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
43	30

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.14.19.72, ec:2.1.1.323	6

Global metrics
13	1.3810	0.0011

Nodes classification
15	3	8	28

Total organisms
432

Eukaryotes	Prokaryotes
90	342

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	90	0	0	342	0

list(REFERENCE = "PMID:23586652", AUTHORS = "Vetter ND, Langill DM, Anjum S, Boisvert-Martel J, Jagdhane RC, Omene E, Zheng H, van Straaten KE, Asiamah I, Krol ES, Sanders DA, Palmer DR", TITLE = "A previously unrecognized kanosamine biosynthesis pathway in Bacillus subtilis.", JOURNAL = c("J Am Chem Soc 135:5970-3 (2013)", "DOI:10.1021/ja4010255")), list(REFERENCE = "PMID:19807062", AUTHORS = "Hollenhorst MA, Clardy J, Walsh CT", TITLE = "The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics.", JOURNAL = c("Biochemistry 48:10467-72 (2009)", "DOI:10.1021/bi9013165")), list(REFERENCE = "PMID:20086163", AUTHORS = "Kumagai T, Koyama Y, Oda K, Noda M, Matoba Y, Sugiyama M", TITLE = "Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae.", JOURNAL = c("Antimicrob Agents Chemother 54:1132-9 (2010)", "DOI:10.1128/AAC.01226-09")), list(REFERENCE = "PMID:25644640", AUTHORS = "Ozcengiz G, Ogulur I", TITLE = "Biochemistry, genetics and regulation of bacilysin biosynthesis and its significance more than an antibiotic.", JOURNAL = c("N Biotechnol 32:612-9 (2015)", "DOI:10.1016/j.nbt.2015.01.006")), list(REFERENCE = "PMID:17335090", AUTHORS = "Sandmann A, Dickschat J, Jenke-Kodama H, Kunze B, Dittmann E, Muller R", TITLE = "A Type II polyketide synthase from the gram-negative Bacterium Stigmatella aurantiaca is involved in Aurachin alkaloid biosynthesis.", JOURNAL = c("Angew Chem Int Ed Engl 46:2712-6 (2007)", "DOI:10.1002/anie.200603513")), list(REFERENCE = "PMID:26359402", AUTHORS = "Lau W, Sattely ES", TITLE = "Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone.", JOURNAL = c("Science 349:1224-8 (2015)", "DOI:10.1126/science.aac7202")), list(REFERENCE = "PMID:27062037", AUTHORS = "Schwarz J, Konjik V, Jankowitsch F, Sandhoff R, Mack M", TITLE = "Identification of the Key Enzyme of Roseoflavin Biosynthesis.", JOURNAL = c("Angew Chem Int Ed Engl 55:6103-6 (2016)", "DOI:10.1002/anie.201600581")), list(REFERENCE = "PMID:12138123", AUTHORS = "Hamano Y, Kuzuyama T, Itoh N, Furihata K, Seto H, Dairi T", TITLE = "Functional analysis of eubacterial diterpene cyclases responsible for biosynthesis of a diterpene antibiotic, terpentecin.", JOURNAL = c("J Biol Chem 277:37098-104 (2002)", "DOI:10.1074/jbc.M206382200")), list(REFERENCE = "PMID:17017767", AUTHORS = "Quaderer R, Omura S, Ikeda H, Cane DE", TITLE = "Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlI, a cytochrome P450 of Streptomyces avermitilis.", JOURNAL = c("J Am Chem Soc 128:13036-7 (2006)", "DOI:10.1021/ja0639214"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00998 Biosynthesis of secondary metabolites - other antibiotics
Metabolism; Biosynthesis of other secondary metabolites

43
NODES

30
EDGES

432
ORGANISMS

13
COMMUNITIES

1.3810
AVG. DEGREE

0.0011
AVG. BETWEENNESS

15
ARTICULATION POINTS

28
OTHER NODES

Filters

Pathway Viewer

43

30

ec:1.14.19.72, ec:2.1.1.323

6

13

1.3810

0.0011

15

3

8

28

432

90

342

0

90

0

0

342

0

Global metrics
Communities	Avg. degree	Avg. betweenness
13	1.3810	0.0011

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00998 Biosynthesis of secondary metabolites - other antibiotics Metabolism; Biosynthesis of other secondary metabolites

43 NODES

30 EDGES

432 ORGANISMS

13 COMMUNITIES

1.3810 AVG. DEGREE

0.0011 AVG. BETWEENNESS

15 ARTICULATION POINTS

28 OTHER NODES