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
55	220

Articulation point with highest impact	Disconnected nodes when remove it
ec:4.2.3.1	43

Global metrics
Communities	Avg. degree	Avg. betweenness
11	8.0000	0.0271

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
8	0	11	47

Serine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In bacteria and plants, threonine is derived from aspartate [MD:M00018].

Class

Metabolism; Amino acid metabolism

Map

Glycine, serine and threonine metabolism

Module

Threonine biosynthesis, aspartate => homoserine => threonine [PATH:map00260], Serine biosynthesis, glycerate-3P => serine [PATH:map00260], Ectoine biosynthesis, aspartate => ectoine [PATH:map00260], Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:map00260], Betaine biosynthesis, choline => betaine [PATH:map00260]

Associated diseases

Primary hyperoxaluria, Cystathioninuria, Homocystinuria, Hypermethioninemia, Nonketotic hyperglycinemia, Guanidinoacetate methyltransferase deficiency, Cerebral creatine deficiency syndrome, Dimethylglycine dehydrogenase deficiency, 3-Phosphoglycerate dehydrogenase (3-PGDH) deficiency, Phosphoserine aminotransferase deficiency, Glycogen storage disease type X, Phosphoserine phosphatase deficiency, Neu-Laxova syndrome

Associated organisms count

Total organisms
6086

Eukaryotes	Prokaryotes
530	5556

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	127	50	5259	297

GO associated terms

GO: 0006544 0006563 0070178 0006566

KO pathway

ko00260

References

list(REFERENCE = "", 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 = "PMID:11823218", AUTHORS = "Kuhlmann AU, Bremer E.", TITLE = "Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp.", JOURNAL = c("Appl Environ Microbiol 68:772-83 (2002)", "DOI:10.1128/AEM.68.2.772-783.2002")), list(REFERENCE = "PMID:10473374", AUTHORS = "Canovas D, Borges N, Vargas C, Ventosa A, Nieto JJ, Santos H.", TITLE = "Role of Ngamma-acetyldiaminobutyrate as an enzyme stabilizer and an intermediate in the biosynthesis of hydroxyectoine.", JOURNAL = "Appl Environ Microbiol 65:3774-9 (1999)"), list(REFERENCE = "PMID:17636255", AUTHORS = "Bursy J, Pierik AJ, Pica N, Bremer E.", TITLE = "Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase.", JOURNAL = c("J Biol Chem 282:31147-55 (2007)", "DOI:10.1074/jbc.M704023200")), list(REFERENCE = "PMID:16707670", AUTHORS = "Garcia-Estepa R, Argandona M, Reina-Bueno M, Capote N, Iglesias-Guerra F, Nieto JJ, Vargas C.", TITLE = "The ectD gene, which is involved in the synthesis of the compatible solute hydroxyectoine, is essential for thermoprotection of the halophilic bacterium Chromohalobacter salexigens.", JOURNAL = c("J Bacteriol 188:3774-84 (2006)", "DOI:10.1128/JB.00136-06")), list(REFERENCE = "PMID:15470257", AUTHORS = "Arevalo-Rodriguez M, Pan X, Boeke JD, Heitman J", TITLE = "FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation.", JOURNAL = c("Eukaryot Cell 3:1287-96 (2004)", "DOI:10.1128/EC.3.5.1287-1296.2004")), list(REFERENCE = "PMID:7639721", AUTHORS = "Rees WD, Hay SM", TITLE = "The biosynthesis of threonine by mammalian cells: expression of a complete bacterial biosynthetic pathway in an animal cell.", JOURNAL = c("Biochem J 309 ( Pt 3):999-1007 (1995)", "DOI:10.1042/bj3090999")), list(REFERENCE = "PMID:11341914", AUTHORS = "Jacques SL, Nieman C, Bareich D, Broadhead G, Kinach R, Honek JF, Wright GD", TITLE = "Characterization of yeast homoserine dehydrogenase, an antifungal target: the invariant histidine 309 is important for enzyme integrity.", JOURNAL = c("Biochim Biophys Acta 1544:28-41 (2001)", "DOI:10.1016/S0167-4838(00)00203-X")), list(REFERENCE = "PMID:15520012", AUTHORS = "Chen X, Jhee KH, Kruger WD", TITLE = "Production of the neuromodulator H2S by cystathionine beta-synthase via the condensation of cysteine and homocysteine.", JOURNAL = c("J Biol Chem 279:52082-6 (2004)", "DOI:10.1074/jbc.C400481200"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00260 Glycine, serine and threonine metabolism
Metabolism; Amino acid metabolism

55
NODES

220
EDGES

6086
ORGANISMS

11
COMMUNITIES

8.0000
AVG. DEGREE

0.0271
AVG. BETWEENNESS

8
ARTICULATION POINTS

47
OTHER NODES

Filters

Pathway Viewer

55

220

ec:4.2.3.1

43

11

8.0000

0.0271

8

0

11

47

6086

530

5556

248

105

127

50

5259

297

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00260 Glycine, serine and threonine metabolism Metabolism; Amino acid metabolism

55 NODES

220 EDGES

6086 ORGANISMS

11 COMMUNITIES

8.0000 AVG. DEGREE

0.0271 AVG. BETWEENNESS

8 ARTICULATION POINTS

47 OTHER NODES