Sand box 326: Difference between revisions

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== Family and Superfamily ==

Research ~~shows~~ that ~~4Q7Q~~ is a member of the ~~SGNH~~ Hydrolase ~~protein~~ super family. ~~BLAST and InterPro both suggested 4Q7Q’s inclusion in this family~~, ~~and~~ the ~~known~~ conserved ~~residues seen from SPRITE analysis—Serine, Glycine, Asparagine, and Histidine—line up~~ with ~~those observed throughout~~ this family.D,~~E Notably, this superfamily is also referred to as the GDSL Hydrolase superfamily~~.~~D,E~~

Research suggests that 3CBW is a member of the Glycoside Hydrolase super family which was found using BLAST. This means that the protein possibly has the ability to hydrolyze glycosidic bonds between two or more carbohydrates. Additionally, 3CBW is also recognized under the beta-mannanase family. This was confirmed with InterPro which showed 3CBW being highly conserved with this family, having over 300 shared amino acids.

~~4Q7Q’s inclusion~~ in this family ~~also supports its SPRITE-derived hypothetical functionality~~. ~~Rhamnogalacturonan Acetylesterase—the enzyme with one~~ of ~~the best SPRITE~~-~~based alignment relative to 4Q7Q—is~~ a ~~member of this family~~.F Proteins in this ~~family are~~ also ~~known for containing a “unique hydrogen bond network~~ that ~~[stabilizes]”~~ the ~~active site~~.F

Using Dali, it was found that 3CBW was similar in structure and sequence to proteins 2QHA (Beta-1,4-mannanase) and 2WHK (Mannan endo-1,4-beta-mannosidase) which come from the bacterial species Bacillus Subtilis. Furthermore, BLAST confirmed that 3CBW is similar to the enzymes that come from this bacterial species in terms of functionality.

Through a search on InterPro, it was determined that 3CBW has a glycosyl hydrolase family 26 domain. This domain consists mostly of endo-beta-1,4-mannanases and typically has a beta/alpha 8-barrel folding motif. Proteins in this domain also tend to have two Glu residues located respectfully on strands beta-4 and beta-7 that act as the catalytic acid/base and nucleophile in a double-displacement mechanism.

Regarding what protein family 4Q7Q belongs to, DALI results suggest it is a part of a sub-family of the greater GDSL/SGNH superfamily. A PDB90% DALI search labels 4Q7Q as a part of the “Lipolytic Protein G-D-S-L Family,” which refers to enzymes that hydrolyze lipid substrates.

== Sequence Analysis (DONE) ==

Sand box 326: Difference between revisions

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@@ Line 15: / Line 15: @@
 == Family and Superfamily ==
-Research shows that 4Q7Q is a member of the SGNH Hydrolase protein super family. BLAST and InterPro both suggested 4Q7Q’s inclusion in this family, and the known conserved residues seen from SPRITE analysis—Serine, Glycine, Asparagine, and Histidine—line up with those observed throughout this family.D,E Notably, this superfamily is also referred to as the GDSL Hydrolase superfamily.D,E
+Research suggests that 3CBW is a member of the Glycoside Hydrolase super family which was found using BLAST. This means that the protein possibly has the ability to hydrolyze glycosidic bonds between two or more carbohydrates. Additionally, 3CBW is also recognized under the beta-mannanase family. This was confirmed with InterPro which showed 3CBW being highly conserved with this family, having over 300 shared amino acids.
-Q7Q’s inclusion in this family also supports its SPRITE-derived hypothetical functionality. Rhamnogalacturonan Acetylesterase—the enzyme with one of the best SPRITE-based alignment relative to 4Q7Q—is a member of this family.F Proteins in this family are also known for containing a “unique hydrogen bond network that [stabilizes]” the active site.F
+Using Dali, it was found that 3CBW was similar in structure and sequence to proteins 2QHA (Beta-1,4-mannanase) and 2WHK (Mannan endo-1,4-beta-mannosidase) which come from the bacterial species Bacillus Subtilis. Furthermore, BLAST confirmed that 3CBW is similar to the enzymes that come from this bacterial species in terms of functionality.
+Through a search on InterPro, it was determined that 3CBW has a glycosyl hydrolase family 26 domain. This domain consists mostly of endo-beta-1,4-mannanases and typically has a beta/alpha 8-barrel folding motif. Proteins in this domain also tend to have two Glu residues located respectfully on strands beta-4 and beta-7 that act as the catalytic acid/base and nucleophile in a double-displacement mechanism.
-Regarding what protein family 4Q7Q belongs to, DALI results suggest it is a part of a sub-family of the greater GDSL/SGNH superfamily. A PDB90% DALI search labels 4Q7Q as a part of the “Lipolytic Protein G-D-S-L Family,” which refers to enzymes that hydrolyze lipid substrates.
 == Sequence Analysis (DONE) ==