Functional Analysis Of 1zkd
Summary Function for Report
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--
LOCATE Data
mouse ortholog Results: soluble non-secreted protein, subcell. location prob. cytoplasm and mitochondrion
Nuclear Protein Localisation Prediction
mouse ortholog Result: NLS 0.07 nonNLS 0.93
human ortholog Result: NLS 0.20 nonNLS 0.80
Expression Profiles from ESTs
Protein is expressed in diverse tissues (brain,liver,lung,pancreas ...)
