ConSurfDB vs. ConSurf

From Proteopedia

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Evolutionary Conservation is introduced at Introduction to Evolutionary Conservation, and treated in somewhat greater depth in the article Conservation, Evolutionary. These describe how conservation patterns in 3D can help to identify functional sites in proteins. Proteopedia displays conservation patterns pre-calculated by ConSurfDB, when available. These are usually based on broad protein families that include sequences of proteins with multiple functions. Consequently, they usually obscure conservation present in a family of proteins with a single function (see Caveats). The present article describes the mechanisms utilized by the ConSurfDB and ConSurf servers, and how to use the latter to reveal conservation within a family of proteins with a single function.

Contents 1 The Two ConSurf Servers 2 Examining Functions of Proteins in ConSurf-DB's MSA 2.1 Example 3 Limiting ConSurf Analysis to Proteins of a Single Function 3.1 Procedure 3.2 Too Many Sequences 3.3 Too Few Sequences 3.4 Too Many Yellow Residues 3.5 Using Your Results 4 The ConSurf-DB Mechanism 4.1 ConSurf-DB Process 4.2 Filtering 4.3 Average Pairwise Distance 5 The ConSurf Server 6 Examples 7 References

The Two ConSurf Servers

There are two ConSurf servers:

• ConSurfDB:
  • In December, 2021: ConSurfDB had not been updated with new entries in the Protein Data Bank since November 4, 2019. To look for more recent updates, at ConSurfDB Home, click More.
  • Has pre-calculated results for every chain in the PDB.
  • Proteopedia's Evolutionary Conservation resource displays results from ConSurfDB.
  • Results typically obscure some conservation related to a protein's function because the analysis typically included proteins of multiple functions (see ConSurfDB Often Obscures Some Functional Sites).

• ConSurf:
  • You submit proteins of interest and wait for the analysis to be completed.
  • Enables you to pick the sequences used in the analysis from a list with checkboxes.
  • Highly flexible with many configurable parameters and several sequence database options.
  • You can upload your own multiple sequence alignment, or phylogenetic tree, for use in the analysis.

Both servers use state-of-the-art methods that are published in peer-reviewed journals. For comparisons with other methods, see Other Evolutionary Conservation Servers.

Both servers permit you to download results. This is a good idea since the continual growth of sequence databases and improvements in analysis algorithms will give at least slightly different results for the same jobs run several months or more apart. Also, results are periodically deleted from the ConSurf server to conserve disk space.

Examining Functions of Proteins in ConSurf-DB's MSA

In December, 2021: ConSurfDB had not been updated with new entries in the Protein Data Bank since November 4, 2019. To look for more recent updates, at ConSurfDB Home, click More.

As explained above, ConSurf-DB typically includes proteins with more than one function in its conservation analysis. Before deciding whether to do a ConSurf Server job that limits the analysis to proteins of a single function, you may want to see what proteins ConSurf-DB included in its analysis. Here is how to see the names (which hopefully reveal the functions) of the proteins included in ConSurf-DB's analysis of a protein chain. (The following steps are based on ConSurfDB as of December, 2021.)

1. Go to consurfdb.tau.ac.il (the DB, distinct from the ConSurf Server).
2. Enter the PDB code (PDB ID) for the protein of interest.
3. Select the chain of interest. If you're not sure, look at the structure in FirstGlance].
4. Click the button Apply.
5. Scroll down and click Homologues, Alignment, and Phylogeny.
6. Notice the number of sequences in the MSA (the number of "hits" upon which "calculations were conducted").
7. Click on the count of hits to view the list of sequences.

If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest.

Example

2vaa is a major histocompatibility complex class I protein (MHC I). ConSurfDB used 300 sequences in its calculation. Starting about halfway down the list of sequence is the first MHC II protein, which has a different function. Early in the list is the first of 14 sequences for hemochromatosis proteins (unrelated in function). The list includes 62 "Ig-like domain-containing" proteins of unknown function. The inclusion of these and many other sequences for proteins with functions that differ from the query will partially mask conservation of residues critical for the specific functions of MHC I proteins. Therefore, you may prefer to run a ConSurf job in which you limit the MSA to MHC I proteins by manual selection.

