Ssu72 Method: Difference between revisions
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==Evolution== | ==Evolution== | ||
===Multiple sequence alignment=== | ===Multiple sequence alignment=== | ||
NCBI’s psiBLASTp search was run on all of the databases (‘nonredundant’) to yield around 200 significant matches. The search was repeated on the SwissProt database to give 24 matching high quality sequences. The Protein Data Bank yielded no significant matches. | NCBI’s psiBLASTp [http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&AUTO_FORMAT=Semiauto&CDD_SEARCH=on&CLIENT=web&COMPOSITION_BASED_STATISTICS=0&DATABASE=pdb&DESCRIPTIONS=500&ENTREZ_QUERY=All+organisms&EXPECT=10&FORMAT_BLOCK_ON_RESPAGE=None&FORMAT_ENTREZ_QUERY=All+organisms&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&GAPCOSTS=11+1&GET_SEQUENCE=on&I_THRESH=0.005&LAYOUT=TwoWindows&MASK_CHAR=0&MASK_COLOR=0&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&QUERY=XTDPSKLAVAVVCSSNXNRSXEAHNFLAKKGFNVRSYGTGERVKLPGXAFDKPNVYEFGTKYEDIYRDLESKDKEFYTQNGLLHXLDRNRRIKKCPERFQDTKEQFDIIVTVEERVYDLVVXHXESXESVDNRPVHVLNVDVVDNAEDALXGAFVITDXINXXAKSTDLDNDIDELIQEFEERRKRVILHSVLFY&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS=Yes&SET_DEFAULTS.x=51&SET_DEFAULTS.y=10&SHOW_LINKOUT=on&SHOW_OVERVIEW=on&WORD_SIZE=3&END_OF_HTTPGET=Yes(1)] search was run on all of the databases (‘nonredundant’) to yield around 200 significant matches. The search was repeated on the SwissProt database to give 24 matching high quality sequences. The Protein Data Bank yielded no significant matches. | ||
The sequences from the ‘nonredundant’ search were aligned using ClustalX. The sequences were well conserved, so a high gap creation penalty (20) was used. Around 30 low matching sequences with large insertions and a few very short sequences were removed, and long sequences were cut to size. (Length was judged relative to the Drosophila sequence of interest.) Closely matched variants from the same organism were removed to reduce redundancy. | The sequences from the ‘nonredundant’ search were aligned using ClustalX. The sequences were well conserved, so a high gap creation penalty (20) was used. Around 30 low matching sequences with large insertions and a few very short sequences were removed, and long sequences were cut to size. (Length was judged relative to the Drosophila sequence of interest.) Closely matched variants from the same organism were removed to reduce redundancy. | ||
Revision as of 14:40, 15 June 2009
Function
The results for the functional component of the analysis were collected from a number of sources. Firstly, a BLAST search was performed using the NCBI database and the 'blastp (protein-protein BLAST)' algorithm (1). Secondly, a literature review was conducted, using the PubMed database (2), on the hits returned from that search. Thirdly, the Drosophila Ssu72 protein, PDB accession number 3FDF_A, was submitted to the ProFunc webserver (3). The automated results returned were then analysed and further searches of PubMed were conducted as necessary - these were dictated by the structural and evolutionary results obtained in their respective sections of this paper.
Structure
Heading
Evolution
Multiple sequence alignment
NCBI’s psiBLASTp [1] search was run on all of the databases (‘nonredundant’) to yield around 200 significant matches. The search was repeated on the SwissProt database to give 24 matching high quality sequences. The Protein Data Bank yielded no significant matches.
The sequences from the ‘nonredundant’ search were aligned using ClustalX. The sequences were well conserved, so a high gap creation penalty (20) was used. Around 30 low matching sequences with large insertions and a few very short sequences were removed, and long sequences were cut to size. (Length was judged relative to the Drosophila sequence of interest.) Closely matched variants from the same organism were removed to reduce redundancy.
The sequences from the SwissProt database were also aligned using ClustalX, with a gap penalty of 20. 8 long sequences were cut to size, and redundant human sequences were removed. The Cryptococcus Neoformans sequence (Q5KIT2.1), derived from gene prediction, was too short to show the residues of the active site. It was replaced with a closely matching longer sequence from RefSeq for the alignment. It was not necessary to replace the sequence for the tree, because the missing residues are so highly conserved.
Tree
The SwissProt sequences were used for the tree. Phylip-3.63 programs were used to generate the tree and bootstrap values. The tree’s structure was compared with the taxonomy provided with NCBI’s psiBLASTp results.
Abstract |
Introduction |
Results |
Discussion |
Method |
References
