troB protein (Paenibacillus polymyxa) - STRING interaction network

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

troB

Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (254 aa)

Predicted Functional Partners:

troA

0.999

troC

0.999

mntD

0.999

adcB

0.941

psaA3

0.933

mntH

0.768

fliY5

0.690

tcyJ

0.690

fliY1

0.690

ytmJ

0.690

Your Current Organism:

Paenibacillus polymyxa

NCBI taxonomy Id: 1406
Other names: ATCC 842, Aerobacillus polymyxa, Bacillus polymyxa, Bacillus sp. NCIM 2538, Bacillus sp. NCIM 2540, Bacillus sp. NCIM 2726, Bacillus sp. RP 2.2, CCUG 7426, CFBP 4258, CIP 66.22, Clostridium polymyxa, DSM 36, Granulobacter polymyxa, HAMBI 635, IAM 13419, IFO 15309, JCM 2507, LMG 13294, LMG:13294, NBRC 15309, NCCB 24016, NCIB 8158, NCIB:8158, NCTC 10343, NRRL B-4317, P. polymyxa, Paenibacillus sp. JCM 8035, Paenibacillus sp. JCM 8036, Paenibacillus sp. JCM 8037, Paenibacillus sp. JCM 8038, Paenibacillus sp. JCM 8039, Paenibacillus sp. WLY78, VKM B-514

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
adcB	mntD	LK13_23570	LK13_19440	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.838
adcB	mntH	LK13_23570	LK13_19400	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	0.522
adcB	psaA3	LK13_23570	LK13_23575	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Zinc ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 9 family.	0.997
adcB	troA	LK13_23570	LK13_19425	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese transporter; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 9 family.	0.915
adcB	troB	LK13_23570	LK13_19430	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.941
adcB	troC	LK13_23570	LK13_19435	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.546
fliY1	fliY5	LK13_17090	LK13_05865	Cysteine ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 3 family.	Amino acid ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.915
fliY1	troB	LK13_17090	LK13_19430	Cysteine ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 3 family.	Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.690
fliY5	fliY1	LK13_05865	LK13_17090	Amino acid ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Cysteine ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 3 family.	0.915
fliY5	troB	LK13_05865	LK13_19430	Amino acid ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.690
mntD	adcB	LK13_19440	LK13_23570	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.838
mntD	mntH	LK13_19440	LK13_19400	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	0.755
mntD	psaA3	LK13_19440	LK13_23575	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Zinc ABC transporter substrate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 9 family.	0.935
mntD	troA	LK13_19440	LK13_19425	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese transporter; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 9 family.	0.999
mntD	troB	LK13_19440	LK13_19430	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
mntD	troC	LK13_19440	LK13_19435	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Manganese ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.978
mntH	adcB	LK13_19400	LK13_23570	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	Zinc ABC transporter permease; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.522
mntH	mntD	LK13_19400	LK13_19440	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	Iron ABC transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.755
mntH	troA	LK13_19400	LK13_19425	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	Manganese transporter; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the bacterial solute-binding protein 9 family.	0.662
mntH	troB	LK13_19400	LK13_19430	Manganese transporter; H(+)-stimulated, divalent metal cation uptake system. Belongs to the NRAMP family.	Manganese ABC transporter ATP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.768

page 1 of 3

Network Stats

number of nodes:

11

number of edges:

52

average node degree:

9.45

avg. local clustering coefficient:

0.958

expected number of edges:

13

PPI enrichment p-value:

1.11e-16

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:0009073

Aromatic amino acid family biosynthetic process

7 of 14

2.2

4.77

4.05e-11

GO:0000162

Tryptophan biosynthetic process

4 of 4

2.5

3.23

7.12e-07

GO:0046417

Chorismate metabolic process

3 of 9

2.02

1.85

0.00020

GO:0008652

Cellular amino acid biosynthetic process

7 of 99

1.35

1.81

7.12e-07

GO:0019438

Aromatic compound biosynthetic process

10 of 203

1.19

1.71

2.70e-09

(more ...)

Molecular Function (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0016829

Lyase activity

6 of 121

1.2

1.08

0.00060

GO:0016835

Carbon-oxygen lyase activity

4 of 46

1.44

1.03

0.0042

GO:0004834

Tryptophan synthase activity

2 of 2

2.5

1.03

0.0133

GO:0004106

Chorismate mutase activity

2 of 2

2.5

1.03

0.0133

GO:0016836

Hydro-lyase activity

3 of 37

1.41

0.7

0.0319

Cellular Component (Gene Ontology)

GO-term

description

count in network

strength

signal

false discovery rate

GO:0005737

Cytoplasm

10 of 1270

0.4

0.28

0.0388

Reference Publications (PubMed)

publication

(year) title

count in network

strength

signal

false discovery rate

PMID:30808357

(2019) Metabolic engineering of microorganisms for production of aromatic compounds.

4 of 8

2.2

2.52

1.05e-05

PMID:34584039

(2021) Recent Advances in Synthetic, Industrial and Biological Applications of Violacein and Its Heterologous Production.

2 of 2

2.5

1.07

0.0109

Local Network Cluster (STRING)

cluster

description

count in network

strength

signal

false discovery rate

CL:1391

Aromatic amino acid biosynthesis, and Anthranilate synthase/para-aminobenzoate synthase like domain

10 of 15

2.32

7.99

3.90e-19

CL:1393

Tryptophan biosynthesis

5 of 6

2.42

4.23

4.38e-09

CL:1407

Chorismate metabolic process

3 of 7

2.13

1.88

0.00022

KEGG Pathways

pathway

description

count in network

strength

signal

false discovery rate

pha00400

Phenylalanine, tyrosine and tryptophan biosynthesis

8 of 18

2.15

5.67

5.08e-14

pha01230

Biosynthesis of amino acids

8 of 113

1.35

2.04

1.36e-08

pha00790

Folate biosynthesis

3 of 24

1.6

1.25

0.0018

pha01110

Biosynthesis of secondary metabolites

8 of 287

0.95

0.97

1.13e-05

pha01100

Metabolic pathways

8 of 632

0.6

0.46

0.0026

Annotated Keywords (UniProt)

keyword

description

count in network

strength

signal

false discovery rate

KW-0057

Aromatic amino acid biosynthesis

7 of 12

2.27

5.34

3.03e-12

KW-0822

Tryptophan biosynthesis

5 of 5

2.5

4.45

2.07e-09

KW-0456

Lyase

9 of 133

1.33

2.1

1.40e-09

Protein Domains (Pfam)

domain

description

count in network

strength

signal

false discovery rate

PF04715

Anthranilate synthase component I, N terminal region

2 of 2

2.5

0.84

0.0299

PF00425

Chorismate binding enzyme

2 of 2

2.5

0.84

0.0299

Protein Domains (SMART)

domain

description

count in network

strength

signal

false discovery rate

SM00830

Chorismate mutase type II

2 of 2

2.5

1.18

0.0068

Enrichment display settings

Enrichment analysis is still ongoing, please wait ...

Server load: low (20%) [HD]

Permalink

Network

Neighborhood

Experiments

Fusion

Databases

Cooccurrence

Textmining

Coexpression

© STRING Consortium 2024

Credits

Access

Info

About