KPV - KEGG Pathway Viewer

Term	Meaning
Metabolic pathway	In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The term network is sometimes defined to mean a graph in which attributes (e.g. names) are associated with the vertices and edges, and the subject that expresses and understands the real-world systems as a network is called network science.
Network/Graphs	In mathematics, graph theory is the study of graphs, which are mathematical structures used to model pairwise relations between objects.
Network visualization	Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Node	In mathematics, and more specifically in graph theory, a vertex (plural vertices) or node is the fundamental unit of which graphs are formed.
Edge	For an undirected graph, an unordered pair of nodes that specify a line joining these two nodes are said to form an edge. For a directed graph, the edge is an ordered pair of nodes. The terms "arc," "branch," "line," "link," and "1-simplex" are sometimes used instead of edge.
KEGG	KEGG: Kyoto Encyclopedia of Genes and Genomes is a Japanese database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
KEGG Pathway	KEGG PATHWAY is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction, reaction and relation.
Pathway code	Each pathway map is identified by the combination of 2-4 letter prefix code and 5 digit number.
Articulation point	In a graph, a vertex is called an articulation point if removing it and all the edges associated with it results in the increase of the number of connected components in the graph.
Articulation point impact	The impact is defined as the number of vertices that get disconnected from the main (largest) surviving connected component after the removal of the articulation point node.
AP node	AP is the abbreviation for Articulation point.
HAP node	AP is the abbreviation for Hub and Articulation point.
HUB node	In network science, a hub is a node with a number of links that greatly exceeds the average.
Other nodes	In the context of this tool, other nodes represent nodes without classification.

00333 Prodigiosin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Prodiginines are red-pigmented natural antibiotics that are produced as secondary metabolites and have received renewed attention because of potential clinical interests. In Serratia sp. or actinomycetes such as Streptomyces coelicolor, the tripyrrole molecules of prodigiosin and undecylprodigiosin are formed by the condensation of 4-methoxy-2,2`-bipyrrole-5-carbaldehyde and either 2-methyl-3-n-amyl-pyrrole [MD:M00837] or 2-undecylpyrrole [MD:M00838]. The Serratia pig gene cluster and the Streptomyces red gene cluster responsible for these biosynthesis pathways have been identified.

Network metrics

Nodes	Edges
2	1

Articulation point with highest impact	Disconnected nodes when remove it
NA	1

Global metrics
Communities	Avg. degree	Avg. betweenness
2	1.0000	1.0000

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
0	0	0	2

Description

Class

Metabolism; Biosynthesis of other secondary metabolites

Map

Prodigiosin biosynthesis

Module

Prodigiosin biosynthesis, L-proline => prodigiosin [PATH:map00333], Undecylprodigiosin biosynthesis, L-proline => undecylprodigiosin [PATH:map00333]

Associated diseases

Associated organisms count

Total organisms
21

Eukaryotes	Prokaryotes
0	21

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	21	0

GO associated terms

KO pathway

ko00333

References

list(REFERENCE = "PMID:15853884", AUTHORS = "Williamson NR, Simonsen HT, Ahmed RA, Goldet G, Slater H, Woodley L, Leeper FJ, Salmond GP", TITLE = "Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces.", JOURNAL = c("Mol Microbiol 56:971-89 (2005)", "DOI:10.1111/j.1365-2958.2005.04602.x")), list(REFERENCE = "PMID:11514230", AUTHORS = "Cerdeno AM, Bibb MJ, Challis GL", TITLE = "Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes.", JOURNAL = c("Chem Biol 8:817-29 (2001)", "DOI:10.1016/S1074-5521(01)00054-0")), list(REFERENCE = "PMID:15528645", AUTHORS = "Harris AK, Williamson NR, Slater H, Cox A, Abbasi S, Foulds I, Simonsen HT, Leeper FJ, Salmond GP", TITLE = "The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation.", JOURNAL = c("Microbiology 150:3547-60 (2004)", "DOI:10.1099/mic.0.27222-0")), list(REFERENCE = "PMID:17109029", AUTHORS = "Williamson NR, Fineran PC, Leeper FJ, Salmond GP", TITLE = "The biosynthesis and regulation of bacterial prodiginines.", JOURNAL = c("Nat Rev Microbiol 4:887-99 (2006)", "DOI:10.1038/nrmicro1531"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00333 Prodigiosin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

2
NODES

1
EDGES

21
ORGANISMS

2
COMMUNITIES

1.0000
AVG. DEGREE

1.0000
AVG. BETWEENNESS

0
ARTICULATION POINTS

2
OTHER NODES

Filters

Pathway Viewer

2

1

NA

1

2

1.0000

1.0000

0

0

0

2

21

0

21

0

0

0

0

21

0

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00333 Prodigiosin biosynthesis Metabolism; Biosynthesis of other secondary metabolites

2 NODES

1 EDGES

21 ORGANISMS

2 COMMUNITIES

1.0000 AVG. DEGREE

1.0000 AVG. BETWEENNESS

0 ARTICULATION POINTS

2 OTHER NODES

Filters

Pathway Viewer

2

1

NA

1

2

1.0000

1.0000

0

0

0

2

21

0

21

0

0

0

0

21

0

KPV - KEGG Pathway Viewer
by Igor Brandão

00333 Prodigiosin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

2
NODES

1
EDGES

21
ORGANISMS

2
COMMUNITIES

1.0000
AVG. DEGREE

1.0000
AVG. BETWEENNESS

0
ARTICULATION POINTS

2
OTHER NODES