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
31	62

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.1.99.9	21

Global metrics
7	4.0000	0.0293

Nodes classification
9	2	6	22

Total organisms
5344

Eukaryotes	Prokaryotes
500	4844

Animals	Plants	Fungi	Protists	Bacteria	Archaea
244	105	123	28	4580	264

list(REFERENCE = "PMID:10753941", AUTHORS = "Tazoe M, Ichikawa K, Hoshino T.", TITLE = "Biosynthesis of vitamin B(6) in rhizobium.", JOURNAL = c("J Biol Chem 275:11300-5 (2000)", "DOI:10.1074/jbc.275.15.11300")), list(REFERENCE = "PMID:9696782", AUTHORS = "Yang Y, Zhao G, Man TK, Winkler ME.", TITLE = "Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5`-phosphate coenzyme biosynthesis in Escherichia coli K-12.", JOURNAL = "J Bacteriol 180:4294-9 (1998)"), list(REFERENCE = "PMID:12269807", AUTHORS = "Yeh JI, Du S, Pohl E, Cane DE.", TITLE = "Multistate binding in pyridoxine 5`-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.", JOURNAL = c("Biochemistry 41:11649-57 (2002)", "DOI:10.1021/bi026292t")), list(REFERENCE = "PMID:10225425", AUTHORS = "Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS.", TITLE = "Vitamin B6 biosynthesis: formation of pyridoxine 5`-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein.", JOURNAL = c("FEBS Lett 449:45-8 (1999)", "DOI:10.1016/S0014-5793(99)00393-2")), list(REFERENCE = "PMID:16157873", AUTHORS = "Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB.", TITLE = "Vitamin B6 biosynthesis in higher plants.", JOURNAL = c("Proc Natl Acad Sci U S A 102:13687-92 (2005)", "DOI:10.1073/pnas.0506228102")), list(REFERENCE = "PMID:22276911", AUTHORS = "Nagase T, Mugo AN, Chu HN, Yoshikane Y, Ohnishi K, Yagi T", TITLE = "The mll6786 gene encodes a repressor protein controlling the degradation pathway for vitamin B6 in Mesorhizobium loti.", JOURNAL = c("FEMS Microbiol Lett 329:116-22 (2012)", "DOI:10.1111/j.1574-6968.2012.02510.x"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00750 Vitamin B6 metabolism
Metabolism; Metabolism of cofactors and vitamins

31
NODES

62
EDGES

5344
ORGANISMS

7
COMMUNITIES

4.0000
AVG. DEGREE

0.0293
AVG. BETWEENNESS

9
ARTICULATION POINTS

22
OTHER NODES

Filters

Pathway Viewer

31

62

ec:1.1.99.9

21

7

4.0000

0.0293

9

2

6

22

5344

500

4844

244

105

123

28

4580

264

Global metrics
Communities	Avg. degree	Avg. betweenness
7	4.0000	0.0293

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00750 Vitamin B6 metabolism Metabolism; Metabolism of cofactors and vitamins

31 NODES

62 EDGES

5344 ORGANISMS

7 COMMUNITIES

4.0000 AVG. DEGREE

0.0293 AVG. BETWEENNESS

9 ARTICULATION POINTS

22 OTHER NODES