format-version: 1.2
data-version: 1.0
date: 25:06:2021 19:45
default-namespace: kegg_pombe_pathway
ontology: kegg_pombe_pathway

[Term]
id: KEGG_PW:spo00740
name: Riboflavin metabolism

[Term]
id: KEGG_PW:spo00565
name: Ether lipid metabolism

[Term]
id: KEGG_PW:spo00909
name: Sesquiterpenoid and triterpenoid biosynthesis
def: "Sesquiterpenoids (C15 terpenoids) are a group of terpenoids consisting of three isoprene units. They are derive from farnesyl diphosphate (FPP) and can be cyclized to produce various skeletal structures. Sesquiterpenoid biosynthesis begins with the loss of diphosphate from FPP under the action of sesquiterpene synthesis enzymes, generating an allylic cation that is highly susceptible to intramolecular attacks. Cyclization of the farnesyl cation may take place onto either of the remaining double bonds with the result that 6-, 10-, or 11-membered rings may be formed. Many sesquiterpenoids have been isolated from plants, fungi, marine organisms, and Streptomyces species. This map shows a few examples of acyclic and cyclic sesquiterpenoids." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03013
name: RNA transport
def: "RNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) via mobile export receptors. The majority of RNAs, such as tRNAs, rRNAs, and U snRNAs, are transported by specific export receptors, which belong to the karyopherin-beta family proteins. A feature of karyopherins is their regulation by the small GTPase Ran. However, general mRNA export is mechanistically different. Nuclear export of mRNAs is functionally coupled to different steps in gene expression processes, such as transcription, splicing, 3'-end formation and even translation." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00100
name: Steroid biosynthesis

[Term]
id: KEGG_PW:spo00620
name: Pyruvate metabolism

[Term]
id: KEGG_PW:spo00053
name: Ascorbate and aldarate metabolism

[Term]
id: KEGG_PW:spo00280
name: Valine, leucine and isoleucine degradation

[Term]
id: KEGG_PW:spo03022
name: Basal transcription factors

[Term]
id: KEGG_PW:spo03430
name: Mismatch repair
def: "DNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preventing mutations from becoming permanent in dividing cells. MMR also suppresses homologous recombination and was recently shown to play a role in DNA damage signaling. Defects in MMR are associated with genome-wide instability, predisposition to certain types of cancer including HNPCC, resistance to certain chemotherapeutic agents, and abnormalities in meiosis and sterility in mammalian systems. The Escherichia coli MMR pathway has been extensively studied and is well characterized. In E. coli, the mismatch-activated MutS-MutL-ATP complex licenses MutH to incise the nearest unmethylated GATC sequence. UvrD and an exonuclease generate a gap. This gap is filled by pol III and DNA ligase. The GATC sites are then methylated by Dam. Several human MMR proteins have been identified based on their homology to E. coli MMR proteins. These include human homologs of MutS and MutL. Although E. coli MutS and MutL proteins are homodimers, human MutS and MutL homologs are heterodimers. The role of hemimethylated dGATC sites as a signal for strand discrimination is not conserved from E. coli to human. Human MMR is presumed to be nick-directed in vivo, and is thought to discriminate daughter and template strands using a strand-specific nick." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00261
name: Monobactam biosynthesis
def: "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:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo04113
name: Meiosis - yeast
def: "During meiosis, a single round of DNA replication is followed by two rounds of chromosome segregation, called meiosis I and meiosis II. At meiosis I, one pair of sister chromatids recombines with, then segregates from, its homologous pair, while the sister chromatids segregate from each other at meoisis II. In yeast, the switch to enter growth phase or meiosis phase is controlled by nutritional signals. At the onset of meiosis, nutritional signaling pathways converge on transcriptional regulation of Ime1. Ime1 is a transcriptional activator to promote expression of early meiosis-specific genes required for pre-meiotic DNA replication and meiotic recombination. Two of the early meiosis-specific genes, a transcriptional activator, Ndt80, and a CDK2 homolog, Ime2, are required for the transcription of middle meiosis-specific genes, which includes B-type cyclin genes and genes involved in spore wall formation. Polo-like kinase Cdc5, whose expression is activated by Ndt80, is required for the critical step in meiotic progression. Cdc5 regulates sister-kinetochore co-orientation by promoting the localization of Mam1 and Lrs4, components of the co-orientation complex, to kinetochores. Cdc5 also phosphorylates the meiotic cohesin subunit Rec8, which is essential for its cleavage and removal by separase. Moreover, Cdc5 promotes the release of protein phosphatase Cdc14 from the nuclezus, which is required for anaphase I spindle disassembly and exit from meiosis I. The centromeric protein Sgo1 is a key regulator of meiotic chromosome segregation. Sgo1 with PP2A may protect pericentromeric but not arm cohesion of sister chromatids during meiosis I. Sgo1 then disappears at meiosis II to allow sister chromatids to separate." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03420
name: Nucleotide excision repair
def: "Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes, uvrAB complex). The following steps of GGR-NER and TCR-NER are similar." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00514
name: Other types of O-glycan biosynthesis
def: "O-linked glycosylation is the attachment of monosaccharides to the hydroxyl groups of amino acids, mostly serine and threonine, and is found in eukaryotes, archaea and bacteria. O-glycans exhibit diverse types of modifications where the innermost monosaccharide is N-acetylgalactosamine (" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00410
name: beta-Alanine metabolism

