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.

Network metrics

Nodes	Edges
46	167

Articulation point with highest impact	Disconnected nodes when remove it
ec:3.1.1.17	42

Global metrics
Communities	Avg. degree	Avg. betweenness
8	7.1739	0.0361

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
6	2	9	40

The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway. One is irreversible oxidative phase in which glucose-6P is converted to ribulose-5P by oxidative decarboxylation, and NADPH is generated [MD:M00006]. The other is reversible non-oxidative phase in which phosphorylated sugars are interconverted to generate xylulose-5P, ribulose-5P, and ribose-5P [MD:M00007]. Phosphoribosyl pyrophosphate (PRPP) formed from ribose-5P [MD:M00005] is an activated compound used in the biosynthesis of histidine and purine/pyrimidine nucleotides. This pathway map also shows the Entner-Doudoroff pathway where 6-P-gluconate is dehydrated and then cleaved into pyruvate and glyceraldehyde-3P [MD:M00008].

Class

Metabolism; Carbohydrate metabolism

Map

Pentose phosphate pathway

Module

Pentose phosphate pathway (Pentose phosphate cycle) [PATH:map00030], PRPP biosynthesis, ribose 5P => PRPP [PATH:map00030], Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:map00030], Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:map00030], Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate [PATH:map00030], D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P [PATH:map00030], Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glycerate-3P [PATH:map00030], Non-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate [PATH:map00030], Formaldehyde assimilation, ribulose monophosphate pathway [PATH:map00030], Pentose phosphate pathway, archaea, fructose 6P => ribose 5P [PATH:map00030], D-Galacturonate degradation (bacteria), D-galacturonate => pyruvate + D-glyceraldehyde 3P [PATH:map00030], Semi-phosphorylative Entner-Doudoroff pathway, gluconate/galactonate => glycerate-3P [PATH:map00030]

Associated diseases

Phosphoribosylpyrophosphate synthetase superactivity, Anemia due to disorders of glutathione metabolism, Arts syndrome, Cortisone reductase deficiency, Ribose 5-phosphate isomerase deficiency, Transaldolase deficiency, Glucose 6-phosphate dehydrogenase deficiency, Glycogen storage disease type XII

Associated organisms count

Total organisms
6064

Eukaryotes	Prokaryotes
531	5533

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	128	50	5236	297

GO associated terms

GO: 0006098

KO pathway

ko00030

References

list(REFERENCE = "(map 3)", AUTHORS = "Nishizuka Y (ed).", TITLE = "[Metabolic Maps] (In Japanese)", JOURNAL = "Tokyo Kagaku Dojin (1980)"), list(REFERENCE = "(map 4)", AUTHORS = "Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).", TITLE = "[Cellular Functions and Metabolic Maps] (In Japanese)", JOURNAL = "Tokyo Kagaku Dojin (1997)"), list(REFERENCE = "", AUTHORS = "Michal G.", TITLE = "Biochemical Pathways", JOURNAL = "Wiley (1999)"), list(REFERENCE = "PMID:12700258", AUTHORS = "Hove-Jensen B, Rosenkrantz TJ, Haldimann A, Wanner BL.", TITLE = "Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.", JOURNAL = c("J Bacteriol 185:2793-801 (2003)", "DOI:10.1128/JB.185.9.2793-2801.2003")), list(REFERENCE = "PMID:16788179", AUTHORS = "Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T, Sakai Y", TITLE = "The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis.", JOURNAL = c("J Bacteriol 188:4698-704 (2006)", "DOI:10.1128/JB.00492-06")), list(REFERENCE = "PMID:16428816", AUTHORS = "Kato N, Yurimoto H, Thauer RK", TITLE = "The physiological role of the ribulose monophosphate pathway in bacteria and archaea.", JOURNAL = c("Biosci Biotechnol Biochem 70:10-21 (2006)", "DOI:10.1271/bbb.70.10")), list(REFERENCE = "PMID:23279921", AUTHORS = "Kouril T, Wieloch P, Reimann J, Wagner M, Zaparty M, Albers SV, Schomburg D, Ruoff P, Siebers B", TITLE = "Unraveling the function of the two Entner-Doudoroff branches in the thermoacidophilic Crenarchaeon Sulfolobus solfataricus P2.", JOURNAL = c("FEBS J 280:1126-38 (2013)", "DOI:10.1111/febs.12106")), list(REFERENCE = "PMID:16458304", AUTHORS = "Reher M, Schonheit P", TITLE = "Glyceraldehyde dehydrogenases from the thermoacidophilic euryarchaeota Picrophilus torridus and Thermoplasma acidophilum, key enzymes of the non-phosphorylative Entner-Doudoroff pathway, constitute a novel enzyme family within the aldehyde dehydrogenase superfamily.", JOURNAL = c("FEBS Lett 580:1198-204 (2006)", "DOI:10.1016/j.febslet.2006.01.029")), list(REFERENCE = "PMID:20023024", AUTHORS = "Reher M, Fuhrer T, Bott M, Schonheit P", TITLE = "The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase.", JOURNAL = c("J Bacteriol 192:964-74 (2010)", "DOI:10.1128/JB.01281-09"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00030 Pentose phosphate pathway
Metabolism; Carbohydrate metabolism

46
NODES

167
EDGES

6064
ORGANISMS

8
COMMUNITIES

7.1739
AVG. DEGREE

0.0361
AVG. BETWEENNESS

6
ARTICULATION POINTS

40
OTHER NODES

Filters

Pathway Viewer

46

167

ec:3.1.1.17

42

8

7.1739

0.0361

6

2

9

40

6064

531

5533

248

105

128

50

5236

297

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00030 Pentose phosphate pathway Metabolism; Carbohydrate metabolism

46 NODES

167 EDGES

6064 ORGANISMS

8 COMMUNITIES

7.1739 AVG. DEGREE

0.0361 AVG. BETWEENNESS

6 ARTICULATION POINTS

40 OTHER NODES