Katie's Assignment - Revision history

Karicheson at 23:37, 6 October 2009

2009-10-06T23:37:17Z

2009-10-06T23:31:55Z

2009-10-06T03:15:56Z

2009-10-01T01:59:02Z

2009-10-01T01:58:39Z

2009-10-01T01:31:25Z

2009-10-01T01:26:52Z

2009-10-01T01:18:51Z

2009-10-01T01:17:50Z

2009-10-01T01:07:52Z

← Older revision		Revision as of 23:37, 6 October 2009
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−	I re did this using ~~tblastx~~ while inserting the protein sequence of our gene and blasting it against translated nucleotide sequences. . . when doing this for both citrate synthase and ACTase I got no hits of similar protein sequences (besides the full protein itself) indicating that no paralogs/genes were missed during annotation.	+	I re did this using tblastn while inserting the protein sequence of our gene and blasting it against translated nucleotide sequences. . . when doing this for both citrate synthase and ACTase I got no hits of similar protein sequences (besides the full protein itself) indicating that no paralogs/genes were missed during annotation.

	3). Note the pathways and systems that these genes play a role in		3). Note the pathways and systems that these genes play a role in

← Older revision		Revision as of 23:31, 6 October 2009
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	Aspartate carbamoyltransferase regulatory unit blasted against out species' genome using Genome Portal, results are below: (no other hits besides the original gene)		Aspartate carbamoyltransferase regulatory unit blasted against out species' genome using Genome Portal, results are below: (no other hits besides the original gene)

		+
		+	I re did this using tblastx while inserting the protein sequence of our gene and blasting it against translated nucleotide sequences. . . when doing this for both citrate synthase and ACTase I got no hits of similar protein sequences (besides the full protein itself) indicating that no paralogs/genes were missed during annotation.

	3). Note the pathways and systems that these genes play a role in		3). Note the pathways and systems that these genes play a role in

@@ Line 190: / Line 190: @@
 [[Citrate Synthase]]
-Malic Enzyme
+Malic Enzyme- I decided last minute not to explore this protein because in further reading of research its comparison to malate dehydrogenase is incorrect and therefore does not establish enough correlation between our species' sequence and the one the researchers studied.  Also in the blastp search I got some malate dehydrogenase results and this enzyme is controlled by salt in a different manner and thus I did not want to explore it for fear of confusion.
-Aspartate Carbamoyltransferase
+[[Aspartate Carbamoyltransferase]]

@@ Line 188: / Line 188: @@
 Is there any section of the salt-loving protein sequences that coincide as compared to non-salt-loving organisms.
-[[Citrate Synthase
+[[Citrate Synthase]]
 ]]
 Malic Enzyme

@@ Line 188: / Line 188: @@
 Is there any section of the salt-loving protein sequences that coincide as compared to non-salt-loving organisms.
-Citrate Synthase
+[[Citrate Synthase
+]]
 Malic Enzyme

← Older revision		Revision as of 01:31, 1 October 2009
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−	6). Blast results of our species' genes: pick halophiles, bacteria, and eukarya to compare nucleotide sequence and protein sequence to (separate salt-loving and non-salt loving)	+	'''6). Blast results of our species' genes: pick halophiles, bacteria, and eukarya to compare nucleotide sequence and protein sequence to (separate salt-loving and non-salt loving)'''
		+
		+	Is there any section of the salt-loving protein sequences that coincide as compared to non-salt-loving organisms.
		+
		+	Citrate Synthase
		+
		+	Malic Enzyme
		+
		+	Aspartate Carbamoyltransferase
		+
		+
		+

← Older revision		Revision as of 01:26, 1 October 2009
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	ClustalW Multiple Alignment between all three enzyme protein sequences in the species studied in the paper (H. salinarium)		ClustalW Multiple Alignment between all three enzyme protein sequences in the species studied in the paper (H. salinarium)
		+
		+	[[Image:cwdata10.jpg]]
		+	[[Image:cwdata11.jpg]]
		+	[[Image:cwdata12.jpg]]

← Older revision		Revision as of 01:18, 1 October 2009
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	'''7). Look for similarities between the genes for these 3 enzymes that are salt dependent.'''		'''7). Look for similarities between the genes for these 3 enzymes that are salt dependent.'''
		+
	ClustalW Multiple Alignment between all three enzyme protein sequences for our species:		ClustalW Multiple Alignment between all three enzyme protein sequences for our species:

← Older revision		Revision as of 01:17, 1 October 2009
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−	7). Look for similarities between the genes for these 3 enzymes that are salt dependent.	+	'''7). Look for similarities between the genes for these 3 enzymes that are salt dependent.'''
		+	ClustalW Multiple Alignment between all three enzyme protein sequences for our species:
		+
		+	[[Image:cwdata4.jpg]]
		+	[[Image:cwdata5.jpg]]
		+	[[Image:cwdata6.jpg]]
		+
		+
		+	ClustalW Multiple Alignment between all three enzyme protein sequences in the species studied in the paper (H. salinarium)

@@ Line 168: / Line 168: @@
 [[Image:cs11.jpg]]
 [[Image:cs12.jpg]]
+[[Image:cs13.jpg]]