Methods 2ece: Difference between revisions
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[[Image:pdb_cartoon_2ece.png|frame|border|left|'''Figure 6''' PDBsum shows the beta and a- helices of SELENBP1 ]] | [[Image:pdb_cartoon_2ece.png|frame|border|left|'''Figure 6''' PDBsum shows the beta and a- helices of SELENBP1 ]] | ||
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Explore SBP features and structural summary here [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61601].The domains of SBP are shown here [http://www.ncbi.nlm.nih.gov/sites/entrez?db=domains&cmd=search&term=2ece] | Explore SBP features and structural summary here [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61601].The domains of SBP are shown here [http://www.ncbi.nlm.nih.gov/sites/entrez?db=domains&cmd=search&term=2ece] | ||
Notice how the domains are similar to the putative Isomerase domains of E.coli below. | Notice how the domains are similar to the putative Isomerase domains of E.coli below. |
Revision as of 08:19, 9 June 2008
STRUCTURAL ANALYSIS
SBP 1 Amino Acid FASTA FORMAT Sequence
>2ECE:A|PDBID|CHAIN|SEQUENCE
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKIVHKVELPYINDELHHFGWNA CSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREPKIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEG EGPGGILMLDHYSFEPLGKWEIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEIPAEPLEGNLPEILKPFKAVP PLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTGKVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNS LYSTWDNQFYPEGLKGWMVKLNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP
WARNING! Given sequence appeared to be a soluble protein, no TM domains found!
Output format is the following:
1st line -> residue numeration
2nd line -> query amino acid sequence
3rd line -> trans-membrane domain prediction (T-TM region, N-soluble part)
MAIVPFKRDPTFYPSPKMAMKAPPEDLAYVACLYTGTGINRADFIAVVDVNPKSETYSKI NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN VHKVELPYINDELHHFGWNACSSALCPNGKPNIERRFLIVPGLRSSRIYIIDTKPNPREP NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN KIIKVIEPEEVKKVSGYSRLHTVHCGPDAIYISALGNEEGEGPGGILMLDHYSFEPLGKW NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN EIDRGDQYLAYDFWWNLPNEVLVSSEWAVPNTIEDGLKLEHLKDRYGNRIHFWDLRKRKR NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN IHSLTLGEENRMALELRPLHDPTKLMGFINMVVSLKDLSSSIWLWFYEDGKWNAEKVIEI NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN PAEPLEGNLPEILKPFKAVPPLVTDIDISLDDKFLYLSLWGIGEVRQYDISNPFKPVLTG NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN KVKLGGIFHRADHPAGHKLTGAPQMLEISRDGRRVYVTNSLYSTWDNQFYPEGLKGWMVK NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN LNANPSGGLEIDKEFFVDFGEARSHQVRLSGGDASSDSYCYP NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Figure 3 SABLE server results.
STRUCTURAL COMPARISONS
Explore SBP features and structural summary here [2].The domains of SBP are shown here [3]
Notice how the domains are similar to the putative Isomerase domains of E.coli below.
1RI6 DOMAINS
2ECE DOMAINS
(Complex Of Bovine Odorant Binding Protein (Obp) With A Selenium Containing Odorant)"Image:Ligand of bovine.png" [[4]]
SEQUENCE ANALYSIS
Selenium binding protein 1 (SELENBP1) SELECTED PROTEIN SIMILARITIES Comparison of sequences in UniGene with selected protein reference sequences. The alignments can suggest function of a gene. [5]