Limiting ConSurf Analysis to Proteins of a Single Function

This section was updated in June, 2017 to correspond to changes in the ConSurf Server.

As explained above, the ConSurf-DB Evolutionary Conservation scene available in Proteopedia often includes proteins with multiple functions. However, the best way to find all functional sites by conservation analysis is to limit the analysis to proteins with a single function. A procedure for doing this follows.

Procedure

1. Go to consurf.tau.ac.il, the ConSurf Server (distinct from ConSurf-DB).
2. Fill out the form. For your first run, all options can be left at their default settings. When you get to the section Select homologs for ConSurf analysis, be sure to check manually.
3. Enter your email address and click the Submit button.
4. After a few minutes, a green message will appear SELECT SEQUENCES. The job cannot continue until you select the sequences.
5. Look at the names of the proteins in the list that has checkboxes, under the header "Sequences producing significant alignments:". Find the first case where the function of the protein is not the same as the protein of interest. Usually you will want to exclude sequences for proteins of different functions.
6. Just below the large red line Please choose which sequences you want to use for ConSurf calculation is a form. Put the number of the last sequence having the same function as the protein of interest in the box "Select the first [ .... ] sequences". Then click on the "Update selection" button.
   1. ConSurf will not accept >500 sequences. 200-250 sequences are plenty. Using more sequences simply loads the server unnecessarily and delays returning your result. If the number of the last sequence having the same function as the query protein is higher than 250, use the radio buttons labeled "only every 2nd, 3rd, ..." to reduce the total number of sequences selected while sampling the full diversity of the desired sequences.
   2. The form is confusingly labeled. If you check an "only every" number, then you will need to divide the number in the slot labeled "Select the first" by the "only every" number you selected. For example, if the first 472 sequences have the same function as the query protein, check "only every 2nd" and enter 236 (namely, 472/2) in the "Select the first" slot.
7. Examine the list of sequences to make sure that only the desired sequences are checked. (Of course you may check or uncheck individual sequences if you wish.)
8. When you are satisfied, scroll to the very bottom of the page and click the Submit button.

Too Many Sequences

ConSurf will list up to 2,000 sequences from which to select. In some cases, these sequences are all too similar. Some proteins will retrieve >5,000 sequences with an expectation value (E value) < 1.0e-4 (1.0 times ten to the -4), the default threshold. Then the 2,000th sequence listed may still be very similar to the first sequence listed. This would be true if the 2,000th sequence has a very small E value, such as 1.0e-100. In such a case, you may wish to try searching the Swiss-Prot database, which is much smaller than the default Uniref-90 database. Start a new job, with the only difference being the database searched.

Too Few Sequences

If the default search for sequence homologs fails to find the minimum of 5 sequences, try repeating the procedure above with one change. Under "Choose parameters to homolog search algorithm", change the Proteins Database to UniProt or NR (larger databases than the default Uniref90).

If the larger database does not give enough sequences, you can use other options to widen the search for sequences, knowing that you will be retrieving sequences less related to the query sequence, likely including proteins with functions differing from that of the query:

• Increase the number of iterations in the search to more than the default of one. Each iteration generates a sequence profile that is used as a query for the next iteration.
• Increase the default E cutoff of 0.0001, for example, to 0.001 or 0.01.
• Increase the "Maximal %ID between sequences" from the default of 95% to perhaps 98%.

Too Many Yellow Residues

If an entire domain of your query protein is   yellow (insufficient data)  , it is because the multiple sequence alignment (MSA) has poor coverage of the yellow domain. In this case, it is best to do separate ConSurf runs for each domain in your protein.

1. Determine sequence numbers for the linkers between domains. This can be done easily by inspection in FirstGlance in Jmol.
2. Using a plain text editor, delete everything in your PDB file except the lines that begin with ATOM or HETATM. (Its OK to leave the lines ANISOU if present.)
3. Based on sequence numbers, separate the domains into different PDB files.
4. Upload each domain to ConSurf as a separate job.

