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Difference between revisions of "User talk:Warren Wakarchuk"
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| + | == Comment on tertiary structural relatedness of GH101 and GH13 == | ||
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Dear Warren, | Dear Warren, | ||
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* You have written, that '[[Glycoside Hydrolase Family 101|the recently solved 3D structure of SpGH101 reveals that this protein surprisingly shares some structural features with GH13 alpha-amylases]]', but it is not so surprising. According to PSI-BLAST searches, GH101 is related to [[GH13]], [[GH31]] and many other (β/α)<sub>8</sub>-barrel glycoside hydrolases [1, 2]. | * You have written, that '[[Glycoside Hydrolase Family 101|the recently solved 3D structure of SpGH101 reveals that this protein surprisingly shares some structural features with GH13 alpha-amylases]]', but it is not so surprising. According to PSI-BLAST searches, GH101 is related to [[GH13]], [[GH31]] and many other (β/α)<sub>8</sub>-barrel glycoside hydrolases [1, 2]. | ||
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3]. | * According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3]. | ||
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References: | References: | ||
| − | + | 1. [http://link.springer.com/article/10.1134/S0026893309040189 D.G. Naumoff and M. Carreras. 2009. PSI Protein Classifier: a new program automating PSI-BLAST search results. Molecular Biology (Engl Transl). V.43. N.4. P.652-664.] | |
| − | 1. [http:// | ||
2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf D.G. Naumoff. 2008. The GH31 family of glycoside hydrolases: subfamily structure and evolutionary connections. The Sixth International Conference on Bioinformatics of Genome Regulation and Structure. June 22-28, 2008. Novosibirsk. Russia. P.169.] | 2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf D.G. Naumoff. 2008. The GH31 family of glycoside hydrolases: subfamily structure and evolutionary connections. The Sixth International Conference on Bioinformatics of Genome Regulation and Structure. June 22-28, 2008. Novosibirsk. Russia. P.169.] | ||
| − | 3. [http:// | + | 3. [http://link.springer.com/article/10.1023/B:MBIL.0000032210.97006.de D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.] |
| − | + | --[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC) | |
| − | + | * Six subfamilies have been recognized in GH101 family [4]. | |
| − | --[[User:Daniil Naumoff|Daniil Naumoff]] | + | References: |
| + | 4. [http://www.worldscinet.com/jbcb/08/0803/S0219720010004628.html D.G. Naumoff. 2010. GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Journal of Bioinformatics and Computational Biology. V.8. N.3. P.437-451.] | ||
| + | --[[User:Daniil Naumoff|Daniil Naumoff]] 21:37, 5 May 2010 (UTC) | ||
Latest revision as of 04:16, 10 December 2013
Dear Warren,
I would like to pay your attention on some data about GH101 family:
- You have written, that 'the recently solved 3D structure of SpGH101 reveals that this protein surprisingly shares some structural features with GH13 alpha-amylases', but it is not so surprising. According to PSI-BLAST searches, GH101 is related to GH13, GH31 and many other (β/α)8-barrel glycoside hydrolases [1, 2].
- According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to family NEW3 of the functionally uncharacterized domains [3].
--Daniil Naumoff 11:36, 10 December 2009 (UTC)
- Six subfamilies have been recognized in GH101 family [4].
References: 4. D.G. Naumoff. 2010. GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Journal of Bioinformatics and Computational Biology. V.8. N.3. P.437-451. --Daniil Naumoff 21:37, 5 May 2010 (UTC)