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System search summary
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Important things to look for when choosing the right system System for your project:
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Introduction
If you have a target protein sequence, the best way to pick the right 3DM system System is using the Find by sequence option. In this article we’ll explain to you what are the important things that you should take into account when picking a 3DM system System to use in your project.
First, from the 3DM dashboard, click on the Find by sequence item - this either in the menu on the left or via the link on the dashboard (Figure 1). Doing so will take you to the system System search page.
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Here, you can simply copy your sequence and click the SEARCH button. You query sequence can be either in the form of a plain amino acid sequence (one-letter codes), or a FASTA sequence. We have to go through a
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A lot of data needs to be inspected to find the right |
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Systems. Therefore, |
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the search might take up to 2 minutes |
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Sequence can be either a plain amino acid sequence (one-letter code) or a FASTA sequence. |
Query sequence coverage
First of all, the The colourful bars at the top of the systems list Systems list that is displayed in the output represent Pfam domains that are found in this sequence and the bars below show you which part of the sequence is covered by the given system. When choosing the right 3DM system we have a 3DM System you need to make sure that the part of sequence we’re that you are interested in is actually covered by this system - this System. This is indicated by the grey bars darker sections in the Query sequence column (if . If part of the bar is light grey, that means it’s this section is not covered by this system):
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System size
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Best protein hit
Yet another things that can help us identify the best system are the System (Figure 2).
For example, in case you are specifically interested in the Malt_amylase_C domain (displayed in green), you can already exclude the second System in the list since it does not cover this domain.
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System size
The next thing to pay attention to is how much data the Systems contain. This can be estimated from the Sequences and Mutations values. In general, the larger the number of sequences, the better a System matches your needs.
Best protein hit
Best protein hit and BLAST e-value- this gives (which is displayed when you expand by clicking the 
on the right side) give you information about how close to your query sequence is the closest protein in this system. In case of this protein all of the systems contain the query sequence - hence the 0 System is to your query sequence. When a System contains your query sequence, the BLAST e-value will be 0 and an
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Detailed
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System view
If When you click on the downward pointing arrows on the right side of a table row, you can unfold the system System view , to see some more information about this particular systemSystem (Figure 3).
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On the left hand side is you can find some overall information about the system itself - System itself, e.g. the number of sequences, mutations, subfamilies, and sequences clusters. Additionally, and a word cloud of protein descriptions in this system (the System is created. The larger the word is displayed, the more abundant it is in protein descriptions). The word cloud can be especially be helpful with the pdb PDB clusters systems Systems that don’t do not have informative names - . In such cases, you can see from look at the word cloud to see what family/domain is covered by the systemSystem.
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In the middle part you can find information about your query sequence. If your sequence is not present in this system a System, you can use the ADD AS PRIVATE PROTEIN button to add your sequence to this systemSystem. In this case Figure 3, the button is disabled because the query sequence is already present in the systemSystem.
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In the right-most part of this view you’ll the row you find information about the best protein hit - , e.g. in which subfamily it is it aligned , and how close is it to the subfamily template (Core core identity) - as . As a rule of thumb you can assume that the closer it is the hit, the higher the alignment quality. If you want to go directly to analysing this protein in the system you can click on either the OPEN PROTEIN DETAIL or the OPEN PROTEIN ANALYSIS button to go the protein detail or protein analysis page, respectively.
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