APY04_2382 protein (Hyphomicrobium sulfonivorans)

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

white nodes:
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

APY04_2382

Periplasmic hemin-binding protein. (312 aa)

Predicted Functional Partners:

hmuV

0.979

APY04_2383

0.975

APY04_1657

0.933

APY04_2949

0.910

APY04_2380

0.823

APY04_2950

0.802

APY04_2381

0.779

APY04_1711

0.778

APY04_1656

0.751

APY04_2654

0.748

Your Current Organism:

Hyphomicrobium sulfonivorans

NCBI taxonomy Id: 121290
Other names: ATCC BAA-113, DSM 13863, H. sulfonivorans, Hyphomicrobium sp. S1, Hyphomicrobium sulfonivorans Borodina et al. 2002, strain S1

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
APY04_1656	APY04_1657	APY04_1656	APY04_1657	Vitamin B12 ABC transporter, ATPase component BtuD.	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.991
APY04_1656	APY04_2382	APY04_1656	APY04_2382	Vitamin B12 ABC transporter, ATPase component BtuD.	Periplasmic hemin-binding protein.	0.751
APY04_1656	APY04_2383	APY04_1656	APY04_2383	Vitamin B12 ABC transporter, ATPase component BtuD.	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.961
APY04_1656	APY04_2949	APY04_1656	APY04_2949	Vitamin B12 ABC transporter, ATPase component BtuD.	Vitamin B12 ABC transporter, permease component BtuC; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.971
APY04_1657	APY04_1656	APY04_1657	APY04_1656	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	Vitamin B12 ABC transporter, ATPase component BtuD.	0.991
APY04_1657	APY04_1711	APY04_1657	APY04_1711	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	Iron-chelator utilization protein.	0.607
APY04_1657	APY04_2382	APY04_1657	APY04_2382	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	Periplasmic hemin-binding protein.	0.933
APY04_1657	APY04_2950	APY04_1657	APY04_2950	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	Vitamin B12 ABC transporter, ATPase component BtuD.	0.985
APY04_1657	hmuV	APY04_1657	APY04_2384	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	ABC-type hemin transport system, ATPase component; Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system.	0.986
APY04_1711	APY04_1657	APY04_1711	APY04_1657	Iron-chelator utilization protein.	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.607
APY04_1711	APY04_2380	APY04_1711	APY04_2380	Iron-chelator utilization protein.	TonB-dependent hemin, ferrichrome receptor.	0.408
APY04_1711	APY04_2382	APY04_1711	APY04_2382	Iron-chelator utilization protein.	Periplasmic hemin-binding protein.	0.778
APY04_1711	APY04_2383	APY04_1711	APY04_2383	Iron-chelator utilization protein.	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.739
APY04_1711	APY04_2654	APY04_1711	APY04_2654	Iron-chelator utilization protein.	Hypothetical protein.	0.497
APY04_1711	APY04_2949	APY04_1711	APY04_2949	Iron-chelator utilization protein.	Vitamin B12 ABC transporter, permease component BtuC; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.500
APY04_1711	hmuV	APY04_1711	APY04_2384	Iron-chelator utilization protein.	ABC-type hemin transport system, ATPase component; Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system.	0.809
APY04_2380	APY04_1711	APY04_2380	APY04_1711	TonB-dependent hemin, ferrichrome receptor.	Iron-chelator utilization protein.	0.408
APY04_2380	APY04_2382	APY04_2380	APY04_2382	TonB-dependent hemin, ferrichrome receptor.	Periplasmic hemin-binding protein.	0.823
APY04_2380	APY04_2383	APY04_2380	APY04_2383	TonB-dependent hemin, ferrichrome receptor.	Hemin ABC transporter, permease protein; Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily.	0.538
APY04_2380	hmuV	APY04_2380	APY04_2384	TonB-dependent hemin, ferrichrome receptor.	ABC-type hemin transport system, ATPase component; Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system.	0.623

page 1 of 4

Network Stats

number of nodes:

