GCA_000988015_00019 protein (Brevundimonas diminuta)

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

GCA_000988015_00019

Unannotated protein. (454 aa)

Predicted Functional Partners:

CD943_12835

0.794

CD943_04210

0.703

CD943_05070

0.703

CD943_03010

0.559

CD943_02140

0.559

CD943_11220

0.559

CD943_01330

0.520

CD943_08990

0.517

GCA_000988015_01011

0.504

polA

0.496

Your Current Organism:

Brevundimonas diminuta

NCBI taxonomy Id: 293
Other names: AJ 2067, ATCC 11568, B. diminuta, BCRC 11894, Bacterium parvulum, CCEB 513, CCRC 11894, CCRC:11894, CECT 317, CIP 63.27, DSM 7234, IAM 12691, IFO 12697, IMET 10409, JCM 2788, LMG 2088, LMG 2089, LMG:2088, LMG:2089, NBRC 12697, NCAIM B.01118, NCCB 76050, NCIB 9393, NCIMB 9393, NCTC 8545, Pseudomonas diminuta

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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
CD943_01330	CD943_02140	GCA_000988015_01294	GCA_000988015_01460	Unannotated protein.	Unannotated protein.	0.577
CD943_01330	CD943_03010	GCA_000988015_01294	GCA_000988015_00562	Unannotated protein.	Unannotated protein.	0.577
CD943_01330	CD943_11220	GCA_000988015_01294	GCA_000988015_01713	Unannotated protein.	Unannotated protein.	0.577
CD943_01330	GCA_000988015_00019	GCA_000988015_01294	GCA_000988015_00019	Unannotated protein.	Unannotated protein.	0.520
CD943_01330	GCA_000988015_01011	GCA_000988015_01294	GCA_000988015_01011	Unannotated protein.	Unannotated protein.	0.992
CD943_02140	CD943_01330	GCA_000988015_01460	GCA_000988015_01294	Unannotated protein.	Unannotated protein.	0.577
CD943_02140	CD943_03010	GCA_000988015_01460	GCA_000988015_00562	Unannotated protein.	Unannotated protein.	0.986
CD943_02140	CD943_04210	GCA_000988015_01460	GCA_000988015_01896	Unannotated protein.	Unannotated protein.	0.496
CD943_02140	CD943_05070	GCA_000988015_01460	GCA_000988015_01940	Unannotated protein.	Unannotated protein.	0.496
CD943_02140	CD943_11220	GCA_000988015_01460	GCA_000988015_01713	Unannotated protein.	Unannotated protein.	0.983
CD943_02140	GCA_000988015_00019	GCA_000988015_01460	GCA_000988015_00019	Unannotated protein.	Unannotated protein.	0.559
CD943_02140	polA	GCA_000988015_01460	GCA_000988015_01496	Unannotated protein.	Unannotated protein; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.563
CD943_03010	CD943_01330	GCA_000988015_00562	GCA_000988015_01294	Unannotated protein.	Unannotated protein.	0.577
CD943_03010	CD943_02140	GCA_000988015_00562	GCA_000988015_01460	Unannotated protein.	Unannotated protein.	0.986
CD943_03010	CD943_04210	GCA_000988015_00562	GCA_000988015_01896	Unannotated protein.	Unannotated protein.	0.496
CD943_03010	CD943_05070	GCA_000988015_00562	GCA_000988015_01940	Unannotated protein.	Unannotated protein.	0.496
CD943_03010	CD943_11220	GCA_000988015_00562	GCA_000988015_01713	Unannotated protein.	Unannotated protein.	0.986
CD943_03010	GCA_000988015_00019	GCA_000988015_00562	GCA_000988015_00019	Unannotated protein.	Unannotated protein.	0.559
CD943_03010	polA	GCA_000988015_00562	GCA_000988015_01496	Unannotated protein.	Unannotated protein; In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity; Belongs to the DNA polymerase type-A family.	0.563
CD943_04210	CD943_02140	GCA_000988015_01896	GCA_000988015_01460	Unannotated protein.	Unannotated protein.	0.496

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

46

average node degree:

8.36

avg. local clustering coefficient:

0.817

expected number of edges:

12

PPI enrichment p-value:

1.52e-13

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:0019557

Histidine catabolic process to glutamate and formate

3 of 3

2.61

2.18

9.31e-05

GO:0019556

Histidine catabolic process to glutamate and formamide

3 of 3

2.61

2.18

9.31e-05

GO:0017000

Antibiotic biosynthetic process

5 of 34

1.77

2.07

2.19e-05

GO:0043648

Dicarboxylic acid metabolic process

4 of 41

1.6

1.48

0.00040

GO:0009064

Glutamine family amino acid metabolic process

4 of 51

1.5

1.31

0.00080

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0031177

Phosphopantetheine binding

5 of 17

2.08

2.97

5.91e-07

GO:0003824

Catalytic activity

11 of 2131

0.32

0.24

0.0448

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005737

Cytoplasm

10 of 1345

0.48

0.36

0.0068

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:363

Histidine metabolism, and Polyamine biosynthesis

4 of 8

2.31

2.77

4.06e-06

CL:729

Phosphopantetheine binding, and Cytochrome P450, B-class

5 of 24

1.93

2.51

3.49e-06

CL:732

Phosphopantetheine binding, and Phosphopantetheine attachment site

3 of 18

1.83

1.43

0.0012

CL:157

Biosynthesis of amino acids, and Arginine and proline metabolism

5 of 111

1.26

1.18

0.00039

CL:751

Phosphopantetheine binding

2 of 5

2.21

1.16

0.0069

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00340

Histidine metabolism

3 of 14

1.94

1.52

0.00094

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005777

Peroxisome

5 of 35

1.76

2.24

6.41e-06

GOCC:0043231

Intracellular membrane-bounded organelle

6 of 208

1.07

0.96

0.00046

GOCC:0043229

Intracellular organelle

7 of 372

0.88

0.76

0.00057

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0369

Histidine metabolism

4 of 4

2.61

3.46

3.02e-07

KW-0596

Phosphopantetheine

5 of 27

1.87

2.71

6.65e-07

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF00501

AMP-binding enzyme

5 of 23

1.94

2.63

1.91e-06

PF00668

Condensation domain

4 of 15

2.03

2.26

2.42e-05

PF13193

AMP-binding enzyme C-terminal domain

4 of 19

1.93

2.11

3.67e-05

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR045851

AMP-binding enzyme, C-terminal domain superfamily

5 of 22

1.96

2.52

4.12e-06

IPR020845

AMP-binding, conserved site

5 of 22

1.96

2.52

4.12e-06

IPR000873

AMP-dependent synthetase/ligase domain

5 of 23

1.94

2.5

4.12e-06

IPR009081

Phosphopantetheine binding ACP domain

5 of 27

1.87

2.43

4.12e-06

IPR036736

ACP-like superfamily

5 of 28

1.86

2.42

4.12e-06

(more ...)

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00823

Phosphopantetheine attachment site

3 of 7

2.24

1.95

0.00018

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