[Term]
id: KEGG_PW:spo00910
name: Nitrogen metabolism
def: "The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00072
name: Synthesis and degradation of ketone bodies

[Term]
id: KEGG_PW:spo00450
name: Selenocompound metabolism

[Term]
id: KEGG_PW:spo00500
name: Starch and sucrose metabolism

[Term]
id: KEGG_PW:spo01240
name: Biosynthesis of cofactors

[Term]
id: KEGG_PW:spo01230
name: Biosynthesis of amino acids
def: "This map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module for conversion of three-carbon compounds from glyceraldehyde-3P to pyruvate [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00260
name: Glycine, serine and threonine metabolism
def: "Serine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00600
name: Sphingolipid metabolism

[Term]
id: KEGG_PW:spo00750
name: Vitamin B6 metabolism

[Term]
id: KEGG_PW:spo03450
name: Non-homologous end-joining
def: "Nonhomologous end joining (NHEJ) eliminates DNA double-strand breaks (DSBs) by direct ligation. NHEJ involves binding of the KU heterodimer to double-stranded DNA ends, recruitment of DNA-PKcs (MRX complex in yeast), processing of ends, and recruitment of the DNA ligase IV (LIG4)-XRCC4 complex, which brings about ligation. A recent study shows that bacteria accomplish NHEJ using just two proteins (Ku and DNA ligase), whereas eukaryotes require many factors. NHEJ repairs DSBs at all stages of the cell cycle, bringing about the ligation of two DNA DSBs without the need for sequence homology, and so is error-prone." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03015
name: mRNA surveillance pathway
def: "The mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go decay (NGD). NMD is a mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In vertebrates, PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Upf3, together with Upf1 and Upf2, may signal the presence of the PTC to the 5'end of the transcript, resulting in decapping and rapid exonucleolytic digestion of the mRNA. In the NSD pathway, which targets mRNAs lacking termination codons, the ribosome is believed to translate through the 3' untranslated region and stall at the end of the poly(A) tail. NSD involves an eRF3-like protein, Ski7p, which is hypothesized to bind the empty A site of the ribosome and recruit the exosome to degrade the mRNA from the 3' end. NGD targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00061
name: Fatty acid biosynthesis

