Documentation and Sources
Introduction to YMDB
YDMB is a detailed database on small molecule from Saccharomyces cerevisiae. Each small molecule entry has extensive information on properties, structure, and biology. Each small molecule can have 1 or more enzymes and transporters associated. Below is a quick definition list to get you started.
- Metabolite
- A naturally occurring molecule typically under 1000 MW.
- Enzyme
- Any protein which catalyzes chemical reactions involving the small molecule.
- Transporter
- A membrane bound protein which shuttles ions, small molecules or macromolecules across membranes, into cells or out of cells.
YMDB also contains experimentally determined concentrations of metabolites. The details of the experimental methods used to determine these concentrations can be found Not Available. Documentation describing our standards for the conversion of literature concentration values can be found Not Available.
Field Documentation and Sources
Data sources indicate the source of the information present in each field. Data sources do not indicate that all sources were used for a particular field and metabolite. Individual metabolite reference information can be found in the "General References" section of each metabolite.
| Field | Description | Sources |
|---|---|---|
| Creation Date | Date/time the entry was created |
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| Update Date | Date/time the entry was last updated |
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| YMDB ID (Primary Accession Number) | Unique YMDB accession number consisting of a 4 letter prefix (YMDB) and a 5 number suffix. This ID is used to access the metabolite entry via the URL. If an entry is deleted, it's YMDB ID will not be reused. |
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| Name | Standard name of metabolite | |
| Description | Description of the metabolite describing general facts. | |
| Kingdom | First level of hierarchical classification.Organic or Inorganic |
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| Super Class | Second level of hierarchical classification. Metabolite with the same super class are considered structurally similar. |
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| Class | Third level of hierarchical classification. Metabolite classes form the major component of the classification system. Metabolite with the same super class are considered structurally similar. |
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| Sub Class | Fourth level of hierarchical classification. Metabolite with the same class are considered structurally similar. |
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| Substituents | Fifth level of hierarchical classification. Metabolite functional groups and substructures. |
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| Synonyms | Alternate names of the metabolite | |
| Chemical IUPAC Name | IUPAC or standard chemical name for the metabolite |
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| Traditional IUPAC Name | Traditional IUPAC or standard chemical name for the metabolite |
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| Chemical Formula | Chemical formula describing atomic or elemental composition |
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| Formal Charge | Molecular formal charge |
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| Average Molecular Weight | Molecular weight in g/mol, determined from molecular formula or sequence |
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| Monoisotopic Molecular Weight | The sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principle (most abundant) isotope for each element instead of the isotopic average mass. |
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| Structure | The 2D chemical structure including links to download and view the structure in various formats. | |
| SMILES | Isomeric SMILES string corresponding to metabolite structure |
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| InChI | Standard InChI identifier |
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| InChI Key | Standard InChI key |
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| CAS Registry Number | Chemical Abstract Service identification number | |
| KEGG Compound ID | Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG) | |
| PubChem Compound ID | NCBI's PubChem database compound identification number | |
| PubChem Substance ID | NCBI's PubChem database subtance identification number | |
| ChemSpider ID | ChemSpider identification number | |
| ChEBI ID | EBI's Chemicals of Biological Interest identification number (if metabolite is in ChEBI) | |
| Wikipedia Link | Link to Wikipedia entry for the given metabolite (if it exists) | |
| State | Physical state (solid, liquid, gas) |
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| Melting Point | Melting point (if solid) or boiling point (if liquid) in degrees Celsius | |
| Experimental Water Solubility | Water solubility in mg/mL or g/L | |
| Predicted Water Solubility | Predicted water solubility in mg/mL | |
| Experimental LogP/Hydrophobicity | Water/octanol partition coefficient (if small molecule) or hydrophobicity score (Gravy score) if protein/peptide | |
| Predicted LogP/Hydrophobicity | Predicted water/octanol partition coefficient |
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| Predicted LogS | Predicted LogS (water solubility) |
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| Experimental LogS | Experimental LogS (water solubility) | |
| pKa | Dissociation constant (pKa) | |
| Experimental QqQ MS/MS Spectrum | Image of experimental QqQ MS/MS spectrum | |
| Experimental 1H NMR Spectrum | Image of experimental 1H NMR Spectrum | |
| Experimental 13C NMR Spectrum | Image of experimental 13C NMR | |
| Experimental 13C HSQC Spectrum | Image of experimental 13C NMR | |
| Experimental 2D TOCSY Spectrum | Image of experimental 2D TOCSY spectrum | |
| Predicted 1H NMR Spectrum | Image of predicted 1H NMR Spectrum |
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| Predicted 13C NMR Spectrum | Image of experimental 13C NMR Spectrum |
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| Metabolite Concentration | Intercellular/Extracellular metabolite concentration found when yeast grown on particular substrate |
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| Pathways | Metabolic Pathways | |
| Cellular Locations | Metabolite subcellular locations |
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| References | General on-line reference to other details about the metabolite |
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Synthesis Reference | Reference describing the compound synthesis |
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Enzyme and Transporter Documentation
| Field | Description | Sources |
|---|---|---|
| Name | Name of the protein or macromolecule (or other small molecule) | |
| Gene Name | Gene name | |
| Synonyms | Alternate names (protein names, abbreviations, etc.) | |
| Protein Sequence | Amino acid sequence | |
| Number of Residues | Number of amino acids in the protein sequence |
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| Molecular Weight (Daltons) | Molecular weight given in Daltons or g/mol |
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| Theoretical pI | Theoretical isoelectric point |
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| GO Classification | Gene ontology classification including function, cellular process and location |
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| General Function | Short 3-4 word summary of the primary functions | |
| Specific Function | Detailed 30-40 word summary of the specific functions | |
| Pathways | Key pathways or processes (from SMPD) that the given molecule is involved in | |
| Reaction | Reaction(s) that the given molecule participates in | |
| Pfam Domain Function | Names and ID numbers of PFAM domains | |
| Signals | Location of signal peptide or other localization signals in the sequence |
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| Transmembrane Regions | Number and location of the transmembrane helices | |
| GenBank ID Protein | GenBank protein ID (if it exists) | |
| UniProt ID/Name | UniProt ID (if it exists) | |
| PDB ID | PDB ID (if it exists) | |
| Cellular Location | Location of the given protein or macromolecule inside or around the cell (cytoplasm, nucleus, membrane, etc.) | |
| Gene Sequence | DNA sequence (from cDNA) of the given molecule | |
| GenBank ID Gene | GenBank database gene identifier and link | |
| Chromosome Location | Location of the molecule on any of the 16 Saccharomyces cerevisiae | |
| Locus | More detailed location of the chromosomal position of the gene | |
| References | Pubmed references |
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