Dear All,
I am trying to find amino acid sequence of beta xylosidase of K. marxianus, but it is not present in NCBI protein database. However, sequence of A. niger's xylosidase is available.
So please suggest me how to make structure, if sequence is not available or provide link, if it is available.
Your suggestions will be appreciated.
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Nilesh
Is the nucleotide sequence known? In this case you may traslate the gene into protein.
Happy working
Luca
Another approach will be first to train andy Gene prediction tool with K. marxianus, then you will get the structure of genes and their translated products, afterwards you can proceed with structure predictions
Dear Dr. Dellafiora,
Thanks you very much for suggestion.
I tried to find out neucleotide sequence but it is not available.
So can you suggest another approach.
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Nilesh
Dear Ashmit.
Thanks for suggestion.
Please send the protocol for gene prediction, if possible.
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Nilesh
You are in for a long haul. Sequence the amino acids (may be 4 or 10) from the C end if it is not possible to do from the N end. Put it in CLUSTL W format and try doing BLAST to find some homology. Then you may go to some common sites like say SwissPROT and you will find different tools (free of charge) by which you can configure a pretty stable (energy wise) secondary or even tertiary structure.
The structure is in the PDB as 3ac0 and 3abz.
http://www.rcsb.org/pdb/explore/explore.do?structureId=3ac0
In Uniprot as D1GCC6_KLUMA. If you need the nucleotide sequence, check NCBI AKFM02000034.1 (gi 806608691)
Dear Dr. Sauder,
Thank you very much for information, But it is glucosidase and I am searching for xylosidase. Can you provide me information for xylosidase, if it is possible.
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Nilesh
If XP_001389416 "exo-1,4-beta-xylosidase xlnD" from A. niger is the sequence you were referring to, then a 6-frame tblastn search against the K. marxianus shotgun genome sequence yields only one hit, the K. marxianus glucosidase sequence I mentioned. Is there a different xylosidase sequence from A. niger that might give a different result?
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