[Term]
id: KEGG_PW:spo00360
name: Phenylalanine metabolism

[Term]
id: KEGG_PW:spo00071
name: Fatty acid degradation

[Term]
id: KEGG_PW:spo00350
name: Tyrosine metabolism

[Term]
id: KEGG_PW:spo00785
name: Lipoic acid metabolism

[Term]
id: KEGG_PW:spo01210
name: 2-Oxocarboxylic acid metabolism
def: "2-Oxocarboxylic acids, also called 2-oxo acids and alpha-keto acids, are the most elementary set of metabolites that includes pyruvate (2-oxopropanoate), 2-oxobutanoate, oxaloacetate (2-oxosuccinate) and 2-oxoglutarate. This diagram illustrates the architecture of chain extension and modification reaction modules for 2-oxocarboxylic acids. The chain extension module" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo04145
name: Phagosome
def: "Phagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is formed when the specific receptors on the phagocyte surface recognize ligands on the particle surface. After formation, nascent phagosomes progressively acquire digestive characteristics. This maturation of phagosomes involves regulated interaction with the other membrane organelles, including recycling endosomes, late endosomes and lysosomes. The fusion of phagosomes and lysosomes releases toxic products that kill most bacteria and degrade them into fragments. However, some bacteria have strategies to escape the bactericidal mechanisms associated with phagocytosis and survive within host phagocytes." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00030
name: Pentose phosphate pathway
def: "The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway. One is irreversible oxidative phase in which glucose-6P is converted to ribulose-5P by oxidative decarboxylation, and NADPH is generated [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03018
name: RNA degradation
def: "The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway, this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway, the exosome, a large multisubunit complex, plays a key role. The exosome exists in archaeal cells, too. In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicases, and additional factors in the RNA-degrading complex." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo01200
name: Carbon metabolism
def: "Carbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. The map contains carbon utilization pathways of glycolysis (" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00680
name: Methane metabolism
def: "Methane is metabolized principally by methanotrophs and methanogens in the global carbon cycle. Methanotrophs consume methane as the only source of carbon, while methanogens produce methane as a metabolic byproduct. Methylotrophs, which are microorganisms that can obtain energy for growth by oxidizing one-carbon compounds, such as methanol and methane, are situated between methanotrophs and methanogens. Methanogens can obtain energy for growth by converting a limited number of substrates to methane under anaerobic conditions. Three types of methanogenic pathways are known: CO2 to methane [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00240
name: Pyrimidine metabolism

[Term]
id: KEGG_PW:spo00052
name: Galactose metabolism

[Term]
id: KEGG_PW:spo03050
name: Proteasome
def: "The proteasome is a protein-destroying apparatus involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. It is capable of degrading a variety of cellular proteins in a rapid and timely fashion and most substrate proteins are modified by ubiquitin before their degradation by the proteasome. The proteasome is a large protein complex consisting of a proteolytic core called the 20S particle and ancillary factors that regulate its activity in various ways. The most common form is the 26S proteasome containing one 20S core particle and two 19S regulatory particles that enable the proteasome to degrade ubiquitinated proteins by an ATP-dependent mechanism. Another form is the immunoproteasome containing two 11S regulatory particles, PA28 alpha and PA28 beta, which are induced by interferon gamma under the conditions of intensified immune response. Other regulatory particles include PA28 gamma and PA200. Although PA28 gamma also belongs to a family of activators of the 20S proteasome, it is localized within the nucleus and forms a homoheptamer. PA28 gamma has been implicated in the regulation of cell cycle progression and apoptosis. PA200 has been identified as a large nuclear protein that stimulates proteasomal hydrolysis of peptides." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00330
name: Arginine and proline metabolism

[Term]
id: KEGG_PW:spo04136
name: Autophagy - other
def: "Autophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either in a housekeeping capacity or during stress and senescence. The process of autophagy could be divided into several stages: induction, vesicle nucleation, elongation and closure, and fusion and digestion. Most essential autophagic machineries are conserved throughout eukaryotes (see" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00062
name: Fatty acid elongation

[Term]
id: KEGG_PW:spo00270
name: Cysteine and methionine metabolism
def: "Cysteine and methionine are sulfur-containing amino acids. Cysteine is synthesized from serine through different pathways in different organism groups. In bacteria and plants, cysteine is converted from serine (via acetylserine) by transfer of hydrogen sulfide [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo01110
name: Biosynthesis of secondary metabolites

[Term]
id: KEGG_PW:spo00520
name: Amino sugar and nucleotide sugar metabolism

[Term]
id: KEGG_PW:spo00630
name: Glyoxylate and dicarboxylate metabolism

[Term]
id: KEGG_PW:spo00380
name: Tryptophan metabolism

[Term]
id: KEGG_PW:spo03410
name: Base excision repair
def: "Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway, thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00051
name: Fructose and mannose metabolism

