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.

00253 Tetracycline biosynthesis
Metabolism; Metabolism of terpenoids and polyketides

Tetracyclines are aromatic polyketide antibiotics produced by Streptomyces species via type II polyketide synthases (PKSs). Tetracyclines contain a linear tetracyclic skeleton, which is formed from a malonamate starter unit and malonyl-CoA extender units through a common polyketide pathway [MD:M00778]. This diagram shows biosynthesis of naturally occurring tetracyclines (tetracycline, oxytetracycline and chlortetracycline) via a common intermediate anhydrotetracycline [MD:M00780 M00823].

Nodes	Edges
11	9

Articulation point with highest impact	Disconnected nodes when remove it
ec:1.14.13.38	4

Global metrics
4	1.6364	0.0232

Nodes classification
5	0	2	6

Total organisms
74

Eukaryotes	Prokaryotes
0	74

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	74	0

list(REFERENCE = "PMID:16959966", AUTHORS = "Petkovic H, Cullum J, Hranueli D, Hunter IS, Peric-Concha N, Pigac J, Thamchaipenet A, Vujaklija D, Long PF", TITLE = "Genetics of Streptomyces rimosus, the oxytetracycline producer.", JOURNAL = c("Microbiol Mol Biol Rev 70:704-28 (2006)", "DOI:10.1128/MMBR.00004-06")), list(REFERENCE = "PMID:20522541", AUTHORS = "Pickens LB, Tang Y", TITLE = "Oxytetracycline biosynthesis.", JOURNAL = c("J Biol Chem 285:27509-15 (2010)", "DOI:10.1074/jbc.R110.130419")), list(REFERENCE = "PMID:16597959", AUTHORS = "Zhang W, Ames BD, Tsai SC, Tang Y", TITLE = "Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase.", JOURNAL = c("Appl Environ Microbiol 72:2573-80 (2006)", "DOI:10.1128/AEM.72.4.2573-2580.2006")), list(REFERENCE = "", AUTHORS = "Dewick PM.", TITLE = "Medicinal Natural Products: A Biosynthetic Approach, Second Edition", JOURNAL = "John Wiley and Sons (2001)"), list(REFERENCE = "PMID:1134373", AUTHORS = "Miller PA, Hash JH", TITLE = "S-adenosylmethionine:dedimethylamino-4-aminoanhydrotetracycline N-methyltransferase.", JOURNAL = c("Methods Enzymol 43:603-6 (1975)", "DOI:10.1016/0076-6879(75)43122-6")), list(REFERENCE = "PMID:1134374", AUTHORS = "Miller PA, Hash JH", TITLE = "ADP; tetracyclin 5a(11a)dehydrogenase.", JOURNAL = c("Methods Enzymol 43:606-7 (1975)", "DOI:10.1016/0076-6879(75)43123-8")), list(REFERENCE = "PMID:19472250", AUTHORS = "Wang P, Zhang W, Zhan J, Tang Y", TITLE = "Identification of OxyE as an ancillary oxygenase during tetracycline biosynthesis.", JOURNAL = c("Chembiochem 10:1544-50 (2009)", "DOI:10.1002/cbic.200900122")), list(REFERENCE = "PMID:18422316", AUTHORS = "Zhang W, Watanabe K, Cai X, Jung ME, Tang Y, Zhan J", TITLE = "Identifying the minimal enzymes required for anhydrotetracycline biosynthesis.", JOURNAL = c("J Am Chem Soc 130:6068-9 (2008)", "DOI:10.1021/ja800951e")), list(REFERENCE = "PMID:10551844", AUTHORS = "Petkovic H, Thamchaipenet A, Zhou LH, Hranueli D, Raspor P, Waterman PG, Hunter IS", TITLE = "Disruption of an aromatase/cyclase from the oxytetracycline gene cluster of Streptomyces rimosus results in production of novel polyketides with shorter chain lengths.", JOURNAL = "J Biol Chem 274:32829-34 (1999)"), list(REFERENCE = "PMID:16148009", AUTHORS = "Peric-Concha N, Borovicka B, Long PF, Hranueli D, Waterman PG, Hunter IS", TITLE = "Ablation of the otcC gene encoding a post-polyketide hydroxylase from the oxytetracyline biosynthetic pathway in Streptomyces rimosus results in novel polyketides with altered chain length.", JOURNAL = c("J Biol Chem 280:37455-60 (2005)", "DOI:10.1074/jbc.M503191200")), list(REFERENCE = "PMID:17631493", AUTHORS = "Zhang W, Watanabe K, Wang CC, Tang Y", TITLE = "Investigation of early tailoring reactions in the oxytetracycline biosynthetic pathway.", JOURNAL = c("J Biol Chem 282:25717-25 (2007)", "DOI:10.1074/jbc.M703437200")), list(REFERENCE = "PMID:8163168", AUTHORS = "Kim ES, Bibb MJ, Butler MJ, Hopwood DA, Sherman DH.", TITLE = "Sequences of the oxytetracycline polyketide synthase-encoding otc genes from Streptomyces rimosus.", JOURNAL = c("Gene 141:141-2 (1994)", "DOI:10.1016/0378-1119(94)90144-9")), list(REFERENCE = "PMID:7612997", AUTHORS = "Dairi T, Nakano T, Aisaka K, Katsumata R, Hasegawa M.", TITLE = "Cloning and nucleotide sequence of the gene responsible for chlorination of tetracycline.", JOURNAL = c("Biosci Biotechnol Biochem 59:1099-106 (1995)", "DOI:10.1271/bbb.59.1099")), list(REFERENCE = "PMID:23621493", AUTHORS = "Wang P, Bashiri G, Gao X, Sawaya MR, Tang Y", TITLE = "Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis.", JOURNAL = c("J Am Chem Soc 135:7138-41 (2013)", "DOI:10.1021/ja403516u")), list(REFERENCE = "PMID:23800859", AUTHORS = "Zhu T, Cheng X, Liu Y, Deng Z, You D", TITLE = "Deciphering and engineering of the final step halogenase for improved chlortetracycline biosynthesis in industrial Streptomyces aureofaciens.", JOURNAL = c("Metab Eng 19:69-78 (2013)", "DOI:10.1016/j.ymben.2013.06.003")), list(REFERENCE = "PMID:15452119", AUTHORS = "Yang W, Moore IF, Koteva KP, Bareich DC, Hughes DW, Wright GD", TITLE = "TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics.", JOURNAL = c("J Biol Chem 279:52346-52 (2004)", "DOI:10.1074/jbc.M409573200"))

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
5	0	2	6

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00253 Tetracycline biosynthesis
Metabolism; Metabolism of terpenoids and polyketides

11
NODES

9
EDGES

74
ORGANISMS

4
COMMUNITIES

1.6364
AVG. DEGREE

0.0232
AVG. BETWEENNESS

5
ARTICULATION POINTS

6
OTHER NODES

Filters

Pathway Viewer

11

9

ec:1.14.13.38

4

4

1.6364

0.0232

5

0

2

6

74

0

74

0

0

0

0

74

0

Global metrics
Communities	Avg. degree	Avg. betweenness
4	1.6364	0.0232

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00253 Tetracycline biosynthesis Metabolism; Metabolism of terpenoids and polyketides

11 NODES

9 EDGES

74 ORGANISMS

4 COMMUNITIES

1.6364 AVG. DEGREE

0.0232 AVG. BETWEENNESS

5 ARTICULATION POINTS

6 OTHER NODES