If yellow residues are sprinkled around in the domain(s) of your query, and you wish to reduce their number, you will need to increase the number of sequences in the MSA from the default of 150.

Using Your Results

The results of this "one protein function" job will usually enable you to identify more functional sites than did the ConSurf-DB result built into Proteopedia.

See below for instructions on how to make a green-link scene in Proteopedia that shows your single-function ConSurf result.

The ConSurf-DB Mechanism

In January 2018: ConSurfDB had not been updated with new entries in the Protein Data Bank since January, 2013.

Because results from the ConSurf DataBase server, ConSurf-DB^[1] are displayed within Proteopedia as Evolutionary Conservation, an overview of its methods is provided here. ConSurf-DB pre-calculates conservation levels for each amino acid in every protein chain in the Protein Data Bank. It went into service in 2008. It uses state-of-the-art methods, all published in peer-reviewed journals^[1].

ConSurf-DB Process

This describes the defaults. Some alternative options are available when the job is submitted.

1. A list of unique protein chains is extracted from the Protein Data Bank. Chains shorter than 30 amino acids are not processed because they do not contain enough information for reliable phylogenetic tree construction. Certain non-standard residues are converted to the closest standard amino acids, for example, selenomethionine MSE is converted to MET. Chains that still have more than 15% non-standard residues are not processed. Chains that could not be processed are colored gray in Proteopedia -- see the color key at the top of this page.
2. The amino acid sequence of each protein chain is submitted to HMMER for collection of related sequences from the UniRef90 database. By default, one iteration is performed using an expectation value^[2] cutoff of 10^-4.
3. The found sequences are then filtered (see below) using a scheme that attempts a balance between limiting the sequences to close homologues, and including distant sequences that do not share structure or function.
4. The filtered sequence set is multiply aligned with MAFFT (a multiple sequence alignment algorithm that out-performs older algorithms such as MUSCLE and CLUSTALW).
5. A phylogenetic tree is constructed from the multiple sequence alignment (MSA) using the Rate4Site program developed by the ConSurf team.
6. Rate4Site then calculates an evolutionary rate for each position in the MSA using a Bayesian approach shown by the ConSurf team to be superior^[3]. "The amino acid evolution is traced using the JTT^[4] substitution model. High evolutionary rate represents a variable position while low rate represents an evolutionarily conserved position."^[1]
7. "The conservation scores are normalized so that the average over all residues is zero, and the standard deviation is one."^[1] Thus, conservation scores are relative, not absolute and comparing them between different protein families might be misleading (see Caveat above).
8. The normalized conservation scores are then divided into nine levels from 1 (highly variable) to 9 (highly conserved).
9. Colors mapped to the nine conservation levels, from turquoise (1) to burgandy (9) are applied to the 3D protein structure visualized in FirstGlance in Jmol. A coloring script for RasMol is also provided.

1. A confidence interval for the conservation level is calculated for each amino acid position in the MSA. When this indicates low reliability, the position is colored yellow, signifying that the data were insufficient to assign a meaningful conservation level.

11. An Average Pairwise Distance (APD) is calculated to describe the diversity of sequences in the MSA (see below).

The results of each stage of the above process may be viewed for each chain at ConSurf-DB. In the initial run (February 2008), roughly 100 computer CPU's were utilized concurrently via a distributed computing system. Processing of the 30,918 unique protein chains in the PDB took about five days, or an average of roughly 30 minutes per chain.

Filtering

Filtering of the sequences gathered for each protein chain is crucial to making the ConSurfDB results maximally informative. Filtering consists of the following steps.

1. Sequences with more than 95% sequence identity to the query sequence are discarded.
2. Sequences shorter than 60% of the query sequence are discarded.
3. Locally aligned sequence fragments that overlap by over 10% are discarded.
4. Redundant sequences (>95% identical) are removed using CD-HIT^[5].
5. A maximum of 300 sequences meeting the above criteria is used (the 300 with the lowest expectation values^[2], that is, most closely related to the query sequence).
6. If the above process yields fewer than 5 sequence homologs, no calculation is performed due to insufficient data. In February, 2008, this occurred for 1,348 chains out of 30,918 (4%).

