EAR61569.1 protein (Neptuniibacter caesariensis)

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:

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Gene Fusion

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[Homology]

Score

EAR61569.1

COG0008 Glutamyl- and glutaminyl-tRNA synthetases. (500 aa)

Predicted Functional Partners:

EAR59478.1

0.990

EAR59464.1

0.989

rplM

0.986

EAR59463.1

0.986

EAR59474.1

0.984

EAR61510.1

0.982

EAR59468.1

0.982

EAR59479.1

0.982

EAR59469.1

0.979

EAR59644.1

0.977

Your Current Organism:

Neptuniibacter caesariensis

NCBI taxonomy Id: 207954
Other names: CCUG 52065, CECT 7075, N. caesariensis, Neptuniibacter caesariensis Arahal et al. 2007, Oceanospirillum sp. MED92, strain MED92

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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
EAR59463.1	EAR59464.1	MED92_18443	MED92_18448	COG0256 Ribosomal protein L18.	COG0097 Ribosomal protein L6P/L9E.	0.999
EAR59463.1	EAR59468.1	MED92_18443	MED92_18468	COG0256 Ribosomal protein L18.	COG0198 Ribosomal protein L24.	0.999
EAR59463.1	EAR59469.1	MED92_18443	MED92_18473	COG0256 Ribosomal protein L18.	COG0093 Ribosomal protein L14.	0.999
EAR59463.1	EAR59474.1	MED92_18443	MED92_18498	COG0256 Ribosomal protein L18.	COG0091 Ribosomal protein L22.	0.999
EAR59463.1	EAR59478.1	MED92_18443	MED92_18518	COG0256 Ribosomal protein L18.	COG0089 Ribosomal protein L23.	0.999
EAR59463.1	EAR59479.1	MED92_18443	MED92_18523	COG0256 Ribosomal protein L18.	COG0088 Ribosomal protein L4.	0.999
EAR59463.1	EAR59644.1	MED92_18443	MED92_04532	COG0256 Ribosomal protein L18.	COG0244 Ribosomal protein L10.	0.999
EAR59463.1	EAR61510.1	MED92_18443	MED92_18428	COG0256 Ribosomal protein L18.	COG0200 Ribosomal protein L15.	0.999
EAR59463.1	EAR61569.1	MED92_18443	MED92_12981	COG0256 Ribosomal protein L18.	COG0008 Glutamyl- and glutaminyl-tRNA synthetases.	0.986
EAR59463.1	rplM	MED92_18443	MED92_15925	COG0256 Ribosomal protein L18.	50S ribosomal protein L13; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.	0.999
EAR59464.1	EAR59463.1	MED92_18448	MED92_18443	COG0097 Ribosomal protein L6P/L9E.	COG0256 Ribosomal protein L18.	0.999
EAR59464.1	EAR59468.1	MED92_18448	MED92_18468	COG0097 Ribosomal protein L6P/L9E.	COG0198 Ribosomal protein L24.	0.999
EAR59464.1	EAR59469.1	MED92_18448	MED92_18473	COG0097 Ribosomal protein L6P/L9E.	COG0093 Ribosomal protein L14.	0.999
EAR59464.1	EAR59474.1	MED92_18448	MED92_18498	COG0097 Ribosomal protein L6P/L9E.	COG0091 Ribosomal protein L22.	0.999
EAR59464.1	EAR59478.1	MED92_18448	MED92_18518	COG0097 Ribosomal protein L6P/L9E.	COG0089 Ribosomal protein L23.	0.999
EAR59464.1	EAR59479.1	MED92_18448	MED92_18523	COG0097 Ribosomal protein L6P/L9E.	COG0088 Ribosomal protein L4.	0.998
EAR59464.1	EAR59644.1	MED92_18448	MED92_04532	COG0097 Ribosomal protein L6P/L9E.	COG0244 Ribosomal protein L10.	0.999
EAR59464.1	EAR61510.1	MED92_18448	MED92_18428	COG0097 Ribosomal protein L6P/L9E.	COG0200 Ribosomal protein L15.	0.999
EAR59464.1	EAR61569.1	MED92_18448	MED92_12981	COG0097 Ribosomal protein L6P/L9E.	COG0008 Glutamyl- and glutaminyl-tRNA synthetases.	0.989
EAR59464.1	rplM	MED92_18448	MED92_15925	COG0097 Ribosomal protein L6P/L9E.	50S ribosomal protein L13; This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.	0.999

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Network Stats

number of nodes:

11

number of edges:

26

average node degree:

4.73

avg. local clustering coefficient:

0.881

expected number of edges:

11

PPI enrichment p-value:

0.000163

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:0006351

Transcription, DNA-templated

5 of 40

1.62

1.67

0.00012

GO:0006352

DNA-templated transcription, initiation

3 of 25

1.6

0.86

0.0177

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016987

Sigma factor activity

3 of 24

1.62

0.7

0.0400

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0000428

DNA-directed RNA polymerase complex

2 of 7

1.98

0.79

0.0321

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:6578

Mixed, incl. RNA polymerase sigma factor 70, ECF, conserved site

5 of 5

2.53

4.04

1.63e-08

CL:6538

Mixed, incl. RNA polymerase sigma factor 70, region 4 type 2, and Formate transport

6 of 29

1.84

2.96

8.31e-08

CL:286

RNA polymerase, and Transcription antitermination

2 of 5

2.13

0.88

0.0226

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

map03020

RNA polymerase

2 of 4

2.22

0.99

0.0145

map02020

Two-component system

5 of 250

0.83

0.49

0.0298

Subcellular Localization (COMPARTMENTS)

compartment

description

count in network

strength

signal

false discovery rate

GOCC:0000428

DNA-directed RNA polymerase complex

5 of 64

1.42

1.41

0.00021

GOCC:0032991

Protein-containing complex

6 of 439

0.66

0.4

0.0336

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0731

Sigma factor

3 of 21

1.68

1.15

0.0041

KW-0240

DNA-directed RNA polymerase

2 of 5

2.13

1.02

0.0120

KW-0804

Transcription

5 of 123

1.13

0.85

0.0039

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF04542

Sigma-70 region 2

3 of 18

1.75

0.92

0.0149

Protein Domains and Features (InterPro)

domain

description

count in network

strength

signal

false discovery rate

IPR013249

RNA polymerase sigma factor 70, region 4 type 2

3 of 11

1.96

1.03

0.0108

IPR039425

RNA polymerase sigma-70 like

3 of 12

1.92

1.02

0.0108

IPR014284

RNA polymerase sigma-70 like domain

3 of 21

1.68

0.85

0.0197

IPR013325

RNA polymerase sigma factor, region 2

3 of 21

1.68

0.85

0.0197

IPR013324

RNA polymerase sigma factor, region 3/4-like

3 of 22

1.66

0.85

0.0197

(more ...)

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