[Term]
id: KEGG_PW:spo00900
name: Terpenoid backbone biosynthesis
def: "Terpenoids, also known as isoprenoids, are a large class of natural products consisting of isoprene (C5) units. There are two biosynthetic pathways, the mevalonate pathway [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00310
name: Lysine degradation

[Term]
id: KEGG_PW:spo00010
name: Glycolysis / Gluconeogenesis
def: "Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabolites: six-carbon compounds of glucose-6P and fructose-6P and three-carbon compounds of glycerone-P, glyceraldehyde-3P, glycerate-3P, phosphoenolpyruvate, and pyruvate [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00780
name: Biotin metabolism
def: "Biotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase. Mammals cannot synthesize biotin, while in bacteria, fungi, and plants it is synthesized from pimelate thioester through different pathways. In E. coli and many organisms, pimelate thioester is derived from malonyl-ACP. The pathway starts with the methylation to malonyl-ACP methyl ester, followed by the fatty acid chain elongation cycle to form pimeloyl-ACP methyl ester, which is then demethylated to form pimeloyl-ACP [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00190
name: Oxidative phosphorylation

[Term]
id: KEGG_PW:spo03030
name: DNA replication
def: "A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. On the leading strand, replication occurs continuously in a 5 to 3 direction, whereas on the lagging strand, DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. In prokaryotes, the leading strand replication apparatus consists of a DNA polymerase (pol III core), a sliding clamp (beta), and a clamp loader (gamma delta complex). The DNA primase (DnaG) is needed to form RNA primers. Normally, during replication of the lagging-strand DNA template, an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I, and the DNA ligase joins the Okazaki fragments. In eukaryotes, three DNA polymerases (alpha, delta, and epsilon) have been identified. DNA primase forms a permanent complex with DNA polymerase alpha. PCNA and RFC function as a clamp and a clamp loader. FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00561
name: Glycerolipid metabolism

[Term]
id: KEGG_PW:spo00970
name: Aminoacyl-tRNA biosynthesis

[Term]
id: KEGG_PW:spo04111
name: Cell cycle - yeast
def: "Mitotic cell cycle progression is accomplished through a reproducible sequence of events, DNA replication (S phase) and mitosis (M phase) separated temporally by gaps (G1 and G2 phases). G1, S, and G2 phases are collectively known as interphase. In yeast Cdc28 is the catalytic subunit of the cyclin-dependent kinase (CDK). At G1 phase Cdc28 associates with G1-cyclins Cln1 to Cln3, while B-type cyclins Clb1 to Clb6 regulate Cdc28 during S, G2, and M phases. Cln3/Cdc28 activity is required for cells to pass through 'start', the commitment point in G1. When Cln3/Cdc28 accumulates more than a certain threshold, SBF (Swi4/Swi6) and MBF (Mbp1/Swi6) are activated, promoting transcription of Cln1, Cln2, and other genes required for S-phase progression. Cln1 and Cln2 interacting with Cdc28 promote activation of B-type cyclin associated CDK, which drives DNA replication and entry into mitosis. Specifically, Cdc28 association with Clb2 and Clb1 promotes entry into mitosis. Cells suffering from DNA damage, spindle misorientation, or spindle assembly defect do not undergo the metaphase-anaphase transition for chromosome segregation and fail to exit from mitosis. The spindle assembly checkpoint activates Mad2, which in turn prevents chromosome segregation by inhibiting degradation of the securin Pds1. Moreover, Pds1 is phosphorylated and stabilized in response to DNA damage in a Chk1-dependent manner. The spindle checkpoint is also involved in the Cdc14 release from the nucleolus. Cdc14 dephosphorylates Swi5, Sic1, and Cdh1, leading to inhibition of Cdc28 and degradation of cyclin required for mitotic exit." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00920
name: Sulfur metabolism
def: "Sulfur is an essential element for life and the metabolism of organic sulfur compounds plays an important role in the global sulfur cycle. Sulfur occurs in various oxidation states ranging from +6 in sulfate to -2 in sulfide (H2S). Sulfate reduction can occur in both an energy consuming assimilatory pathway and an energy producing dissimilatory pathway. The assimilatory pathway, which is found in a wide range of organisms, produces reduced sulfur compounds for the biosynthesis of S-containing amino acids and does not lead to direct excretion of sulfide. In the dissimilatory pathway, which is restricted to obligatory anaerobic bacterial and archaeal lineages, sulfate (or sulfur) is the terminal electron acceptor of the respiratory chain producing large quantities of inorganic sulfide. Both pathways start from the activation of sulfate by reaction with ATP to form adenylyl sulfate (APS). In the assimilatory pathway [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00660
name: C5-Branched dibasic acid metabolism

