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
79	222

Articulation point with highest impact	Disconnected nodes when remove it
ec:4.4.1.1	49

Global metrics
Communities	Avg. degree	Avg. betweenness
9	5.6203	0.0308

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
13	2	16	66

Cysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted from serine (via acetylserine) by transfer of hydrogen sulfide [MD:M00021]. In animals, methionine-derived homocysteine is used as sulfur source and its condensation product with serine (cystathionine) is converted to cysteine [MD:M00338]. Cysteine is metabolized to pyruvate in multiple routes. Methionine is an essential amino acid, which animals cannot synthesize. In bacteria and plants, methionine is synthesized from aspartate [MD:M00017]. S-Adenosylmethionine (SAM), synthesized from methionine and ATP, is a methyl group donor in many important transfer reactions including DNA methylation for regulation of gene expression. SAM may also be used to regenerate methionine in the methionine salvage pathway [MD:M00034].

Class

Metabolism; Amino acid metabolism

Map

Cysteine and methionine metabolism

Module

Methionine biosynthesis, apartate => homoserine => methionine [PATH:map00270], Cysteine biosynthesis, serine => cysteine [PATH:map00270], Methionine salvage pathway [PATH:map00270], Methionine degradation [PATH:map00270], Cysteine biosynthesis, homocysteine + serine => cysteine [PATH:map00270], Ethylene biosynthesis, methionine => ethylene [PATH:map00270], Cysteine biosynthesis, methionine => cysteine [PATH:map00270]

Associated diseases

Cystathioninuria, Homocystinuria, Hypermethioninemia, Snyder-Robinson syndrome, Methylcobalamin deficiency type G, Tatton-Brown-Rahman syndrome

Associated organisms count

Total organisms
6084

Eukaryotes	Prokaryotes
527	5557

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	124	50	5261	296

GO associated terms

GO: 0006534 0006555

KO pathway

ko00270

References

list(REFERENCE = "PMID:15102328", AUTHORS = "Sekowska A, Denervaud V, Ashida H, Michoud K, Haas D, Yokota A, Danchin A", TITLE = "Bacterial variations on the methionine salvage pathway.", JOURNAL = c("BMC Microbiol 4:9 (2004)", "DOI:10.1186/1471-2180-4-9")), list(REFERENCE = "PMID:14551435", AUTHORS = "Ashida H, Saito Y, Kojima C, Kobayashi K, Ogasawara N, Yokota A.", TITLE = "A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO.", JOURNAL = c("Science 302:286-90 (2003)", "DOI:10.1126/science.1086997")), list(REFERENCE = "PMID:12022921", AUTHORS = "Sekowska A, Danchin A.", TITLE = "The methionine salvage pathway in Bacillus subtilis.", JOURNAL = c("BMC Microbiol 2:8 (2002)", "DOI:10.1186/1471-2180-2-8")), list(REFERENCE = "PMID:12670965", AUTHORS = "Berger BJ, English S, Chan G, Knodel MH.", TITLE = "Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis.", JOURNAL = c("J Bacteriol 185:2418-31 (2003)", "DOI:10.1128/JB.185.8.2418-2431.2003")), list(REFERENCE = "PMID:17169919", AUTHORS = "Goyer A, Collakova E, Shachar-Hill Y, Hanson AD", TITLE = "Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway.", JOURNAL = c("Plant Cell Physiol 48:232-42 (2007)", "DOI:10.1093/pcp/pcl055")), list(REFERENCE = "PMID:17030798", AUTHORS = "Rebeille F, Jabrin S, Bligny R, Loizeau K, Gambonnet B, Van Wilder V, Douce R, Ravanel S", TITLE = "Methionine catabolism in Arabidopsis cells is initiated by a gamma-cleavage process and leads to S-methylcysteine and isoleucine syntheses.", JOURNAL = c("Proc Natl Acad Sci U S A 103:15687-92 (2006)", "DOI:10.1073/pnas.0606195103")), list(REFERENCE = "PMID:18625006", AUTHORS = "Pirkov I, Norbeck J, Gustafsson L, Albers E", TITLE = "A complete inventory of all enzymes in the eukaryotic methionine salvage pathway.", JOURNAL = c("FEBS J 275:4111-20 (2008)", "DOI:10.1111/j.1742-4658.2008.06552.x")), list(REFERENCE = "PMID:18391471", AUTHORS = "Ashida H, Saito Y, Kojima C, Yokota A", TITLE = "Enzymatic characterization of 5-methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway in Bacillus subtilis.", JOURNAL = c("Biosci Biotechnol Biochem 72:959-67 (2008)", "DOI:10.1271/bbb.70651")), list(REFERENCE = "PMID:10613873", AUTHORS = "Kitabatake M, So MW, Tumbula DL, Soll D", TITLE = "Cysteine biosynthesis pathway in the archaeon Methanosarcina barkeri encoded by acquired bacterial genes?", JOURNAL = c("J Bacteriol 182:143-5 (2000)", "DOI:10.1128/JB.182.1.143-145.2000")), list(REFERENCE = "PMID:12644499", AUTHORS = "Mino K, Ishikawa K", TITLE = "Characterization of a novel thermostable O-acetylserine sulfhydrylase from Aeropyrum pernix K1.", JOURNAL = c("J Bacteriol 185:2277-84 (2003)", "DOI:10.1128/JB.185.7.2277-2284.2003")), list(REFERENCE = "PMID:18520135", AUTHORS = "Tanabe S", TITLE = "Development of assay methods for endogenous inorganic sulfur compounds and sulfurtransferases and evaluation of the physiological functions of bound sulfur.", JOURNAL = c("Yakugaku Zasshi 128:881-900 (2008)", "DOI:10.1248/yakushi.128.881")), 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:19270684", AUTHORS = "Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL", TITLE = "Transition state analogs of 5`-methylthioadenosine nucleosidase disrupt quorum sensing.", JOURNAL = c("Nat Chem Biol 5:251-7 (2009)", "DOI:10.1038/nchembio.153"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00270 Cysteine and methionine metabolism
Metabolism; Amino acid metabolism

79
NODES

222
EDGES

6084
ORGANISMS

9
COMMUNITIES

5.6203
AVG. DEGREE

0.0308
AVG. BETWEENNESS

13
ARTICULATION POINTS

66
OTHER NODES

Filters

Pathway Viewer

79

222

ec:4.4.1.1

49

9

5.6203

0.0308

13

2

16

66

6084

527

5557

248

105

124

50

5261

296

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00270 Cysteine and methionine metabolism Metabolism; Amino acid metabolism

79 NODES

222 EDGES

6084 ORGANISMS

9 COMMUNITIES

5.6203 AVG. DEGREE

0.0308 AVG. BETWEENNESS

13 ARTICULATION POINTS

66 OTHER NODES