11

number of edges:

32

average node degree:

5.82

avg. local clustering coefficient:

0.813

expected number of edges:

28

PPI enrichment p-value:

0.244

your network does not have 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:0006099

Tricarboxylic acid cycle

10 of 20

2.29

7.77

7.28e-19

GO:0006091

Generation of precursor metabolites and energy

11 of 119

1.56

3.51

3.27e-15

GO:0044238

Primary metabolic process

11 of 1488

0.46

0.37

0.0019

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000104

Succinate dehydrogenase activity

4 of 4

2.59

3.15

1.20e-06

GO:0036440

Citrate synthase activity

2 of 2

2.59

1.12

0.0090

GO:0008177

Succinate dehydrogenase (ubiquinone) activity

2 of 2

2.59

1.12

0.0090

GO:0004775

succinate-CoA ligase (ADP-forming) activity

2 of 2

2.59

1.12

0.0090

GO:0016417

S-acyltransferase activity

2 of 3

2.42

1.11

0.0090

(more ...)

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:1990204

Oxidoreductase complex

4 of 15

2.02

2.38

1.23e-05

GO:1902494

Catalytic complex

5 of 88

1.35

1.39

0.00012

GO:0045239

Tricarboxylic acid cycle enzyme complex

2 of 3

2.42

1.38

0.0028

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:23902230

(2013) Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains.

3 of 18

1.82

1.84

0.00011

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1985

Tricarboxylic acid cycle

8 of 11

2.46

7.28

4.74e-16

CL:1982

Citrate cycle (TCA cycle), and FAD-dependent oxidoreductase 2, FAD binding domain

9 of 24

2.17

6.5

1.93e-16

CL:1980

Mixed, incl. Citrate cycle (TCA cycle), and Pyruvate metabolism

11 of 51

1.93

5.87

1.90e-18

CL:1981

Citrate cycle (TCA cycle), and Pyruvate metabolism

10 of 42

1.97

5.77

6.68e-17

CL:1987

Succinate dehydrogenase activity

4 of 5

2.5

3.43

2.66e-07

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map00020

Citrate cycle (TCA cycle)

10 of 20

2.29

8.11

6.57e-20

map01200

Carbon metabolism

10 of 113

1.54

3.24

1.61e-13

map00190

Oxidative phosphorylation

4 of 39

1.61

1.74

6.77e-05

map00650

Butanoate metabolism

4 of 40

1.59

1.73

6.77e-05

map01120

Microbial metabolism in diverse environments

10 of 317

1.09

1.47

2.29e-09

(more ...)

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0045239

Tricarboxylic acid cycle enzyme complex

4 of 6

2.42

3.03

1.51e-06

GOCC:1990204

Oxidoreductase complex

5 of 28

1.85

2.56

1.51e-06

GOCC:0045273

Respiratory chain complex II

3 of 5

2.37

2.25

5.48e-05

GOCC:0045281

Succinate dehydrogenase complex

2 of 2

2.59

1.56

0.0014

GOCC:0045274

Plasma membrane respiratory chain complex II

2 of 2

2.59

1.56

0.0014

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0816

Tricarboxylic acid cycle

6 of 12

2.29

4.65

2.14e-10

KW-0450

Lipoyl

2 of 4

2.29

1.08

0.0102

KW-0012

Acyltransferase

3 of 54

1.34

0.72

0.0257

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF01127

Succinate dehydrogenase/Fumarate reductase transmembrane subunit

2 of 2

2.59

0.91

0.0227

PF00549

CoA-ligase

2 of 2

2.59

0.91

0.0227

PF00285

Citrate synthase, C-terminal domain

2 of 2

2.59

0.91

0.0227

PF02817

e3 binding domain

2 of 3

2.42

0.9

0.0227

PF00198

2-oxoacid dehydrogenases acyltransferase (catalytic domain)

2 of 3

2.42

0.9

0.0227

(more ...)

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