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.

00130 Ubiquinone and other terpenoid-quinone biosynthesis
Metabolism; Metabolism of cofactors and vitamins

Ubiquinone (UQ), also called coenzyme Q, and plastoquinone (PQ) are electron carriers in oxidative phosphorylation and photosynthesis, respectively. The quinoid nucleus of ubiquinone is derived from the shikimate pathway; 4-hydroxybenzoate is directly formed from chorismate in bacteria, while it can be formed from either chorismate or tyrosine in yeast. The following biosynthesis of terpenoid moiety involves reactions of prenylation, decarboxylation, and three hydroxylations alternating with three methylations. The order of these reactions are somewhat different between bacteria and yeast. Phylloquinone (vitamin K1), menaquinone (vitamin K2), and tocopherol (vitamin E) are fat-soluble vitamins. Phylloquinone is a compound present in all photosynthetic plants serving as a cofactor for photosystem I-mediated electron transport. Menaquinone is an obligatory component of the electron-transfer pathway in bacteria.

Nodes	Edges
44	49

Articulation point with highest impact	Disconnected nodes when remove it
ec:2.2.1.9, ec:5.4.4.2	14

Global metrics
8	2.2273	0.0062

Nodes classification
24	6	9	20

Total organisms
5214

Eukaryotes	Prokaryotes
495	4719

Animals	Plants	Fungi	Protists	Bacteria	Archaea
244	105	120	26	4510	209

list(REFERENCE = "PMID:12908086", AUTHORS = "Ward MJ, Fu QS, Rhoads KR, Yeung CH, Spormann AM, Criddle CS.", TITLE = "A derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by aerobically grown Shewanella oneidensis MR-1.", JOURNAL = c("Appl Microbiol Biotechnol 63:571-7 (2004)", "DOI:10.1007/s00253-003-1407-3")), list(REFERENCE = "PMID:14499605", AUTHORS = "Monzingo AF, Gao J, Qiu J, Georgiou G, Robertus JD.", TITLE = "The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing.", JOURNAL = c("J Mol Biol 332:1015-24 (2003)", "DOI:10.1016/S0022-2836(03)00970-7")), list(REFERENCE = "PMID:11470786", AUTHORS = "Johnson TW, Zybailov B, Jones AD, Bittl R, Zech S, Stehlik D, Golbeck JH, Chitnis PR.", TITLE = "Recruitment of a foreign quinone into the A1 site of photosystem I. In vivo replacement of plastoquinone-9 by media-supplemented naphthoquinones in phylloquinone biosynthetic pathway mutants of Synechocystis sp. PCC 6803.", JOURNAL = c("J Biol Chem 276:39512-21 (2001)", "DOI:10.1074/jbc.M104040200")), list(REFERENCE = "PMID:12615349", AUTHORS = "Wade Johnson T, Naithani S, Stewart C Jr, Zybailov B, Daniel Jones A, Golbeck JH, Chitnis PR.", TITLE = "The menD and menE homologs code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA synthase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803.", JOURNAL = c("Biochim Biophys Acta 1557:67-76 (2003)", "DOI:10.1016/S0005-2728(02)00396-1")), list(REFERENCE = "PMID:12721307", AUTHORS = "Gin P, Hsu AY, Rothman SC, Jonassen T, Lee PT, Tzagoloff A, Clarke CF.", TITLE = "The Saccharomyces cerevisiae COQ6 gene encodes a mitochondrial flavin-dependent monooxygenase required for coenzyme Q biosynthesis.", JOURNAL = c("J Biol Chem 278:25308-16 (2003)", "DOI:10.1074/jbc.M303234200")), list(REFERENCE = "PMID:18284213", AUTHORS = "Jiang M, Chen X, Guo ZF, Cao Y, Chen M, Guo Z.", TITLE = "Identification and Characterization of (1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate Synthase in the Menaquinone Biosynthesis of Escherichia coli.", JOURNAL = c("Biochemistry 47:3426-34 (2008)", "DOI:10.1021/bi7023755")), list(REFERENCE = "PMID:17760421", AUTHORS = "Jiang M, Cao Y, Guo ZF, Chen M, Chen X, Guo Z.", TITLE = "Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity.", JOURNAL = c("Biochemistry 46:10979-89 (2007)", "DOI:10.1021/bi700810x")), list(REFERENCE = "PMID:17956107", AUTHORS = "Jiang M, Chen M, Cao Y, Yang Y, Sze KH, Chen X, Guo Z.", TITLE = "Determination of the stereochemistry of 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate, a key intermediate in menaquinone biosynthesis.", JOURNAL = c("Org Lett 9:4765-7 (2007)", "DOI:10.1021/ol702126m")), list(REFERENCE = "PMID:18801996", AUTHORS = "Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T", TITLE = "An alternative menaquinone biosynthetic pathway operating in microorganisms.", JOURNAL = c("Science 321:1670-3 (2008)", "DOI:10.1126/science.1160446")), list(REFERENCE = "PMID:12232327", AUTHORS = "Loscher R, Heide L", TITLE = "Biosynthesis of p-Hydroxybenzoate from p-Coumarate and p-Coumaroyl-Coenzyme A in Cell-Free Extracts of Lithospermum erythrorhizon Cell Cultures.", JOURNAL = c("Plant Physiol 106:271-279 (1994)", "DOI:10.1104/pp.106.1.271")), list(REFERENCE = "PMID:11583838", AUTHORS = "Meganathan R", TITLE = "Ubiquinone biosynthesis in microorganisms.", JOURNAL = c("FEMS Microbiol Lett 203:131-9 (2001)", "DOI:10.1111/j.1574-6968.2001.tb10831.x")), list(REFERENCE = "PMID:14508009", AUTHORS = "Cheng Z, Sattler S, Maeda H, Sakuragi Y, Bryant DA, DellaPenna D", TITLE = "Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes.", JOURNAL = c("Plant Cell 15:2343-56 (2003)", "DOI:10.1105/tpc.013656")), list(REFERENCE = "PMID:16989822", AUTHORS = "Sadre R, Gruber J, Frentzen M", TITLE = "Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis.", JOURNAL = c("FEBS Lett 580:5357-62 (2006)", "DOI:10.1016/j.febslet.2006.09.002")), list(REFERENCE = "PMID:12523993", AUTHORS = "Hofius D, Sonnewald U.", TITLE = "Vitamin E biosynthesis: biochemistry meets cell biology.", JOURNAL = c("Trends Plant Sci 8:6-8 (2003)", "DOI:10.1016/S1360-1385(02)00002-X")), list(REFERENCE = "PMID:16233343", AUTHORS = "Kawamukai M", TITLE = "Biosynthesis, bioproduction and novel roles of ubiquinone.", JOURNAL = c("J Biosci Bioeng 94:511-7 (2002)", "DOI:10.1016/S1389-1723(02)80188-8")), list(REFERENCE = "PMID:21239697", AUTHORS = "Tie JK, Jin DY, Straight DL, Stafford DW", TITLE = "Functional study of the vitamin K cycle in mammalian cells.", JOURNAL = c("Blood 117:2967-74 (2011)", "DOI:10.1182/blood-2010-08-304303")), list(REFERENCE = "PMID:23113660", AUTHORS = "Zhou L, Wang JY, Wu J, Wang J, Poplawsky A, Lin S, Zhu B, Chang C, Zhou T, Zhang LH, He YW", TITLE = "The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways.", JOURNAL = c("Mol Microbiol 87:80-93 (2013)", "DOI:10.1111/mmi.12084"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00130 Ubiquinone and other terpenoid-quinone biosynthesis
Metabolism; Metabolism of cofactors and vitamins

44
NODES

49
EDGES

5214
ORGANISMS

8
COMMUNITIES

2.2273
AVG. DEGREE

0.0062
AVG. BETWEENNESS

24
ARTICULATION POINTS

20
OTHER NODES

Filters

Pathway Viewer

44

49

ec:2.2.1.9, ec:5.4.4.2

14

8

2.2273

0.0062

24

6

9

20

5214

495

4719

244

105

120

26

4510

209

Global metrics
Communities	Avg. degree	Avg. betweenness
8	2.2273	0.0062

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00130 Ubiquinone and other terpenoid-quinone biosynthesis Metabolism; Metabolism of cofactors and vitamins

44 NODES

49 EDGES

5214 ORGANISMS

8 COMMUNITIES

2.2273 AVG. DEGREE

0.0062 AVG. BETWEENNESS

24 ARTICULATION POINTS

20 OTHER NODES