1‐Tutorial
Alternate URL: https://cqb.pku.edu.cn/zyli/info/1017/1176.htm
Each siderophore has an individual page including detailed information.
The URL of page is related to SIDERITE ID.
For example, the URL to Piscibactin (SID00095) is http://siderite.bdainformatics.org/database?conditions=%5B%5D&query=&sid=SID00095.
The SIDERITE ID can be found in download.
See below for an explanation of the detailed information content.
The indexing interface of the SIDERITE database guides users quickly to find the desired siderophore, which is visualized siderophore molecules by TMAP.
The source code of indexing interface construction: https://github.com/RuolinHe/SIDERITE/tree/main/TAMP/SIDERITE
Hover over and click the nodes to explore the chemical space of siderophores.
You can change the color label of siderophores with a specific property by the legend region on the bottom right.
Use "ctrl" + scroll wheel on the mouse to adjust the size of tree.
Enjoy it!
| Properties | Description | Possible value or value type |
|---|---|---|
| Biosynthetic Type | Biosynthetic type of siderophores | Hybrid NRPS/NIS, Hybrid NRPS/PKS, NIS, NRPS, PKS |
| Kingdom of Source | Kingdom of siderophore producers | Animal, Bacteria, Bacteria/Fungi, Fungi, Plant |
| Siderophore Large Class | Large class of siderophore classification | Integer |
| Precursor | Precursors of siderophores | String |
| Phylum | Phylum of siderophore producer | String |
| Siderophore Small Class | Small class of siderophore classification | Float |
| Theoretical denticity | Theoretical denticity of siderophores | Integer |
| Count | Counts of siderophores in all siderophore records | Integer |
| Number of Monomers | Number of monomers comprised of siderophores | Integer |
| Coverage of Monomers | Coverage of monomers generated by rBAN | Float |
| Molecular Weight | Molecular weight of siderophores | Float |
| Number of Hydroxamate | Number of hydroxamate ligand in siderophores | Integer |
| Number of Catecholate | Number of catecholate ligand in siderophores | Integer |
| Number of Phenolate | Number of phenolate ligand in siderophores (except catecholate) | Integer |
| Number of Carboxylate | Number of carboxylate ligand in siderophores (except alpha-hydroxycarboxylate and carboxylate in citrate) | Integer |
| Number of Carboxylate in Citrate | Number of carboxylate in citrate ligand in siderophores | Integer |
| Number of Alpha-Hydroxycarboxylate | Number of alpha-hydroxycarboxylate ligand in siderophores | Integer |
| Number of Hydroxyphenyloxazoline | Number of hydroxyphenyloxazoline ligand in siderophores | Integer |
| Number of Hydroxyphenylthiazoline | Number of hydroxyphenylthiazoline ligand in siderophores | Integer |
| Number of Alpha-Aminocarboxylate | Number of alpha-aminocarboxylate ligand in siderophores | Integer |
| Number of Alpha-Hydroxyimidazole | Number of alpha-hydroxyimidazole ligand in siderophores | Integer |
| Number of Alpha-Hydroxycarboxylate in Citrate | Number of alpha-hydroxycarboxylate in citrate ligand in siderophores | Integer |
| Number of Diazeniumdiolate | Number of diazeniumdiolate ligand in siderophores | Integer |
| Number of 2-Nitrosophenol | Number of 2-Nitrosophenol ligand in siderophores | Integer |
| Predicted logS | Predicted logS by SolTranNet, where S is the aqueous solubility in mol/L (or M). | Float |
| Predicted diffusion coefficient | Predicted diffusion coefficient by SEGWE calculator | Float |
The indexing interface example：
SIDERITE supports Fast Search, Advanced Search and Similarity Search.
SIDERITE offers fast fuzzy search functionality based on partial siderophore names. It could be any of the possible names for the siderophores with many names.
Example: Madurastatin C1 or MBJ-0034 both target to SID00582
And you also needn't type complete siderophore name.
The advanced search feature includes various conditions, including siderophore ID, siderophore name, functional group, biosynthetic type, monomer name, number of monomers, monomer coverage, theoretical denticity, molecular weight, species, source (kingdom), source (phylum), and class.
"Siderophore ID" is a unique ID starting with "SID" such as SID00001.
"Class" is the clustering class of siderophore. Read the original paper for the precise definition of class. In general, similar siderophores will be in the same class. Each siderophore is assigned a unique class id x.y.z, where z stands for the z-th record within the group. For example, enterobactin has the id 1.22.2. In this ID, “1” means the 1st large cluster. “22” means the 22nd group within the 1st large cluster. “2” means the 2nd record in the 1.22 cluster.
"Siderophore name" has been described in Fast Search.
Other conditions have been described in Supported Properties of Indexing Interface.
Multiple conditions could be combined by the "+Add Condition" button.
| Logical Operations | Description |
|---|---|
| = | Equal |
| <> | Unequal |
| > | Greater than |
| >= | Not less than (greater than or equal) |
| < | Less than |
| <= | Not greater than (less than or equal) |
| LIKE (%) | Fuzzy matching |
| NOT LIKE | Non-fuzzy (exact) matching |
| IN | Included |
| NOT IN | Not included |
| FIND IN SET | Search in the input list |
Notice: You must click "Search" button to start searching. "Enter" doesn't work.
Similarity search is another important way to access the siderophore resource in the SIDERITE, which helps users to find similar siderophores in the SIDERITE with the desired molecule. And it also can be used to determine whether it has potential iron-binding activity.
Users can type the SMILES of molecule or draw in the SMILES editor. If this molecule has potential iron-binding activity predicted by our method based on functional group search and doesn't exist in the SIDERITE database, it will be reported as new in the result. Users can choose to upload this molecule to the SIDERITE database. Furthermore, the result will return similar siderophores with the query molecule in the SIDERITE.
The similarity search supports Tanimoto, Dice and Tversky similarity and the user can set a cut-off threshold to filter the result with low similarity.
Notice:SIDERITE database won't record the molecule entered by user unless the user choose to upload it into database. After manual review, new molecule will be included in the SIDERITE and contributors will be recorded.