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| Browse by Superfamily | Browse by Reaction | Search by Enzyme | Search by Reaction |
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| SFLD General Instructions | ||
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Browsing Searching
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Browsing the SFLD superfamilies You can browse through the hierarchy of the SFLD superfamilies by clicking on the Browse by Superfamily link located on the main page. A table listing the superfamilies currently in the SFLD database is displayed:
Clicking on a superfamily of interest will display the summary page of that particular superfamily. The superfamily summary page includes a short description about the superfamily and a list of the subgroups (if any) and families that comprise the superfamily. You can browse further down the hierarchy by clicking on one of the subgroups or on one of the families. For example, if you wish to look at the enolase superfamily, you will get the enolase superfamily summary page. If you wish to look at the methylaspartate ammonia-lyase family, one of the families comprising the enolase superfamily, the link will take you to the methylaspartate ammonia-lyase family summary page. The family page has an active site image if structures are available, a reaction picture, and a list of enzymes that comprise the family. Clicking on the active site image will open a Chimera session. On both the superfamily and family summary pages, you can align a sequence to the superfamily or family, view the master alignment for the superfamily or family, and view the superfamily or family as a dendogram. Also, you can get a FASTA format file of all the sequences in a family. All these functions are located in a gray box towards the bottom of the page:
As you browse, the level of hierarchy is indicated at the top of the webpage. For example, if you choose to look at the methylaspartate ammonia-lyase enzyme that is listed on the methylaspartate ammonia-lyase family summary page, the top of the webpage will have the following display:
This display tells you that you are looking at the methylaspartate ammonia-lyase enzyme functional domain, which is part of the methylaspartate ammonia-lyase family, which is part of the enolase superfamily. This particular enzyme does not fall under a subgroup. You can view a list of all reactions catalyzed by the enzymes in the SFLD database by clicking on the Browse by Reaction link located on the main page. A table is displayed that lists the reaction names, the associated E.C. numbers, superfamilies, and families.
Clicking on any reaction name will display a reaction picture and associated partial reaction pictures. At the bottom the page, a list of enzyme functional domains performing the specific reaction is displayed.
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You can search the SFLD using protein information or chemical structure information. In the future, you will be able to search the SFLD using structural information. Search by Enzyme You can search for a protein by its sequence, its name, or its NCBI GI number. Click on the Search by Enzyme link on the main page to start your search. To search by protein name, enter the name in the box labled Name and click on the Search button located underneath the box. To search a protein by its GI number, enter the GI number in the box labeled GI Number and click on the corresponding Search button. To search for a protein using its sequence, input the sequence in the box labeled �Protein Sequence�.
Once the protein sequence is entered, click on the Search button. A list of sequence search results is displayed with its HMMER e-value. Here are the results for the sequence entered above:
Click on the name to view the superfamily, subgroup, or family summary page. Click on the "View alignment" link to view the alignment to the Hidden Markov Model (HMM). This is the page that is shown when the first "View Alignment" link next to the enolase (subgroup) hit is clicked:
The query sequence is located at the top of the alignment. You can
view the the raw MSF file by clicking on the
"Raw MSF file" link or view the alignment in
Chimera by clicking on the
Chimera icon Click on the arrow next to the "View" button to select a color scheme to view the alignment. Use the bars located on the right and bottom of the alignment to scroll up and down or left and right to view the entire alignment. A chart of the functional residues of the subgroup is located under the alignment. These functional residues are highlighted in white in the alignment (not shown in the above picture). The evidence codes are also listed in this chart. The You can search for a protein using chemical structure information. Click on the Search by Reaction link on the main page to begin your search. You can enter the Enzyme Commission (E.C.) Number in the box labeled "Enzyme Commission Number".
You can also enter a SMILES/SMARTS string. Check the box next to "Search only overall reactions" to exclude partial reactions from your search. For example, to search for reactions that involve acetic acid, enter the appropriate SMILES string and click on the search button.
You can also draw out acetic acid using the JME Molecular Editor Java applet. This Java applet does not work on all browsers. Click on the Search button to start the search.
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