Lab Journal - Task 4 (PAH)

Explore structural alignments

To explore different tools for building structural alignments the webservers themselves are used. For all tools the default parameters are kept.
As there are often more than one chain for the proteins we decided to take chain A for both our query 2pah and all different targets.

SAP or CE
First, we wanted to do the structural alignment with the SAP webserver, but we did get an Error with this program. So we only used CE. Nevertheless, we tried SAP later again and this time it worked, but still we did not include it here.

Evaluate sequence alignments

The perl script hhmakemodel can be found in /usr/share/hhsuite/scripts. It needs an input file in form of a result file from hhsearch with hit list and alignments (-i).

So, first an hhr file was created with the FASTA file of our protein PAH and the pdb database. The output file was called hhsearch_PAH.hhr. Furthermore, we set the maximal reported lines in summary and alignments to 10000:
hhsearch -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -Z 10000 -B 10000

26 entries were found. Two of them were also used in explore structural alignments: 1j8u, 3luy. For hhmakemodel.pl we one time choose eight entries thereby trying to get the whole range of e-values and scores on default it would only take the first (-m):

No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
 1 1phz_A Protein (phenylalanine  100.0  7E-165  3E-169 1181.8   0.0  429    1-429     1-429 (429)
 2 1j8u_A Phenylalanine-4-hydroxy 100.0  3E-135  1E-139  951.9   0.0  325  103-427     1-325 (325)
 6 2v27_A Phenylalanine hydroxyla 100.0 3.6E-74 1.4E-78  528.8   0.0  231  172-406    13-248 (275)
 7 2qmx_A Prephenate dehydratase;  98.2 1.1E-09   4E-14   98.4   0.0   67   33-99    199-266 (283)
 9 3luy_A Probable chorismate mut  98.1 3.3E-09 1.2E-13   97.7   0.0   67   33-99    206-274 (329)
12 1qey_A MNT-C, protein (regulat  54.0     3.4 0.00013   28.3   0.0   12  189-200    18-29  (31)
19 1wyp_A Calponin 1; CH domain,   29.4      15 0.00057   29.7   0.0   68  201-269    47-115 (136)
26 1a6s_A GAG polyprotein; core p  20.6      29  0.0011   28.0   0.0   42  141-196    42-83  (87)

The second time we choose all 26 pdbs. Additionally a database had to be chosen, which includes those pdb entries (-d) and finally the models are written in PDB-format to model_PAH.pdb (-ts):
perl /usr/share/hhsuite/scripts/hhmakemodel.pl -i /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 1 2 6 7 9 12 19 26 -ts /mnt/home/student/waldraffs/Masterpraktikum/Task4/model_PAH.pdb