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.

00550 Peptidoglycan biosynthesis
Metabolism; Glycan biosynthesis and metabolism

Peptidoglycan is a macromolecule made of long aminosugar strands cross-linked by short peptides. It forms the cell wall in bacteria surrounding the cytoplasmic membrane. The glycan strands are typically comprised of repeating N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) disaccharides. Each MurNAc is linked to a peptide of three to five amino acid residues. Disaccharide subunits are first assembled on the cytoplasmic side of the bacterial membrane on a polyisoprenoid anchor (lipid I and II). Polymerization of disaccharide subunits by transglycosylases and cross-linking of glycan strands by transpeptidases occur on the other side of the membrane. Bacterial cell wall biosynthesis inhibitors form a major class of antibiotics.

Network metrics

Nodes	Edges
20	22

Articulation point with highest impact	Disconnected nodes when remove it
ec:2.7.8.13	13

Global metrics
Communities	Avg. degree	Avg. betweenness
5	2.2000	0.0531

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
9	2	4	11

Description

Class

Metabolism; Glycan biosynthesis and metabolism

Map

Peptidoglycan biosynthesis

Module

Associated diseases

Associated organisms count

Total organisms
5049

Eukaryotes	Prokaryotes
0	5049

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	0	0	0	5049	0

GO associated terms

KO pathway

ko00550

References

list(REFERENCE = "PMID:18081839", AUTHORS = "Bouhss A, Trunkfield AE, Bugg TD, Mengin-Lecreulx D", TITLE = "The biosynthesis of peptidoglycan lipid-linked intermediates.", JOURNAL = c("FEMS Microbiol Rev 32:208-33 (2008)", "DOI:10.1111/j.1574-6976.2007.00089.x")), list(REFERENCE = "PMID:18077448", AUTHORS = "Lloyd AJ, Gilbey AM, Blewett AM, De Pascale G, El Zoeiby A, Levesque RC, Catherwood AC, Tomasz A, Bugg TD, Roper DI, Dowson CG", TITLE = "Characterization of tRNA-dependent peptide bond formation by MurM in the synthesis of Streptococcus pneumoniae peptidoglycan.", JOURNAL = c("J Biol Chem 283:6402-17 (2008)", "DOI:10.1074/jbc.M708105200")), list(REFERENCE = "PMID:18266853", AUTHORS = "Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D", TITLE = "Cytoplasmic steps of peptidoglycan biosynthesis.", JOURNAL = c("FEMS Microbiol Rev 32:168-207 (2008)", "DOI:10.1111/j.1574-6976.2008.00104.x")), list(REFERENCE = "PMID:11699883", AUTHORS = "van Heijenoort J", TITLE = "Recent advances in the formation of the bacterial peptidoglycan monomer unit.", JOURNAL = c("Nat Prod Rep 18:503-19 (2001)", "DOI:10.1039/a804532a")), list(REFERENCE = "PMID:11320055", AUTHORS = "van Heijenoort J", TITLE = "Formation of the glycan chains in the synthesis of bacterial peptidoglycan.", JOURNAL = c("Glycobiology 11:25R-36R (2001)", "DOI:10.1093/glycob/11.3.25R"))

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00550 Peptidoglycan biosynthesis
Metabolism; Glycan biosynthesis and metabolism

20
NODES

22
EDGES

5049
ORGANISMS

5
COMMUNITIES

2.2000
AVG. DEGREE

0.0531
AVG. BETWEENNESS

9
ARTICULATION POINTS

11
OTHER NODES

Filters

Pathway Viewer

20

22

ec:2.7.8.13

13

5

2.2000

0.0531

9

2

4

11

5049

0

5049

0

0

0

0

5049

0

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00550 Peptidoglycan biosynthesis Metabolism; Glycan biosynthesis and metabolism

20 NODES

22 EDGES

5049 ORGANISMS

5 COMMUNITIES

2.2000 AVG. DEGREE

0.0531 AVG. BETWEENNESS

9 ARTICULATION POINTS

11 OTHER NODES

Filters

Pathway Viewer

20

22

ec:2.7.8.13

13

5

2.2000

0.0531

9

2

4

11

5049

0

5049

0

0

0

0

5049

0

KPV - KEGG Pathway Viewer
by Igor Brandão

00550 Peptidoglycan biosynthesis
Metabolism; Glycan biosynthesis and metabolism

20
NODES

22
EDGES

5049
ORGANISMS

5
COMMUNITIES

2.2000
AVG. DEGREE

0.0531
AVG. BETWEENNESS

9
ARTICULATION POINTS

11
OTHER NODES