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
14	10

Articulation point with highest impact	Disconnected nodes when remove it
ec:3.1.3.101	4

Global metrics
4	1.4286	0.0055

Nodes classification
6	2	3	8

Total organisms
3756

Eukaryotes	Prokaryotes
0	3756

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	3590	166

list(REFERENCE = "PMID:17390001", AUTHORS = "Flatt PM, Mahmud T", TITLE = "Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds.", JOURNAL = c("Nat Prod Rep 24:358-92 (2007)", "DOI:10.1039/b603816f")), list(REFERENCE = "PMID:17661520", AUTHORS = "Mahmud T, Flatt PM, Wu X", TITLE = "Biosynthesis of unusual aminocyclitol-containing natural products.", JOURNAL = c("J Nat Prod 70:1384-91 (2007)", "DOI:10.1021/np070210q")), list(REFERENCE = "PMID:22944206", AUTHORS = "Wendler S, Hurtgen D, Kalinowski J, Klein A, Niehaus K, Schulte F, Schwientek P, Wehlmann H, Wehmeier UF, Puhler A", TITLE = "The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism.", JOURNAL = c("J Biotechnol 167:178-89 (2013)", "DOI:10.1016/j.jbiotec.2012.08.011")), list(REFERENCE = "PMID:22443545", AUTHORS = "Schwientek P, Szczepanowski R, Ruckert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Puhler A", TITLE = "The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.", JOURNAL = c("BMC Genomics 13:112 (2012)", "DOI:10.1186/1471-2164-13-112")), list(REFERENCE = "PMID:17003911", AUTHORS = "Deng Z, Bai L", TITLE = "Antibiotic biosynthetic pathways and pathway engineering--a growing research field in China.", JOURNAL = c("Nat Prod Rep 23:811-27 (2006)", "DOI:10.1039/b611140h")), list(REFERENCE = "PMID:21766819", AUTHORS = "Asamizu S, Yang J, Almabruk KH, Mahmud T", TITLE = "Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis.", JOURNAL = c("J Am Chem Soc 133:12124-35 (2011)", "DOI:10.1021/ja203574u")), list(REFERENCE = "PMID:18648803", AUTHORS = "Choi WS, Wu X, Choeng YH, Mahmud T, Jeong BC, Lee SH, Chang YK, Kim CJ, Hong SK", TITLE = "Genetic organization of the putative salbostatin biosynthetic gene cluster including the 2-epi-5-epi-valiolone synthase gene in Streptomyces albus ATCC 21838.", JOURNAL = c("Appl Microbiol Biotechnol 80:637-45 (2008)", "DOI:10.1007/s00253-008-1591-2")), list(REFERENCE = "PMID:19101977", AUTHORS = "Wu X, Flatt PM, Xu H, Mahmud T", TITLE = "Biosynthetic gene cluster of cetoniacytone A, an unusual aminocyclitol from the endosymbiotic Bacterium Actinomyces sp. Lu 9419.", JOURNAL = c("Chembiochem 10:304-14 (2009)", "DOI:10.1002/cbic.200800527"))

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
6	2	3	8

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00525 Acarbose and validamycin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

14
NODES

10
EDGES

3756
ORGANISMS

4
COMMUNITIES

1.4286
AVG. DEGREE

0.0055
AVG. BETWEENNESS

6
ARTICULATION POINTS

8
OTHER NODES

Filters

Pathway Viewer

14

10

ec:3.1.3.101

4

4

1.4286

0.0055

6

2

3

8

3756

0

3756

0

0

0

0

3590

166

Global metrics
Communities	Avg. degree	Avg. betweenness
4	1.4286	0.0055

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00525 Acarbose and validamycin biosynthesis Metabolism; Biosynthesis of other secondary metabolites

14 NODES

10 EDGES

3756 ORGANISMS

4 COMMUNITIES

1.4286 AVG. DEGREE

0.0055 AVG. BETWEENNESS

6 ARTICULATION POINTS

8 OTHER NODES

Filters

Pathway Viewer

14

10

ec:3.1.3.101

4

4

1.4286

0.0055

6

2

3

8

3756

0

3756

0

0

0

0

3590

166

KPV - KEGG Pathway Viewer
by Igor Brandão

00525 Acarbose and validamycin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

14
NODES

10
EDGES

3756
ORGANISMS

4
COMMUNITIES

1.4286
AVG. DEGREE

0.0055
AVG. BETWEENNESS

6
ARTICULATION POINTS

8
OTHER NODES