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.

Nodes	Edges
18	13

Articulation point with highest impact	Disconnected nodes when remove it
ec:3.1.2.32	4

Global metrics
6	1.4444	0.0123

Nodes classification
7	1	4	11

Total organisms
645

Eukaryotes	Prokaryotes
0	645

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	627	18

list(REFERENCE = "PMID:23897464", AUTHORS = "Xu N, Ahuja EG, Janning P, Mavrodi DV, Thomashow LS, Blankenfeldt W", TITLE = "Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis.", JOURNAL = c("Acta Crystallogr D Biol Crystallogr 69:1403-13 (2013)", "DOI:10.1107/S0907444913008354")), list(REFERENCE = "PMID:20352425", AUTHORS = "Pierson LS 3rd, Pierson EA", TITLE = "Metabolism and function of phenazines in bacteria: impacts on the behavior of bacteria in the environment and biotechnological processes.", JOURNAL = c("Appl Microbiol Biotechnol 86:1659-70 (2010)", "DOI:10.1007/s00253-010-2509-3")), list(REFERENCE = "PMID:19053436", AUTHORS = "Ahuja EG, Janning P, Mentel M, Graebsch A, Breinbauer R, Hiller W, Costisella B, Thomashow LS, Mavrodi DV, Blankenfeldt W", TITLE = "PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis.", JOURNAL = c("J Am Chem Soc 130:17053-61 (2008)", "DOI:10.1021/ja806325k")), list(REFERENCE = "PMID:19658148", AUTHORS = "Mentel M, Ahuja EG, Mavrodi DV, Breinbauer R, Thomashow LS, Blankenfeldt W", TITLE = "Of two make one: the biosynthesis of phenazines.", JOURNAL = c("Chembiochem 10:2295-304 (2009)", "DOI:10.1002/cbic.200900323")), list(REFERENCE = "PMID:15502343", AUTHORS = "Parsons JF, Calabrese K, Eisenstein E, Ladner JE", TITLE = "Structure of the phenazine biosynthesis enzyme PhzG.", JOURNAL = c("Acta Crystallogr D Biol Crystallogr 60:2110-3 (2004)", "DOI:10.1107/S0907444904022474")), list(REFERENCE = "PMID:11591691", AUTHORS = "Mavrodi DV, Bonsall RF, Delaney SM, Soule MJ, Phillips G, Thomashow LS", TITLE = "Functional analysis of genes for biosynthesis of pyocyanin and phenazine-1-carboxamide from Pseudomonas aeruginosa PAO1.", JOURNAL = c("J Bacteriol 183:6454-65 (2001)", "DOI:10.1128/JB.183.21.6454-6465.2001"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00405 Phenazine biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

18
NODES

13
EDGES

645
ORGANISMS

6
COMMUNITIES

1.4444
AVG. DEGREE

0.0123
AVG. BETWEENNESS

7
ARTICULATION POINTS

11
OTHER NODES

Filters

Pathway Viewer

18

13

ec:3.1.2.32

4

6

1.4444

0.0123

7

1

4

11

645

0

645

0

0

0

0

627

18

Global metrics
Communities	Avg. degree	Avg. betweenness
6	1.4444	0.0123

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00405 Phenazine biosynthesis Metabolism; Biosynthesis of other secondary metabolites

18 NODES

13 EDGES

645 ORGANISMS

6 COMMUNITIES

1.4444 AVG. DEGREE

0.0123 AVG. BETWEENNESS

7 ARTICULATION POINTS

11 OTHER NODES