Functional Analysis Of 1zkd: Difference between revisions
No edit summary |
No edit summary |
||
| Line 31: | Line 31: | ||
added sequence of 1zkd to fasta file --> saved file as "search150507_1.fasta" | added sequence of 1zkd to fasta file --> saved file as "search150507_1.fasta" | ||
MSA still very messy --> NEXT: BLAST search for 1zkd and mouse and human orthologs. Build MSA from the resulting sequences from BLAST search ! | MSA still very messy --> NEXT: BLAST search for 1zkd and mouse and human orthologs. Build MSA from the resulting sequences from BLAST search ! | ||
Revision as of 06:52, 15 May 2007
Best scores for Methyltransferase: in SSM (Secondary Structure Matching), LIG(Ligand Template Matches) and REV (Reverse Template Matches)
Superfamily search against HMM library found motif similar to S-adenosyl-L-methionine-dependent methyltransferases (1g8a) which is a RNA binding protein:
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1g8a
http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=53335
No DNA-binding motifs (Helix-turn-helix) were found in the ProFunc search.
Search against NCBI Protein Database for "S-adenosyl-L-methionine-dependent Methyltransferase" limited to RefSeq Sequences
101 hits --> saved all as FASTA file "search150507.fasta"
deleted sequences of excessive length from fasta file:
gi15234111 gi88860170 gi77360608 gi119501377 gi126138018
added sequence of 1zkd to fasta file --> saved file as "search150507_1.fasta"
MSA still very messy --> NEXT: BLAST search for 1zkd and mouse and human orthologs. Build MSA from the resulting sequences from BLAST search !