[Term]
id: KEGG_PW:spo00300
name: Lysine biosynthesis

[Term]
id: KEGG_PW:spo04011
name: MAPK signaling pathway - yeast
def: "The S. cerevisiae genome encodes multiple MAP kinase orthologs. One (Fus3) mediates cellular response to peptide pheromones. Another (Kss1) permits adjustment to nutrient limiting conditions. A third (Hog1) is necessary for survival under hyperosmotic conditions. A fourth (Slt2/Mpk1) is required for repair of injuries to the cell wall. As in mammalian cells, these pathways consist of a conserved module in which three kinases phosphorylate each other in sequence. The MAPK is phosphorylated by the MAPK/ERK kinase (MAPKK/MEK), which is itself phosphorylated by a MEK kinase (MAPKKK/MEKK)." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00515
name: Mannose type O-glycan biosynthesis
def: "Biosynthesis of mammalian O-mannosyl glycans is initiated by the transfer of mannose from mannose-P-Dol to serine or threonine residue, followed by extensions with N-acetylglucosamine (GlcNAc) and galactose (Gal) to generate core M1, M2 and M3 glycans. Core M1 and M2 glycans can then be further attached by fucose residues, sialic acid terminals and sulfatded glucuroinc acid terminals. Core M3 glycan is involved in the synthesis of alpha-dystroglycan, a heavily glycosylated protein found in muscle and brain tissues. Core M3 glycan contains a tandem repeat of ribitol 5-phosphate (Rbo5P) and -alpha3-GlcA-beta3-Xyl- repeating structures. Defects of genes encoding core glycans and modified core M3 glycans are associated with various congenital diseases, such as muscular dystrophies caused by reduced O-mannosylation of alpha-dystroglycan in skeletal muscles [DS:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00563
name: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
def: "Cell surface proteins can be attached to the cell membrane via the glycolipid structure called glycosylphosphatidylinositol (GPI) anchor. Hundreds of GPI-anchored proteins have been identified in many eukaryotes ranging from protozoa and fungi to mammals. All protein-linked GPI anchors share a common core structure, characterized by the substructure Man (a1-4) GlcN (a1-6) myo-inositol-1P-lipid. Biosynthesis of GPI anchors proceeds in three stages: (i) preassembly of a GPI precursor in the ER membrane, (ii) attachment of the GPI to the C-terminus of a newly synthesized protein in the lumen of the ER, and (iii) lipid remodeling and/or carbohydrate side-chain modifications in the ER and the Golgi. Defects of GPI anchor biosynthesis gene result in a genetic disorder, paroxysmal nocturnal hemoglobinuria." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03060
name: Protein export
def: "The protein export is the active transport of proteins from the cytoplasm to the exterior of the cell, or to the periplasmic compartment in Gram-negative bacteria. The sec dependent pathway is the general protein export system that transports newly synthesized proteins into or across the cell membrane. The translocation channel is formed from a conserved trimeric membrane protein complex, called the Sec61/SecY complex. The twin-arginine translocation (Tat) pathway is another protein transport system that transports folded proteins in bacteria, archaea, and chloroplasts. Many Tat systems comprise three functionally different membrane proteins, TatA, TatB, and TatC, but TatA and TatE seem to have overlapping functions, with TatA having by far the more important role." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo04141
name: Protein processing in endoplasmic reticulum
def: "The endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylated. Correctly folded proteins are packaged into transport vesicles that shuttle them to the Golgi complex. Misfolded proteins are retained within the ER lumen in complex with molecular chaperones. Proteins that are terminally misfolded bind to BiP and are directed toward degradation through the proteasome in a process called ER-associated degradation (ERAD). Accumulation of misfolded proteins in the ER causes ER stress and activates a signaling pathway called the unfolded protein response (UPR). In certain severe situations, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00760
name: Nicotinate and nicotinamide metabolism

