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.

00261 Monobactam biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

Monobactams are beta-lactam antibiotics containing a monocyclic beta-lactam nucleus, which is structurally different from penicillin and cephalosporin core structures with another fused ring. This diagram shows biosynthesis of nocardicin A, a naturally occurring monobactam, via the pentapeptide formed by condensation of L-4-hydroxyphenylglycine (L-pHPG), L-arginine and L-serine [MD:M00736]. Other naturally occurring monobactams are also shown but the biosynthetic pathway is not yet fully characterized. Sulfazecin and other 3-aminomonobactamic acid derivatives are derived from serine or threonine, and tabtoxinine-beta-lactam is a phytotoxin. Aztreonam, a synthetic monobactam originally isolated as SQ 26,180 from Chromobacterium violaceum, is the first clinically used monobactam.

Nodes	Edges
9	6

Articulation point with highest impact	Disconnected nodes when remove it
NA	1

Global metrics
4	1.3333	0.0060

Nodes classification
0	0	2	9

Total organisms
5465

Eukaryotes	Prokaryotes
241	5224

Animals	Plants	Fungi	Protists	Bacteria	Archaea
0	105	122	14	4969	255

list(REFERENCE = "PMID:23135477", AUTHORS = "Hamed RB, Gomez-Castellanos JR, Henry L, Ducho C, McDonough MA, Schofield CJ", TITLE = "The enzymes of beta-lactam biosynthesis.", JOURNAL = c("Nat Prod Rep 30:21-107 (2013)", "DOI:10.1039/c2np20065a")), list(REFERENCE = "PMID:15271351", AUTHORS = "Gunsior M, Breazeale SD, Lind AJ, Ravel J, Janc JW, Townsend CA", TITLE = "The biosynthetic gene cluster for a monocyclic beta-lactam antibiotic, nocardicin A.", JOURNAL = c("Chem Biol 11:927-38 (2004)", "DOI:10.1016/j.chembiol.2004.04.012")), list(REFERENCE = "PMID:15252031", AUTHORS = "Kelly WL, Townsend CA", TITLE = "Mutational analysis and characterization of nocardicin C-9` epimerase.", JOURNAL = c("J Biol Chem 279:38220-7 (2004)", "DOI:10.1074/jbc.M405450200")), list(REFERENCE = "PMID:15629944", AUTHORS = "Kelly WL, Townsend CA", TITLE = "Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis.", JOURNAL = c("J Bacteriol 187:739-46 (2005)", "DOI:10.1128/JB.187.2.739-746.2005")), list(REFERENCE = "PMID:9804844", AUTHORS = "Reeve AM, Breazeale SD, Townsend CA", TITLE = "Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis.", JOURNAL = c("J Biol Chem 273:30695-703 (1998)", "DOI:10.1074/jbc.273.46.30695")), list(REFERENCE = "PMID:12105888", AUTHORS = "Kelly WL, Townsend CA", TITLE = "Role of the cytochrome P450 NocL in nocardicin A biosynthesis.", JOURNAL = c("J Am Chem Soc 124:8186-7 (2002)", "DOI:10.1021/ja025926g")), list(REFERENCE = "PMID:11137816", AUTHORS = "Hubbard BK, Thomas MG, Walsh CT", TITLE = "Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics.", JOURNAL = c("Chem Biol 7:931-42 (2000)", "DOI:10.1016/S1074-5521(00)00043-0")), list(REFERENCE = "PMID:25624104", AUTHORS = "Gaudelli NM, Long DH, Townsend CA", TITLE = "beta-Lactam formation by a non-ribosomal peptide synthetase during antibiotic biosynthesis.", JOURNAL = c("Nature 520:383-7 (2015)", "DOI:10.1038/nature14100")), list(REFERENCE = "PMID:24531841", AUTHORS = "Gaudelli NM, Townsend CA", TITLE = "Epimerization and substrate gating by a TE domain in beta-lactam antibiotic biosynthesis.", JOURNAL = c("Nat Chem Biol 10:251-8 (2014)", "DOI:10.1038/nchembio.1456")), list(REFERENCE = "PMID:22365611", AUTHORS = "Davidsen JM, Townsend CA", TITLE = "In vivo characterization of nonribosomal peptide synthetases NocA and NocB in the biosynthesis of nocardicin A.", JOURNAL = c("Chem Biol 19:297-306 (2012)", "DOI:10.1016/j.chembiol.2011.10.020")), list(REFERENCE = "PMID:23330869", AUTHORS = "Davidsen JM, Bartley DM, Townsend CA", TITLE = "Non-ribosomal propeptide precursor in nocardicin A biosynthesis predicted from adenylation domain specificity dependent on the MbtH family protein NocI.", JOURNAL = c("J Am Chem Soc 135:1749-59 (2013)", "DOI:10.1021/ja307710d")), list(REFERENCE = "PMID:6805424", AUTHORS = "O`Sullivan J, Gillum AM, Aklonis CA, Souser ML, Sykes RB", TITLE = "Biosynthesis of monobactam compounds: origin of the carbon atoms in the beta-lactam ring.", JOURNAL = c("Antimicrob Agents Chemother 21:558-64 (1982)", "DOI:10.1128/AAC.21.4.558")), list(REFERENCE = "PMID:6859838", AUTHORS = "O`Sullivan J, Souser ML, Kao CC, Aklonis CA", TITLE = "Sulfur metabolism in the biosynthesis of monobactams.", JOURNAL = c("Antimicrob Agents Chemother 23:598-602 (1983)", "DOI:10.1128/AAC.23.4.598")), list(REFERENCE = "PMID:16506699", AUTHORS = "Kinscherf TG, Willis DK", TITLE = "The biosynthetic gene cluster for the beta-lactam antibiotic tabtoxin in Pseudomonas syringae.", JOURNAL = c("J Antibiot (Tokyo) 58:817-21 (2005)", "DOI:10.1038/ja.2005.109")), list(REFERENCE = "PMID:22994681", AUTHORS = "Wencewicz TA, Walsh CT", TITLE = "Pseudomonas syringae self-protection from tabtoxinine-beta-lactam by ligase TblF and acetylase Ttr.", JOURNAL = c("Biochemistry 51:7712-25 (2012)", "DOI:10.1021/bi3011384")), list(REFERENCE = "PMID:23770908", AUTHORS = "Arai T, Arimura Y, Ishikura S, Kino K", TITLE = "L-amino acid ligase from Pseudomonas syringae producing tabtoxin can be used for enzymatic synthesis of various functional peptides.", JOURNAL = c("Appl Environ Microbiol 79:5023-9 (2013)", "DOI:10.1128/AEM.01003-13")), list(REFERENCE = "PMID:1515668", AUTHORS = "Engst K, Shaw PD", TITLE = "Identification of a lysA-like gene required for tabtoxin biosynthesis and pathogenicity in Pseudomonas syringae pv. tabaci strain PTBR2.024.", JOURNAL = "Mol Plant Microbe Interact 5:322-9 (1992)"), list(REFERENCE = "PMID:8990304", AUTHORS = "Liu L, Shaw PD", TITLE = "Characterization of dapB, a gene required by Pseudomonas syringae pv. tabaci BR2.024 for lysine and tabtoxinine-beta-lactam biosynthesis.", JOURNAL = c("J Bacteriol 179:507-13 (1997)", "DOI:10.1128/JB.179.2.507-513.1997")), list(REFERENCE = "PMID:9294453", AUTHORS = "Liu L, Shaw PD", TITLE = "A possible role for acetylated intermediates in diaminopimelate and tabtoxinine-beta-lactam biosynthesis in Pseudomonas syringae pv. tabaci BR2.024.", JOURNAL = c("J Bacteriol 179:5922-7 (1997)", "DOI:10.1128/JB.179.18.5922-5927.1997")), list(REFERENCE = "PMID:2881927", AUTHORS = "Unkefer CJ, London RE, Durbin RD, Uchytil TF, Langston-Unkefer PJ", TITLE = "The biosynthesis of tabtoxinine-beta-lactam. Use of specifically 13C-labeled glucose and 13C NMR spectroscopy to identify its biosynthetic precursors.", JOURNAL = "J Biol Chem 262:4994-9 (1987)")

Nodes classification
Articulation points (AP)	Hub & AP	Hubs	Other nodes
0	0	2	9

KPV - KEGG Pathway Viewer
by Igor Brandão

Loading..

00261 Monobactam biosynthesis
Metabolism; Biosynthesis of other secondary metabolites

9
NODES

6
EDGES

5465
ORGANISMS

4
COMMUNITIES

1.3333
AVG. DEGREE

0.0060
AVG. BETWEENNESS

0
ARTICULATION POINTS

9
OTHER NODES

Filters

Pathway Viewer

9

6

NA

1

4

1.3333

0.0060

0

0

2

9

5465

241

5224

0

105

122

14

4969

255

Global metrics
Communities	Avg. degree	Avg. betweenness
4	1.3333	0.0060

KPV - KEGG Pathway Viewer by Igor Brandão

Loading..

00261 Monobactam biosynthesis Metabolism; Biosynthesis of other secondary metabolites

9 NODES

6 EDGES

5465 ORGANISMS

4 COMMUNITIES

1.3333 AVG. DEGREE

0.0060 AVG. BETWEENNESS

0 ARTICULATION POINTS

9 OTHER NODES