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.

00402 Benzoxazinoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Benzoxazinoids (hydroxamic acids) are plant secondary metabolites that serve as important factors for host resistance against microbial pathogens and insects and for allelopathic effects. They are found in grass family and some eudicot families. The predominant benzoxazinoids are DIBOA and its 7-methoxy derivative DIMBOA, which are stored as glucosides in vacuoles. In maize, benzoxazinoid biosynthesis branches off from tryptophan biosynthesis at indole-3-glycerol phosphate, which is converted to indole by indole-3-glycerol phosphate lyase, BX1. Subsequently four cytochrome P450 monooxygenases (BX2-BX5) catalyze the introduction of four oxygen atoms into the indole moiety, yielding DIBOA. After glucosylation by UDP-glucosyltransferase (BX8/BX9), the glucoside is further modified by hydroxylation and O-methylation at C-7 to form DIMBOA-glucoside.

Network metrics

Nodes	Edges
8	7

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.14.14.110, ec:1.14.14.109	4

Global metrics
Communities	Avg. degree	Avg. betweenness
3	1.7500	0.1667

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

Description

Class

Metabolism; Biosynthesis of other secondary metabolites

Map

Benzoxazinoid biosynthesis

Module

Associated diseases

Associated organisms count

Total organisms
4

Eukaryotes	Prokaryotes
4	0

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	4	0	0	0	0

GO associated terms

KO pathway

ko00402

References

list(REFERENCE = "PMID:11106389", AUTHORS = "Frey M, Stettner C, Pare PW, Schmelz EA, Tumlinson JH, Gierl A.", TITLE = "An herbivore elicitor activates the gene for indole emission in maize.", JOURNAL = c("Proc Natl Acad Sci U S A 97:14801-6 (2000)", "DOI:10.1073/pnas.260499897")), list(REFERENCE = "PMID:11556781", AUTHORS = "Gierl A, Frey M.", TITLE = "Evolution of benzoxazinone biosynthesis and indole production in maize.", JOURNAL = c("Planta 213:493-8 (2001)", "DOI:10.1007/s004250100594")), list(REFERENCE = "PMID:16260753", AUTHORS = "Nomura T, Ishihara A, Yanagita RC, Endo TR, Iwamura H.", TITLE = "Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat.", JOURNAL = c("Proc Natl Acad Sci U S A 102:16490-5 (2005)", "DOI:10.1073/pnas.0505156102")), list(REFERENCE = "PMID:9235894", AUTHORS = "Frey M, Chomet P, Glawischnig E, Stettner C, Grun S, Winklmair A, Eisenreich W, Bacher A, Meeley RB, Briggs SP, Simcox K, Gierl A.", TITLE = "Analysis of a chemical plant defense mechanism in grasses.", JOURNAL = c("Science 277:696-9 (1997)", "DOI:10.1126/science.277.5326.696")), list(REFERENCE = "PMID:12620350", AUTHORS = "Frey M, Huber K, Park WJ, Sicker D, Lindberg P, Meeley RB, Simmons CR, Yalpani N, Gierl A.", TITLE = "A 2-oxoglutarate-dependent dioxygenase is integrated in DIMBOA-biosynthesis.", JOURNAL = c("Phytochemistry 62:371-6 (2003)", "DOI:10.1016/S0031-9422(02)00556-3")), list(REFERENCE = "PMID:11851909", AUTHORS = "von Rad U, Huttl R, Lottspeich F, Gierl A, Frey M.", TITLE = "Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize.", JOURNAL = c("Plant J 28:633-42 (2001)", "DOI:10.1046/j.1365-313x.2001.01161.x")), list(REFERENCE = "PMID:16666853", AUTHORS = "Bailey BA, Larson RL", TITLE = "Hydroxamic Acid glucosyltransferases from maize seedlings.", JOURNAL = c("Plant Physiol 90:1071-6 (1989)", "DOI:10.1104/pp.90.3.1071")), list(REFERENCE = "PMID:18192444", AUTHORS = "Jonczyk R, Schmidt H, Osterrieder A, Fiesselmann A, Schullehner K, Haslbeck M, Sicker D, Hofmann D, Yalpani N, Simmons C, Frey M, Gierl A", TITLE = "Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7.", JOURNAL = c("Plant Physiol 146:1053-63 (2008)", "DOI:10.1104/pp.107.111237")), list(REFERENCE = "PMID:19577780", AUTHORS = "Frey M, Schullehner K, Dick R, Fiesselmann A, Gierl A", TITLE = "Benzoxazinoid biosynthesis, a model for evolution of secondary metabolic pathways in plants.", JOURNAL = c("Phytochemistry 70:1645-51 (2009)", "DOI:10.1016/j.phytochem.2009.05.012"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00402 Benzoxazinoid biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

8
NODES

7
EDGES

4
ORGANISMS

3
COMMUNITIES

1.7500
AVG. DEGREE

0.1667
AVG. BETWEENNESS

6
ARTICULATION POINTS

2
OTHER NODES

Filters

Pathway Viewer

8

7

ec:1.14.14.110, ec:1.14.14.109

4

3

1.7500

0.1667

6

2

2

2

4

4

0

0

4

0

0

0

0

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00402 Benzoxazinoid biosynthesis Metabolism; Biosynthesis of other secondary metabolites

8 NODES

7 EDGES

4 ORGANISMS

3 COMMUNITIES

1.7500 AVG. DEGREE

0.1667 AVG. BETWEENNESS

6 ARTICULATION POINTS

2 OTHER NODES