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Guided Tour

1. Classify Your Protein

In the following example, we start with the following unidentified protein sequence:

MGRSIRLFATFFLIAMLFLSTEMGPM
TSAEARTCESQSHRFHGTCVRESNCA
SVCQTEGFIGGNCRAFRRRCFCTRNC

We then entered it in Classify Your Protein's "Paste your protein sequence" field:
"Paste Your Protein" field

 

2: Cluster Card Page

We then submitted the sequence, which brought us to the Cluster Card Page for the Cluster that best matches the sequence.
In this case, the Cluster is cluster number 273515.
This cluster contains 74 proteins  +1  your "Hypothetical protein".

Cluster Card

 

3: View Proteins of Cluster

The cluster's proteins can be viewed by clicking on View Proteins of Cluster on the upper-left hand corner of the Cluster Card page.

Cluster Card: View Proteins

Clicking on the "sort by Escores with your protein" button next to the unidentified sequence [in this case "Hypothetical Protein"] will sort the other proteins in the cluster according to their BLAST E-score with the sequence.

 

4: Keywords Appearances

To obtain the biological characteristics of these proteins, we go to the Get Keywords Appearances section.
In this case, we choose to view InterPro Family keywords:

Keywords Appearances

In this case, there are first two relevant InterPro Family keywords.

For example: Gamma Purothionin - we see that 50 of this cluster's proteins have this keyword, and only 1 other protein in the database have this keyword.
This seems to indicate that the unidentified sequence may be a Gamma Purothionin- type protein.

 

5: Cluster Similarity Distribution (Not Supported in Current Version 6.1)

In order to explore this sequence's biological properties more deeply, we decide to view the Cluster Similarity Distribution by clicking on the icon Cluster Similarity Distribution icon at the top of the Cluster Card page. This opens a new window:

Cluster Similarity Distribution

Clicking "proceed" next to the Display similarity distributions section brings us to the similarity matrix for the proteins in this cluster (including the unidentified protein sequence we added):

Cluster Similarity Distribution

 

6: BLAST

The color in each square of the matrix indicates the BLAST E-score for the pair of proteins appearing in the correspoding row and column of the square. Clicking on a specific square will open a window displaying the BLAST results and alignment for the corresponding pair of proteins.

BLAST result

In this example, by clicking on the uppermost of the low-E-score squares, shows that the similarity between THG_PETIN [ProtoNet ID is P-70672].

 

7: Browse Cluster in tree

Clicking on the Browse Cluster in tree button at the top of the main Cluster Card page.
In order to confirm some of our above-mentioned conjectures, we decide to "climb" the Protonet tree, by using the ProtoBrowser option by clicking on the button found in the Browse Cluster in Tree section.

This opens a new window of the ProtoBrowser:

ProtoBrowser

To climb the tree, we click on the "up arrow" at the top of the tree. This moves us up in the Protonet tree display.

ProtoBrowser

 

8: Cluster Card page for the newly-chosen cluster

Clicking on a cluster will load the Cluster Card page for the newly-chosen cluster.

Cluster Card page for the newly-chosen cluster

In this case, we choose Cluster 286462. On the Cluster Card page for Cluster 286462, we see that there are 153 proteins in the cluster.

 

9: Keywords Appearances for the newly-chosen cluster

To obtain the biological characteristics of this larger cluster of proteins, we go to the Get Keywords Appearances section. In this case, we choose to view Interpro keywords (keywords regarding functional domains and families):

Get Keywords Appearances: Interpro keywords of Cluster 224897

In this case, there are 3 relevant Interpro keywords: However none of them are assigned to a majority of the cluster's proteins.
Therefore, it is difficult to reach any conclusions regarding this set of proteins.

 

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