Average Pairwise Distance

An Average Pairwise Distance (APD) is calculated to describe the diversity of sequences in the MSA generated during the processing of each chain. A value of 0.01 means that on average, there is one amino acid replacement for every 100 positions. Optimally informative results are obtained when the APD is between roughly 0.5 and 1.5. APD values > 1.5 suggest that it is likely that proteins of diverse functions were included in the MSA, thus masking some degree of conservation in the query protein.

The ConSurf Server

The ConSurf Server, first available in 2001^[6][7][8] with many subsequent enhancements, can calculate and display the conservation pattern for 3D structures completely automatically. It should be used whenever the pre-calculated result at the ConSurf-DB needs improvement (for example, see above), or if you have your own multiple sequence alignment (MSA) that you wish to use. The default settings of ConSurf may need to be adjusted in order to get an optimally informative result. The main adjustment needed is to gather an adequate number of sequences for proteins of the same function as your protein of interest (see above).

Like ConSurf-DB, the ConSurf Server uses the same state-of-the-art methods, all of which are published in peer-reviewed journal articles. Unlike ConSurf-DB's pre-calculated results the ConSurf Server permits considerable customization. For example, the user may specify the number of sequences to use, choose the database from which sequences are obtained, set the Expectation cutoff^[2], set the number of HMMER iterations, or submit their own multiple sequence alignment, or phylogenetic tree. Also you can upload your own PDB file, which enables you to process unpublished data, theoretical models, or "trimmed" chains, e.g. a domain of interest from a multiple-domain chain.

In brief, the ConSurf Server uses the following process by default:

1. Obtains the protein sequence for the specified PDB code (or uploaded PDB file) and chain.
2. Gathers closely related sequences from UNIREF90 (or another database that you specify) with an HMMER search (or other algorithm that you specify). E value cutoff^[2], number of iterations, and number of sequences to use are configurable.
3. Filters the sequences, by default eliminating those redundant at 95% or higher identity with each other, and those with less than 35% sequence identity to the query sequence. These percentages are adjustable.
4. Optionally enables the user to manually select which sequences will be used, from a list with checkboxes. In particular, this enables users to limit the analysis to proteins having the same function as the protein of interest (see above).
5. Does a multiple sequence alignment with MAFFT. (Or you can choose a different algorithm or upload your own MSA.)
6. Constructs a phylogenetic tree using neighbor joining with ML distance. (Or you can choose a different algorithm or upload your own tree.)
7. Calculates a conservation score with confidence interval for each amino acid. Classifies the conservation scores into nine levels, and maps them to standard conservation level colors (see color key at the top of this page). Marks residues for which the conservation score confidence interval is too large, hence the conservation score is unreliable ("insufficient data").
8. Displays the protein, colored by conservation, in interactive 3D, using the NGL Viewer, FirstGlance in Jmol, Chimera, or PyMOL.

Examples

This example needs to be updated. It is on my list to do. Eric Martz 09:13, 25 April 2010 (IDT) (The remainder of this page was updated December, 2021.)

Evolutionary conservation reported by ConSurf-DB for Major Histocompatibility Class I alpha chain in 2vaa. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

At right is the pattern of evolutionary conservation and variability reported by ConSurf-DB for the alpha chain of Major Histocompatibility Complex Class I (chain A of 2vaa).

Because the scene at the right contains no amino acids marked insufficient data, and no chains with no data, the yellow and gray colors need not be included in the color key. For all the available variations of the ConSurf color key, see Help:Color_Keys#ConSurf.

2vaa contains three chains. Here, ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B) and the peptide (chain P) are shown as gray backbone traces. See also How to Insert a ConSurf Result Into a Proteopedia Green Link.

Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on

• Lac repressor
• Avian Influenza Neuraminidase, Tamiflu and Relenza
• Mechanosensitive channels: opening and closing

References