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.

00521 Streptomycin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Streptomycin is an aminocyclitol-aminoglycoside antibiotic produced by Streptomyces griseus. Streptomycin consists of aminocyclitol (streptidine), 6-deoxyhexose (streptose), and N-methyl-L-glucosamine moieties, which are formed by independent biosynthetic pathways. All of the moieties are derived from D-glucose. The streptidine moiety is synthesized via myo-inositol, which is then oxidized at C-1 and transaminated to give scyllo-inosamine. After phosphorylation, the compound is transamidinated by arginine. The same procedure is repeated at the C-3 position. The streptose moiety is made from D-glucose via a dTDP-glucose pathway. The exact biosynthetic route for the N-methyl-L-glucosamine moiety is unknown, though the biosynthetic gene cluster have been proposed.

Network metrics

Nodes	Edges
15	15

Articulation point with highest impact	Disconnected nodes when remove it
ec:5.5.1.4	6

Global metrics
Communities	Avg. degree	Avg. betweenness
5	2.0000	0.0355

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
10	2	3	5

Description

Class

Metabolism; Biosynthesis of other secondary metabolites

Map

Streptomycin biosynthesis

Module

dTDP-L-rhamnose biosynthesis [PATH:map00521]

Associated diseases

D08531, Streptomycin (INN)

Associated organisms count

Total organisms
5066

Eukaryotes	Prokaryotes
0	5066

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	4778	288

GO associated terms

GO: 0019872

KO pathway

ko00521

References

list(REFERENCE = "PMID:19362651", AUTHORS = "Wehmeier UF, Piepersberg W", TITLE = "Enzymology of aminoglycoside biosynthesis-deduction from gene clusters.", JOURNAL = c("Methods Enzymol 459:459-91 (2009)", "DOI:10.1016/S0076-6879(09)04619-9")), list(REFERENCE = "PMID:17390001", AUTHORS = "Flatt PM, Mahmud T", TITLE = "Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds.", JOURNAL = c("Nat Prod Rep 24:358-92 (2007)", "DOI:10.1039/b603816f")), list(REFERENCE = "PMID:1698764", AUTHORS = "Walker JB", TITLE = "Possible evolutionary relationships between streptomycin and bluensomycin biosynthetic pathways: detection of novel inositol kinase and O-carbamoyltransferase activities.", JOURNAL = c("J Bacteriol 172:5844-51 (1990)", "DOI:10.1128/JB.172.10.5844-5851.1990")), list(REFERENCE = "PMID:2995326", AUTHORS = "Ohnuki T, Imanaka T, Aiba S", TITLE = "Self-cloning in Streptomyces griseus of an str gene cluster for streptomycin biosynthesis and streptomycin resistance.", JOURNAL = "J Bacteriol 164:85-94 (1985)"), list(REFERENCE = "PMID:9238101", AUTHORS = "Ahlert J, Distler J, Mansouri K, Piepersberg W", TITLE = "Identification of stsC, the gene encoding the L-glutamine:scyllo-inosose aminotransferase from streptomycin-producing Streptomycetes.", JOURNAL = c("Arch Microbiol 168:102-13 (1997)", "DOI:10.1007/s002030050475")), list(REFERENCE = "PMID:1377151", AUTHORS = "Distler J, Mansouri K, Mayer G, Stockmann M, Piepersberg W", TITLE = "Streptomycin biosynthesis and its regulation in Streptomycetes.", JOURNAL = c("Gene 115:105-11 (1992)", "DOI:10.1016/0378-1119(92)90547-3")), list(REFERENCE = "PMID:1654502", AUTHORS = "Mansouri K, Piepersberg W.", TITLE = "Genetics of streptomycin production in Streptomyces griseus: nucleotide sequence of five genes, strFGHIK, including a phosphatase gene.", JOURNAL = c("Mol Gen Genet 228:459-69 (1991)", "DOI:10.1007/BF00260640")), list(REFERENCE = "PMID:9922132", AUTHORS = "Fritsche E, Bergner A, Humm A, Piepersberg W, Huber R", TITLE = "Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: an enzyme involved in streptomycin biosynthesis.", JOURNAL = c("Biochemistry 37:17664-72 (1998)", "DOI:10.1021/bi981949p"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00521 Streptomycin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

15
NODES

15
EDGES

5066
ORGANISMS

5
COMMUNITIES

2.0000
AVG. DEGREE

0.0355
AVG. BETWEENNESS

10
ARTICULATION POINTS

5
OTHER NODES

Filters

Pathway Viewer

15

15

ec:5.5.1.4

6

5

2.0000

0.0355

10

2

3

5

5066

0

5066

0

0

0

0

4778

288

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00521 Streptomycin biosynthesis Metabolism; Biosynthesis of other secondary metabolites

15 NODES

15 EDGES

5066 ORGANISMS

5 COMMUNITIES

2.0000 AVG. DEGREE

0.0355 AVG. BETWEENNESS

10 ARTICULATION POINTS

5 OTHER NODES

Filters

Pathway Viewer

15

15

ec:5.5.1.4

6

5

2.0000

0.0355

10

2

3

5

5066

0

5066

0

0

0

0

4778

288

KPV - KEGG Pathway Viewer
by Igor Brandão

00521 Streptomycin biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

15
NODES

15
EDGES

5066
ORGANISMS

5
COMMUNITIES

2.0000
AVG. DEGREE

0.0355
AVG. BETWEENNESS

10
ARTICULATION POINTS

5
OTHER NODES