[Term]
id: KEGG_PW:spo03040
name: Spliceosome
def: "After transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, the spliceosome. The standard spliceosome is made up of five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6 snRNPs, and several spliceosome-associated proteins (SAPs). Spliceosomes are not a simple stable complex, but a dynamic family of particles that assemble on the mRNA precursor and help fold it into a conformation that allows transesterification to proceed. Various spliceosome forms (e.g. A-, B- and C-complexes) have been identified." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo04070
name: Phosphatidylinositol signaling system

[Term]
id: KEGG_PW:spo00250
name: Alanine, aspartate and glutamate metabolism

[Term]
id: KEGG_PW:spo00640
name: Propanoate metabolism

[Term]
id: KEGG_PW:spo00460
name: Cyanoamino acid metabolism

[Term]
id: KEGG_PW:spo04144
name: Endocytosis
def: "Endocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins entering through clathrin-dependent endocytosis (CDE) have sequences in their cytoplasmic domains that bind to the APs (adaptor-related protein complexes) and enable their rapid removal from the PM. In addition to APs and clathrin, there are numerous accessory proteins including dynamin. Depending on the various proteins that enter the endosome membrane, these cargoes are sorted to distinct destinations. Some cargoes, such as nutrient receptors, are recycled back to the PM. Ubiquitylated membrane proteins, such as activated growth-factor receptors, are sorted into intraluminal vesicles and eventually end up in the lysosome lumen via multivesicular endosomes (MVEs). There are distinct mechanisms of clathrin-independent endocytosis (CIE) depending upon the cargo and the cell type." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo04120
name: Ubiquitin mediated proteolysis
def: "Protein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to proteins being degraded is performed by a reaction cascade consisting of three enzymes, named E1 (ubiquitin activating enzyme), E2 (ubiquitin conjugating enzyme), and E3 (ubiquitin ligase). Each E3 has specificity to its substrate, or proteins to be targeted by ubiquitination. Many E3s are discovered in eukaryotes and they are classified into four types: HECT type, U-box type, single RING-finger type, and multi-subunit RING-finger type. Multi-subunit RING-finger E3s are exemplified by cullin-Rbx E3s and APC/C. They consist of a RING-finger-containing subunit (RBX1 or RBX2) that functions to bind E2s, a scaffold-like cullin molecule, adaptor proteins, and a target recognizing subunit that binds substrates." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo03440
name: Homologous recombination
def: "Homologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves the generation of a single-stranded region of DNA, followed by strand invasion, formation of a Holliday junction, DNA synthesis using the intact strand as a template, branch migration and resolution. It is investigated that RecA/Rad51 family proteins play a central role. The breast cancer susceptibility protein Brca2 and the RecQ helicase BLM (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity, at least in part, through HR." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00230
name: Purine metabolism

[Term]
id: KEGG_PW:spo00480
name: Glutathione metabolism

[Term]
id: KEGG_PW:spo00730
name: Thiamine metabolism

[Term]
id: KEGG_PW:spo00332
name: Carbapenem biosynthesis
def: "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:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00430
name: Taurine and hypotaurine metabolism

[Term]
id: KEGG_PW:spo00860
name: Porphyrin and chlorophyll metabolism

[Term]
id: KEGG_PW:spo00472
name: D-Arginine and D-ornithine metabolism

[Term]
id: KEGG_PW:spo01212
name: Fatty acid metabolism

[Term]
id: KEGG_PW:spo04146
name: Peroxisome
def: "Peroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contribute to many crucial metabolic processes such as fatty acid oxidation, biosynthesis of ether lipids and free radical detoxification. The biogenesis of peroxisomes starts with the early peroxins PEX3, PEX16 and PEX19 and proceeds via several steps. The import of membrane proteins into peroxisomes needs PEX19 for recognition, targeting and insertion via docking at PEX3. Matrix proteins in the cytosol are recognized by peroxisomal targeting signals (PTS) and transported to the docking complex at the peroxisomal membrane. Peroxisomes' deficiencies lead to severe and often fatal inherited peroxisomal disorders (PD). PDs are usually classified in two groups. The first group is disorders of peroxisome biogenesis which include Zellweger syndrome, and the second group is single peroxisomal enzyme deficiencies." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00790
name: Folate biosynthesis

