User talk:Warren Wakarchuk - Revision history

Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */

2013-12-10T11:16:15Z

Comment on tertiary structural relatedness of GH101 and GH13

Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */

2010-06-18T11:28:46Z

Comment on tertiary structural relatedness of GH101 and GH13

Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */

2010-05-05T21:37:44Z

Comment on tertiary structural relatedness of GH101 and GH13

Harry Brumer: some formatting changes, deleted non-peer-reviewed information

2009-12-15T17:01:27Z

some formatting changes, deleted non-peer-reviewed information

Harry Brumer at 16:38, 15 December 2009

2009-12-15T16:38:51Z

Daniil Naumoff at 07:43, 14 December 2009

2009-12-14T07:43:23Z

Daniil Naumoff: Created page with 'Dear Warren, I would like to pay your attention on some data about GH101 family: * You have written, that '[[Glycoside Hydrolase Family 101|the recently solved 3D structure…'

2009-12-10T11:36:26Z

Created page with 'Dear Warren, I would like to pay your attention on some data about GH101 family: * You have written, that '[[Glycoside Hydrolase Family 101|the recently solved 3D structure…'

New page

Dear Warren,

I would like to pay your attention on some data about [[GH101]] family:

* 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 (beta/alpha)<sub>8</sub>-barrel glycoside hydrolases [1].
* 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 [2].
* Six subfamilies have been recognized in GH101 family [3, 4].

References:

1. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]

2. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]

3. [http://mccmb.genebee.msu.su/2009/MCCMB09_Proceedings.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases and their homologues. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB’09). July 20-23, 2009. Moscow. Russia. P.251-252.]

4. [http://www.springerlink.com/content/5464020317174jx9/fulltext.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases (Abstracts of 20th International Symposium on Glycoconjugates Glycans "GLYCO XX", November 29 – December 4, 2009, San Juan, Puerto Rico, USA). Glycoconjugate Journal. V.26. N.7. P.847.]

--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)

@@ Line 20: / Line 20: @@
 References:
-. [http://www.worldscinet.com/jbcb/00/0001/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. (in press)]
+. [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)

← Older revision		Revision as of 21:37, 5 May 2010
Line 16:		Line 16:

	--[[User:Daniil Naumoff\|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)		--[[User:Daniil Naumoff\|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)
		+
		+	* Six subfamilies have been recognized in GH101 family [4].
		+
		+	References:
		+	4. [http://www.worldscinet.com/jbcb/00/0001/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. (in press)]
		+
		+	--[[User:Daniil Naumoff\|Daniil Naumoff]] 21:37, 5 May 2010 (UTC)

@@ Line 5: / Line 5: @@
 * 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].
@@ Line 17: / Line 15: @@
 . [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf 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)

@@ Line 9: / Line 9: @@
 References:
-. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]
+. [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.]
 . [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.]
-. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]
+. [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)

@@ Line 3: / Line 3: @@
 I would like to pay your attention on some data about [[GH101]] family:
-* 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 (beta/alpha)<sub>8</sub>-barrel glycoside hydrolases [1].
+* 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 [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].
-* Six subfamilies have been recognized in GH101 family [3, 4].
+* Six subfamilies have been recognized in GH101 family [4, 5].
@@ Line 13: / Line 13: @@
 . [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]
-. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]
+. [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.]
-. [http://mccmb.genebee.msu.su/2009/MCCMB09_Proceedings.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases and their homologues. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB’09). July 20-23, 2009. Moscow. Russia. P.251-252.]
+. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]
-. [http://www.springerlink.com/content/5464020317174jx9/fulltext.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases (Abstracts of 20th International Symposium on Glycoconjugates Glycans "GLYCO XX", November 29 – December 4, 2009, San Juan, Puerto Rico, USA). Glycoconjugate Journal. V.26. N.7. P.847.]
+. [http://mccmb.genebee.msu.su/2009/MCCMB09_Proceedings.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases and their homologues. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB’09). July 20-23, 2009. Moscow. Russia. P.251-252.]
 --[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)