Functional Analysis Of 1zkd: Difference between revisions
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ncbi entry [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=27229156 mouse ortholog LOC73694][http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=21396487 human ortholog LOC55471][http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=67464609 1zkd Rhodopseudomonas palustris] | ncbi entry [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=27229156 mouse ortholog LOC73694][http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=21396487 human ortholog LOC55471][http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=67464609 1zkd Rhodopseudomonas palustris] | ||
[[blastp mouse ortholog results e-value cut off e-48]] [[blastp human ortholog results e-value cut off e-47]] [[blastp 1zkd R.pelustris results e-value cut off e-48]] | [[blastp mouse ortholog results e-value cut off e-48]] | ||
[[blastp human ortholog results e-value cut off e-47]] | |||
[[blastp 1zkd R.pelustris results e-value cut off e-48]] | |||
Revision as of 06:08, 22 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 !
ncbi entry mouse ortholog LOC73694human ortholog LOC554711zkd Rhodopseudomonas palustris
blastp mouse ortholog results e-value cut off e-48
blastp human ortholog results e-value cut off e-47 blastp 1zkd R.pelustris results e-value cut off e-48