[Term]
id: KEGG_PW:spo01040
name: Biosynthesis of unsaturated fatty acids

[Term]
id: KEGG_PW:spo00130
name: Ubiquinone and other terpenoid-quinone biosynthesis
def: "Ubiquinone (UQ), also called coenzyme Q, and plastoquinone (PQ) are electron carriers in oxidative phosphorylation and photosynthesis, respectively. The quinoid nucleus of ubiquinone is derived from the shikimate pathway; 4-hydroxybenzoate is directly formed from chorismate in bacteria, while it can be formed from either chorismate or tyrosine in yeast. The following biosynthesis of terpenoid moiety involves reactions of prenylation, decarboxylation, and three hydroxylations alternating with three methylations. The order of these reactions are somewhat different between bacteria and yeast. Phylloquinone (vitamin K1), menaquinone (vitamin K2), and tocopherol (vitamin E) are fat-soluble vitamins. Phylloquinone is a compound present in all photosynthetic plants serving as a cofactor for photosystem I-mediated electron transport. Menaquinone is an obligatory component of the electron-transfer pathway in bacteria." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00770
name: Pantothenate and CoA biosynthesis

[Term]
id: KEGG_PW:spo03010
name: Ribosome

[Term]
id: KEGG_PW:spo00562
name: Inositol phosphate metabolism

[Term]
id: KEGG_PW:spo00340
name: Histidine metabolism

[Term]
id: KEGG_PW:spo00513
name: Various types of N-glycan biosynthesis

[Term]
id: KEGG_PW:spo04138
name: Autophagy - yeast
def: "Autophagy is a non-selective and bulk intracellular degradation system of eukaryotic cells and is highly conserved from yeast to human. In this process, the double-membrane vesicle, known as autophagosome, is formed and sequesters organelles or portions of cytosol. The autophagosome is subsequently fused with the vacuole for breakdown by resident hydrolases, and the resulting metabolites are delivered for reuse. In yeast, nutrient withdrawal is the primary stimulus that induces autophagy. Autophagy plays a central role in normal development and cell homeostasis of yeast." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00510
name: N-Glycan biosynthesis
def: "N-glycans or asparagine-linked glycans are major constituents of glycoproteins in eukaryotes. N-glycans are covalently attached to asparagine with the consensus sequence of Asn-X-Ser/Thr by an N-glycosidic bond, GlcNAc b1- Asn. Biosynthesis of N-glycans begins on the cytoplasmic face of the ER membrane with the transferase reaction of UDP-GlcNAc and the lipid-like precursor P-Dol (dolichol phosphate) to generate GlcNAc a1- PP-Dol. After sequential addition of monosaccharides by ALG glycosyltransferases [MD:" [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00564
name: Glycerophospholipid metabolism

[Term]
id: KEGG_PW:spo04122
name: Sulfur relay system
def: "Ubiquitin and ubiquitin-like proteins (Ubls) are signalling messengers that control many cellular functions, such as cell proliferation, apoptosis, and DNA repair. It is suggested that Ub-protein modification evolved from prokaryotic sulfurtransfer systems. Molybdenum cofactor (Moco) and thiamin are sulfur-containing cofactors whose biosynthesis includes a key sulfur transfer step that uses unique sulfur carrier proteins, MoaD and ThiS. Ubiquitin, MoaD, and ThiS are all structurally related proteins whose C-termini are activated through adenylation by homologous E1-like enzymes. s2T biosynthesis may share similar chemistry with Moco and thiamin synthesis. In Saccharomyces cerevisiae, Urm1 and Uba4 function as part of a ubl protein conjugation system, though they have sequence homology to bacterial sulfur-transfer enzymes and the ability to function in sulfur transfer." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo01100
name: Metabolic pathways

