34921643

(2021) Floral organ-specific proteome profiling of the floral ornamental orchid (Cymbidium goeringii) reveals candidate proteins related to floral organ development.

6 of 64

2.39

5.15

3.07e-11

(more ...)

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:25402

Mixed, incl. Osmosensory signaling pathway, and Negative regulation of protein serine/threonine phosphatase activity

6 of 12

3.12

7.22

4.38e-14

CL:8062

Polyamine biosynthesis, and Aminotransferases, class-I, pyridoxal-phosphate-binding site

5 of 17

2.89

5.42

7.51e-11

CL:25416

Osmosensory signaling pathway, and 1-aminocyclopropane-1-carboxylate oxidase activity

4 of 5

3.32

4.91

1.20e-09

CL:8086

1-aminocyclopropane-1-carboxylate oxidase activity, and Aminotransferases, class-I, pyridoxal-phosphate-binding site

3 of 5

3.2

3.26

1.20e-06

CL:8065

Polyamine biosynthesis, and 1-aminocyclopropane-1-carboxylate metabolic process

2 of 10

2.72

1.34

0.0037

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

dct00270

Cysteine and methionine metabolism

5 of 77

2.23

3.88

9.40e-09

dct04016

MAPK signaling pathway - plant

5 of 115

2.06

3.44

3.26e-08

dct01110

Biosynthesis of secondary metabolites

5 of 829

1.2

1.13

0.00033

dct01100

Metabolic pathways

5 of 1519

0.94

0.69

0.0045

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0043684

Type IV secretion system complex

3 of 3

3.42

3.32

1.00e-06

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00155

Aminotransferase class I and II

5 of 27

2.69

4.75

9.51e-10

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR004838

Aminotransferases, class-I, pyridoxal-phosphate-binding site

5 of 14

2.97

5.28

1.63e-10

IPR004839

Aminotransferase, class I/classII

5 of 27

2.69

4.66

1.40e-09

IPR015422

Pyridoxal phosphate-dependent transferase, small domain

5 of 62

2.33

3.69

4.46e-08

IPR015424

Pyridoxal phosphate-dependent transferase

5 of 74

2.25

3.51

7.79e-08

IPR015421

Pyridoxal phosphate-dependent transferase, major domain

5 of 75

2.25

3.5

7.79e-08

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00338

Basic region leucin zipper

3 of 63

2.1

1.59

0.00085

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