Sequence/structure analysis

[sillitoe]

For 3.20.20.190 (and hopefully 2.30.29.30) provide:

• sequence alignments (based on structure)
• structure superpositions (including HETATMs)

[tonyelewis]

Attaching 3.20.20.190.zip (GitHub's preferred format) containing files arising from aligning+superposing the s-reps of 3.20.20.190 [v4.1.0]:

• 3.20.20.190.faa - a FASTA alignment
• 3.20.20.190.html - an HTML rendering of the alignment:
  • rainbow colouring (blue → red) shows the position on the alignment (N → C)
  • colour saturation shows structural similarity
• 3.20.20.190.pml - a PyMOL superposition:
  • F1 – F3 keys change the colouring scheme
  • black sticks are atoms in non-polymer organic compounds, accessible under the organic selection
  • core/noncore selections identify structurally well-conserved/poorly-conserved residues respectively (so, for example, clicking noncore → H (Hide) → everything leaves only the core showing)
  • alignment shows lines between aligned residues and can be activated by selecting alignment and then clicking S (Show) → dashes (note: the distorted cartoon representation can miss the alignment lines whereas the ribbon representation touches them precisely)
• 3.20.20.190.superposed_pdbs.tar.gz - a .tar.gz of a directory of the superposed PDB files

These files should contain all residues and all pertinent ATOM / HETATM records (including, eg MSE HETATM records). Please shout if you spot any absences.

Here's an image of the superposition:

[tonyelewis]

At present, cath-tools's high-quality alignment procedure is a bit slow to handle the 116 s-reps in 2.30.29.30 but I'm happy to generate derived files if someone gives me an alignment.

[nathaliereuter]

Dear Tony and Ian,

would it be possible to obtain the same types of alignments (structure and sequence) for the superfamily of PH domains, i.e. Superfamily 2.30.29.30? It is a fairly big family with many structure representatives....

Best,
Nathalie

[tonyelewis]

We haven't been able to look into vastly speeding up the heavy-refining process we previously used (above) but we have added a light-refining process. This can leave the alignment more gappy than it should be (ie it doesn't always align residues that should be aligned) but it should do a pretty good job of aligning core residues.

I've performed this light-refining structural alignment for 2.30.29.30 with v4.2.0 data. You can get the results from this file : 2.30.29.30.4_2_0.light_refining.tar.gz.

For a short time, I'll also leave the individual files on my account on the UCL server:

• 2.30.29.30.4_2_0.light_refining.fa - FASTA alignment
• 2.30.29.30.4_2_0.light_refining.html - HTML rendering of alignment
• 2.30.29.30.4_2_0.light_refining.pml - PyMOL script containing superposition (very slow to load)
• 2.30.29.30.4_2_0.light_refining.pymol_draw.jpg PyMOL image of the superposition

[nathaliereuter]

Thank you very much Tony, this is extremely helpful. The extra gaps in the sequence alignment should not be much of a problem for us, we'll have a look at it.

[hkabbech]

Dear Tony,

Thank you for the files. I'm working with Nathalie on a project based on these structural alignments.
Please, may you add the directory of the superposed PDB files for the 2.30.29.30 superfamily ?

Kind regards,
Helene

[tonyelewis]

Yes - here are the PDBs: 2.30.29.30.4_2_0.light_refining.pdbs.tar.gz

...and here's a PyMOL ray-traced image of the superposition:

[nathaliereuter]

Thank you!