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.

00332 Carbapenem biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Carbapenems are broad-spectrum beta-lactam antibiotics, which are often considered as the antibiotics of last resort. A naturally occurring carbapenem, thienamycin, was first discovered in Streptomyces cattleya. This diagram shows how a simple carbapenem, carbapenem-3-carboxylate, is synthesized from malonyl-CoA and pyrroline-5-carboxylate [MD:M00675]. For structurally complex carbapenems, such as thienamycin, olivanic acid, epi-thienamycin and carbapenems of the OA-6129 group, uncertainty remains about the mechanism and timing for the inversion of the C-5 carbapenam bridgehead, the desaturation of the C-2/C-3 bond and the attachment of the C-2 and C-6 side chains.

Nodes	Edges
5	3

Articulation point with highest impact	Disconnected nodes when remove it
ec:6.3.3.6	2

Global metrics
2	1.2000	0.0167

Nodes classification
1	0	1	4

Total organisms
4310

Eukaryotes	Prokaryotes
130	4180

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	4	119	7	4106	74

list(REFERENCE = "PMID:12848554", AUTHORS = "Stapon A, Li R, Townsend CA", TITLE = "Carbapenem biosynthesis: confirmation of stereochemical assignments and the role of CarC in the ring stereoinversion process from L-proline.", JOURNAL = c("J Am Chem Soc 125:8486-93 (2003)", "DOI:10.1021/ja034248a")), list(REFERENCE = "PMID:15174175", AUTHORS = "Sleeman MC, Smith P, Kellam B, Chhabra SR, Bycroft BW, Schofield CJ", TITLE = "Biosynthesis of carbapenem antibiotics: new carbapenam substrates for carbapenem synthase (CarC).", JOURNAL = c("Chembiochem 5:879-82 (2004)", "DOI:10.1002/cbic.200300908")), list(REFERENCE = "PMID:14625287", AUTHORS = "Sleeman MC, Schofield CJ", TITLE = "Carboxymethylproline synthase (CarB), an unusual carbon-carbon bond-forming enzyme of the crotonase superfamily involved in carbapenem biosynthesis.", JOURNAL = c("J Biol Chem 279:6730-6 (2004)", "DOI:10.1074/jbc.M311824200")), list(REFERENCE = "PMID:19090510", AUTHORS = "Hamed RB, Batchelar ET, Mecinovic J, Claridge TD, Schofield CJ", TITLE = "Evidence that thienamycin biosynthesis proceeds via C-5 epimerization: ThnE catalyzes the formation of (2S,5S)-trans-carboxymethylproline.", JOURNAL = c("Chembiochem 10:246-50 (2009)", "DOI:10.1002/cbic.200800652")), list(REFERENCE = "PMID:21913298", AUTHORS = "Bodner MJ, Li R, Phelan RM, Freeman MF, Moshos KA, Lloyd EP, Townsend CA", TITLE = "Definition of the common and divergent steps in carbapenem beta-lactam antibiotic biosynthesis.", JOURNAL = c("Chembiochem 12:2159-65 (2011)", "DOI:10.1002/cbic.201100366")), list(REFERENCE = "PMID:12147472", AUTHORS = "Derzelle S, Duchaud E, Kunst F, Danchin A, Bertin P", TITLE = "Identification, characterization, and regulation of a cluster of genes involved in carbapenem biosynthesis in Photorhabdus luminescens.", JOURNAL = c("Appl Environ Microbiol 68:3780-9 (2002)", "DOI:10.1128/AEM.68.8.3780-3789.2002")), list(REFERENCE = "PMID:21263049", AUTHORS = "Rodriguez M, Nunez LE, Brana AF, Mendez C, Salas JA, Blanco G", TITLE = "Mutational analysis of the thienamycin biosynthetic gene cluster from Streptomyces cattleya.", JOURNAL = c("Antimicrob Agents Chemother 55:1638-49 (2011)", "DOI:10.1128/AAC.01366-10")), list(REFERENCE = "PMID:3988730", AUTHORS = "Williamson JM, Inamine E, Wilson KE, Douglas AW, Liesch JM, Albers-Schonberg G", TITLE = "Biosynthesis of the beta-lactam antibiotic, thienamycin, by Streptomyces cattleya.", JOURNAL = "J Biol Chem 260:4637-47 (1985)"), list(REFERENCE = "PMID:12725858", AUTHORS = "Nunez LE, Mendez C, Brana AF, Blanco G, Salas JA", TITLE = "The biosynthetic gene cluster for the beta-lactam carbapenem thienamycin in Streptomyces cattleya.", JOURNAL = c("Chem Biol 10:301-11 (2003)", "DOI:10.1016/S1074-5521(03)00069-3")), list(REFERENCE = "PMID:20017478", AUTHORS = "Bodner MJ, Phelan RM, Freeman MF, Li R, Townsend CA", TITLE = "Non-heme iron oxygenases generate natural structural diversity in carbapenem antibiotics.", JOURNAL = c("J Am Chem Soc 132:12-3 (2010)", "DOI:10.1021/ja907320n")), list(REFERENCE = "PMID:18678912", AUTHORS = "Freeman MF, Moshos KA, Bodner MJ, Li R, Townsend CA", TITLE = "Four enzymes define the incorporation of coenzyme A in thienamycin biosynthesis.", JOURNAL = c("Proc Natl Acad Sci U S A 105:11128-33 (2008)", "DOI:10.1073/pnas.0804500105")), list(REFERENCE = "PMID:22706025", AUTHORS = "Buller AR, Labonte JW, Freeman MF, Wright NT, Schildbach JF, Townsend CA", TITLE = "Autoproteolytic activation of ThnT results in structural reorganization necessary for substrate binding and catalysis.", JOURNAL = c("J Mol Biol 422:508-18 (2012)", "DOI:10.1016/j.jmb.2012.06.012")), list(REFERENCE = "PMID:24420617", AUTHORS = "Li R, Lloyd EP, Moshos KA, Townsend CA", TITLE = "Identification and characterization of the carbapenem MM 4550 and its gene cluster in Streptomyces argenteolus ATCC 11009.", JOURNAL = c("Chembiochem 15:320-31 (2014)", "DOI:10.1002/cbic.201300319"))

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
1	0	1	4

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00332 Carbapenem biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

5
NODES

3
EDGES

4310
ORGANISMS

2
COMMUNITIES

1.2000
AVG. DEGREE

0.0167
AVG. BETWEENNESS

1
ARTICULATION POINTS

4
OTHER NODES

Filters

Pathway Viewer

5

3

ec:6.3.3.6

2

2

1.2000

0.0167

1

0

1

4

4310

130

4180

0

4

119

7

4106

74

Global metrics
Communities	Avg. degree	Avg. betweenness
2	1.2000	0.0167

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00332 Carbapenem biosynthesis Metabolism; Biosynthesis of other secondary metabolites

5 NODES

3 EDGES

4310 ORGANISMS

2 COMMUNITIES

1.2000 AVG. DEGREE

0.0167 AVG. BETWEENNESS

1 ARTICULATION POINTS

4 OTHER NODES