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
85	217

Articulation point with highest impact	Disconnected nodes when remove it
ec:4.1.1.19, ec:1.5.1.1+_1, ec:2.6.1.1+_2	82

Global metrics
Communities	Avg. degree	Avg. betweenness
11	5.0588	0.0097

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
16	3	17	69

Proline biosynthesis, glutamate => proline [PATH:map00330], Creatine pathway [PATH:map00330], Polyamine biosynthesis, arginine => agmatine => putrescine => spermidine [PATH:map00330], Polyamine biosynthesis, arginine => ornithine => putrescine [PATH:map00330], GABA biosynthesis, eukaryotes, putrescine => GABA [PATH:map00330], GABA biosynthesis, prokaryotes, putrescine => GABA [PATH:map00330], Arginine succinyltransferase pathway, arginine => glutamate [PATH:map00330]

Associated diseases

Hyperargininemia, Ornithinaemia, Hyperprolinemia, Snyder-Robinson syndrome, Guanidinoacetate methyltransferase deficiency, Cerebral creatine deficiency syndrome

Associated organisms count

Total organisms
5836

Eukaryotes	Prokaryotes
523	5313

Animals	Plants	Fungi	Protists	Bacteria	Archaea
248	105	123	47	5015	298

GO associated terms

GO: 0006525 0006560

KO pathway

ko00330

References

list(REFERENCE = "PMID:5288244", AUTHORS = "Haake P, Allen GW.", TITLE = "Studies on phosphorylation by phosphoroguanidinates. The mechanism of action of creatine: ATP transphosphorylase (creatine kinase).", JOURNAL = c("Proc Natl Acad Sci U S A 68:2691-3 (1971)", "DOI:10.1073/pnas.68.11.2691")), list(REFERENCE = "PMID:16499623", AUTHORS = "Kurihara S, Oda S, Kumagai H, Suzuki H.", TITLE = "Gamma-glutamyl-gamma-aminobutyrate hydrolase in the putrescine utilization pathway of Escherichia coli K-12.", JOURNAL = c("FEMS Microbiol Lett 256:318-23 (2006)", "DOI:10.1111/j.1574-6968.2006.00137.x")), list(REFERENCE = "PMID:15590624", AUTHORS = "Kurihara S, Oda S, Kato K, Kim HG, Koyanagi T, Kumagai H, Suzuki H.", TITLE = "A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12.", JOURNAL = c("J Biol Chem 280:4602-8 (2005)", "DOI:10.1074/jbc.M411114200"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00330 Arginine and proline metabolism
Metabolism; Amino acid metabolism

85
NODES

217
EDGES

5836
ORGANISMS

11
COMMUNITIES

5.0588
AVG. DEGREE

0.0097
AVG. BETWEENNESS

16
ARTICULATION POINTS

69
OTHER NODES

Filters

Pathway Viewer

85

217

ec:4.1.1.19, ec:1.5.1.1+_1, ec:2.6.1.1+_2

82

11

5.0588

0.0097

16

3

17

69

5836

523

5313

248

105

123

47

5015

298

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00330 Arginine and proline metabolism Metabolism; Amino acid metabolism

85 NODES

217 EDGES

5836 ORGANISMS

11 COMMUNITIES

5.0588 AVG. DEGREE

0.0097 AVG. BETWEENNESS

16 ARTICULATION POINTS

69 OTHER NODES