OSB07962.1 protein (Paraclostridium bifermentans)

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

OSB07962.1

Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology. (445 aa)

Predicted Functional Partners:

OSB07963.1

0.912

OSB08002.1

0.911

OSB07964.1

0.911

OSB07975.1

0.888

OSB07973.1

0.842

OSB07967.1

0.809

OSB07979.1

0.791

OSB07966.1

0.709

OSB12409.1

0.708

OSB10472.1

0.692

Your Current Organism:

Paraclostridium bifermentans

NCBI taxonomy Id: 1490
Other names: ATCC 638, BCRC 14542, Bacillus bifermentans, Bacillus bifermentans sporogenes, Bacillus centrosporogenes, CCRC 14542, CCRC:14542, CCUG 36626, CIP 104309, Clostridium bifermentans, DSM 14991, Martellillus bifermentans, NCIMB 10716, NCTC 13019, P. bifermentans

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
OSB07962.1	OSB07963.1	B2H97_15955	B2H97_15960	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Phage capsid protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.912
OSB07962.1	OSB07964.1	B2H97_15955	B2H97_15965	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.911
OSB07962.1	OSB07966.1	B2H97_15955	B2H97_15975	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.709
OSB07962.1	OSB07967.1	B2H97_15955	B2H97_15980	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Phage coat protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.809
OSB07962.1	OSB07973.1	B2H97_15955	B2H97_16015	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.842
OSB07962.1	OSB07975.1	B2H97_15955	B2H97_16025	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Tail tape measure protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.888
OSB07962.1	OSB07979.1	B2H97_15955	B2H97_16045	Terminase; 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
OSB07962.1	OSB08002.1	B2H97_15955	B2H97_15950	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.911
OSB07962.1	OSB10472.1	B2H97_15955	B2H97_05745	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.692
OSB07962.1	OSB12409.1	B2H97_15955	B2H97_04750	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.708
OSB07963.1	OSB07962.1	B2H97_15960	B2H97_15955	Phage capsid protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Terminase; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.912
OSB07963.1	OSB07964.1	B2H97_15960	B2H97_15965	Phage capsid 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.	0.984
OSB07963.1	OSB07966.1	B2H97_15960	B2H97_15975	Phage capsid 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
OSB07963.1	OSB07967.1	B2H97_15960	B2H97_15980	Phage capsid protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Phage coat protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.936
OSB07963.1	OSB07973.1	B2H97_15960	B2H97_16015	Phage capsid 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.	0.897
OSB07963.1	OSB07975.1	B2H97_15960	B2H97_16025	Phage capsid protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Tail tape measure protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.947
OSB07963.1	OSB07979.1	B2H97_15960	B2H97_16045	Phage capsid 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.	0.763
OSB07963.1	OSB08002.1	B2H97_15960	B2H97_15950	Phage capsid 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.	0.727
OSB07963.1	OSB10472.1	B2H97_15960	B2H97_05745	Phage capsid 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.	0.717
OSB07963.1	OSB12409.1	B2H97_15960	B2H97_04750	Phage capsid 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.	0.740

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Network Stats

number of nodes:

11

number of edges:

55

average node degree:

10

avg. local clustering coefficient:

1

expected number of edges:

25

PPI enrichment p-value:

9.09e-08

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:0006412

Translation

11 of 128

1.69

4.18

7.28e-16

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0019843

rRNA binding

11 of 44

2.15

7.64

8.20e-21

GO:0003735

Structural constituent of ribosome

11 of 57

2.04

6.81

5.26e-20

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005840

Ribosome

11 of 60

2.01

6.72

3.27e-20

GO:0015935

Small ribosomal subunit

3 of 8

2.33

2.45

1.91e-05

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:37185344

(2023) Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.

7 of 31

2.11

4.47

8.07e-11

PMID:28083017

(2016) Distribution of Hydrogenases in Cyanobacteria: A Phylum-Wide Genomic Survey.

6 of 20

2.23

4.29

9.18e-10

PMID:26096579

(2015) Neutral red-mediated microbial electrosynthesis by Escherichia coli, Klebsiella pneumoniae, and Zymomonas mobilis.

5 of 49

1.76

2.2

8.48e-06

PMID:37991636

(2023) De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain.

3 of 36

1.67

0.93

0.0127

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:169

Ribosome

11 of 31

2.3

8.83

4.54e-22

CL:209

Small ribosomal subunit, and Ribosome

5 of 11

2.41

4.38

1.92e-09

CL:172

rRNA-binding

5 of 16

2.25

3.92

8.47e-09

CL:211

Small ribosomal subunit, and Ribosomal protein S13-like, H2TH

4 of 5

2.65

3.89

4.47e-08

CL:174

rRNA-binding

4 of 11

2.31

3.21

4.60e-07

(more ...)

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

reh03010

Ribosome

11 of 55

2.05

7.06

1.00e-20

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0005840

Ribosome

10 of 52

2.04

6.21

1.65e-17

GOCC:0015935

Small ribosomal subunit

6 of 13

2.42

5.42

8.57e-12

GOCC:0044391

Ribosomal subunit

7 of 27

2.17

5.17

2.04e-12

GOCC:0022626

Cytosolic ribosome

5 of 21

2.13

3.68

1.42e-08

GOCC:0022627

Cytosolic small ribosomal subunit

4 of 9

2.4

3.53

1.25e-07

(more ...)

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0699

rRNA-binding

11 of 40

2.19

8.13

8.94e-22

KW-0689

Ribosomal protein

11 of 55

2.05

7.06

1.01e-20

KW-0820

tRNA-binding

2 of 17

1.82

0.84

0.0239

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