[Term]
id: KEGG_PW:spo00040
name: Pentose and glucuronate interconversions

[Term]
id: KEGG_PW:spo00220
name: Arginine biosynthesis

[Term]
id: KEGG_PW:spo04130
name: SNARE interactions in vesicular transport

[Term]
id: KEGG_PW:spo04139
name: Mitophagy - yeast
def: "Mitophagy, which refers to the selective elimination of impaired or excessive mitochondria, is considered to be the main mechanism for mitochondria quality and quantity control. In yeast, oxidative stress or inhibition of TOR induces expression of Agt32, the indispensable mitochondrial outer membrane receptor. Direct phosphorylation of Atg32 by CK2 triggers mitophagy, and two mitogen-activated protein kinase (MAPK) signal transduction pathways are also important in this process. Atg11 is an adaptor protein for selective autophagy, and recruits the cargo to the phagophore assembly site (PAS), where the autophagosome is generated. Then Atg32-Atg8 interaction enhances the formation of the autophagosome surrounding the mitochondria, which finally fuses with vacuoles for degradation. Atg32-Atg11 interaction may also be regulated by Yme1-mediated processing of Atg32, as well as by mitochondrial fission machinery. Some factors have been suggested to positively or negatively regulate the mitophagy via different mechanisms, including Atg1, Atg33, Mss4, Fmc1, Mdm38, Mip1, and Ubp3-Bre5 deubiquitination complex." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00650
name: Butanoate metabolism

[Term]
id: KEGG_PW:spo03008
name: Ribosome biogenesis in eukaryotes
def: "Ribosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It requires hundreds of factors not present in the mature particle. In the absence of these proteins, ribosome biogenesis is stalled and cell growth is terminated even under optimal growth conditions. The primary pre-rRNA transcript is assembled into the 90S pre-ribosome, which contains both 40S and 60S assembly factors. Within this complex, the pre-rRNA is cleaved. pre-60S ribosomes are subjected to several sequential processing steps in the nucleoplasm involving numerous assembly intermediates before it is exported to the cytoplasm and matured into the 60S ribosomal subunit. The pre-40S ribosome is matured to the small ribosomal subunit in the cytoplasm by cleavage." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo02010
name: ABC transporters
def: "The ATP-binding cassette (ABC) transporters form one of the largest known protein families, and are widespread in bacteria, archaea, and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions, sugars, lipids, sterols, peptides, proteins, and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments, two peripheral proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand, in a typical eukaryotic ABC transporter, the membrane spanning protein and the ATP-binding protein are fused, forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD)." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00290
name: Valine, leucine and isoleucine biosynthesis

[Term]
id: KEGG_PW:spo00670
name: One carbon pool by folate

[Term]
id: KEGG_PW:spo00511
name: Other glycan degradation

[Term]
id: KEGG_PW:spo00440
name: Phosphonate and phosphinate metabolism
def: "Natural products containing carbon-phosphorous bonds, so-called C-P compounds, are derivatives of phosphonate and phosphinate with substitution of alkyl group for hydrogen of phosphorus-hydrogen bonds. C-P compounds have been found in many organisms, but only protists and bacteria, mostly Actinobacteria, have biosynthetic capacity. A common reaction in the biosynthetic pathway is C-P bond forming reaction from phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy) catalyzed by PEP phosphomutase. 2-Aminoethylphosphonate (AEP) is the most abundant C-P compound in the natural world. AEP derivatives include phosphonoprotein, phosphonoglycan, and phosphonolipid. Other known C-P compounds are bioactive substances used in medicine (antibiotics) and agriculture (herbicide) such as fosfomycin, FR-33289, rhizocticin, and bialaphos." [KEGG:KEGG]

[Term]
id: KEGG_PW:spo00590
name: Arachidonic acid metabolism

[Term]
id: KEGG_PW:spo03020
name: RNA polymerase

[Term]
id: KEGG_PW:spo00400
name: Phenylalanine, tyrosine and tryptophan biosynthesis

[Term]
id: KEGG_PW:spo00020
name: Citrate cycle (TCA cycle)
def: "The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data, many organisms seem to lack genes for the full cycle [MD:" [KEGG:KEGG]