Claudia's Assignment - Revision history

Clcarcelen: /* Genome Comparisons */

2009-10-01T15:28:55Z

‎Genome Comparisons

Clcarcelen at 15:27, 1 October 2009

2009-10-01T15:27:43Z

Clcarcelen at 15:23, 1 October 2009

2009-10-01T15:23:14Z

Clcarcelen at 13:45, 1 October 2009

2009-10-01T13:45:09Z

Clcarcelen at 06:15, 1 October 2009

2009-10-01T06:15:00Z

Show changes

Clcarcelen: /* Introduction */

2009-10-01T05:11:15Z

‎Introduction

Clcarcelen at 05:10, 1 October 2009

2009-10-01T05:10:42Z

Clcarcelen: /* Introduction */

2009-10-01T04:55:29Z

‎Introduction

Clcarcelen at 04:44, 1 October 2009

2009-10-01T04:44:23Z

Clcarcelen at 03:12, 1 October 2009

2009-10-01T03:12:53Z

← Older revision		Revision as of 15:28, 1 October 2009
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	[http://mic.sgmjournals.org/cgi/content/abstract/145/12/3431 TRAP Transporters]<br>		[http://mic.sgmjournals.org/cgi/content/abstract/145/12/3431 TRAP Transporters]<br>
−	[[Image:TRAP.~~jpg~~]]	+	[[Image:TRAP.png]]

← Older revision		Revision as of 15:27, 1 October 2009
Line 223:		Line 223:

	[http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Subsystems;subsystem=ECF_class_transporters ECF Transporters Comparison Chart]		[http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Subsystems;subsystem=ECF_class_transporters ECF Transporters Comparison Chart]
		+
		+	[http://mic.sgmjournals.org/cgi/content/abstract/145/12/3431 TRAP Transporters]<br>
		+	[[Image:TRAP.jpg]]

← Older revision		Revision as of 15:23, 1 October 2009
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	I altered my course of interest by deciding to look into the hits resulting in matches with ''Zea mays'', since the salt-tolerance of this important agricultural product is an area of interest for the benefit of the population as whole.<br>		I altered my course of interest by deciding to look into the hits resulting in matches with ''Zea mays'', since the salt-tolerance of this important agricultural product is an area of interest for the benefit of the population as whole.<br>
	Furthermore, I chose to compare the genomes of the recurring hits listed above, and study the transporters that occur in both.<br>		Furthermore, I chose to compare the genomes of the recurring hits listed above, and study the transporters that occur in both.<br>
		+
		+	==Genome Comparisons==
		+
		+	''Halomicrobium mukohataei'' & ''Haloarcula marismortui''<br>
		+	Shared 652 genes based on function of (838 defined).<br>
		+	Shared Membrane Transport genes: 3 TRAP Transporters, 4 ECF Transporters, 2 Potassium Homeostasis Transporters, & 5 Transporters of Nickel & Cobalt.<br>
		+	Did not share any ABC Transporters.
		+
		+	''Halomicrobium mukohataei'' & ''Halorubrum lacusprofundi''<br>
		+	RAST/SEED comparison unavailable.
		+
		+	''Halomicrobium mukohataei'' & ''Halorhabdus utahensis''<br>
		+	Shared 444 genes based on function (of 622 defined).<br>
		+	Shared 3 Membrane Transport genes involved in Potassium Homeostasis.<br>
		+	Did not share Membrane Transport genes encoding ECF Transporter genes or transporters for Nickel & Cobalt.
		+
		+
		+	''Halomicrobium mukohataei'' & ''Halobacterium salinarum''<br>
		+	RAST/SEED comparison unavailable.
		+
		+	''Halomicrobium mukohataei'' & ''Halobacterium sp.''<br>
		+	Shared 570 genes based on function (of 792 defined).<br>
		+	Shared 7 Membrane Transport genes, 3 TRAP Transporters, 1 ECF Transporter, 2 Potassium Homeostasis Transporters, & 1 Transport of Nickel & Cobalt.<br>
		+	Did not share a few Potassium Homeostasis Transporters, and shared no ABC Transporters.
		+
		+	''Halomicrobium mukohataei'' & ''Natronomonoas pharaonis''<br>
		+	Shared 578 genes based on function (of 769 defined).<br>
		+	Shared Membrane Transport genes: 2 ABC Transporters, 3 TRAP Transporters, & 3 Potassium Homeostasis Transporters.<br>
		+	Did not share most ABC transporters & did not share a few ECF & TRAP Transporters.<br>
		+
		+	[http://en.wikipedia.org/wiki/ABC-transporter ABC Transporters]<br>
		+	[[Image:ABC Trans.jpg]]
		+
		+	[http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Subsystems;subsystem=ECF_class_transporters ECF Transporters Comparison Chart]

@@ Line 1: / Line 1: @@
 ==Introduction==
 From the background information on our species, ''Halomicrobium mukohataei'', we know that our organism is not only a halophile, or salt-loving, but also that the organism in fact requires a high salinity environment to survive. This trait is unique and compelling because of the harsh environment and the many pumps and mechanisms that must be present for an living organism to survive. However, our organism is not the only one to have such adaptations. There are a number of halophile species as well as a number of salt-tolerant organisms, including a number of bacteria and a few yeasts.<br>
 Originally, I wanted to look into the genes that encoded adaptations to the high-salinity environment, specifically ion (cation) pumps. Of the proteins with known functions, our organism appears to encode 21 different proteins functioning as ion or ion-dependent pumps. I wanted to investigate these pumps, and their roles within the organism's metabolic pathways.
 ==Cation Pumps==
@@ Line 162: / Line 163: @@
 [[Image:Pic18.png]]<br>
 [[Image:Pic19.png]]<br>

@@ Line 1: / Line 1: @@
 ==Introduction==
 From the background information on our species, ''Halomicrobium mukohataei'', we know that our organism is not only a halophile, or salt-loving, but also that the organism in fact requires a high salinity environment to survive. This trait is unique and compelling because of the harsh environment and the many pumps and mechanisms that must be present for an living organism to survive. However, our organism is not the only one to have such adaptations. There are a number of halophile species as well as a number of salt-tolerant organisms, including a number of bacteria and a few yeasts.<br>
-Originally, I wanted to look into the genes that encoded adaptations to the high-salinity environment, specifically ion (cation) pumps. Of the proteins with known functions, our organism appears to encode 22 different proteins functioning as ion or ion-dependent pumps. I wanted to investigate these pumps, and their roles within the organism's metabolic pathways.
+Originally, I wanted to look into the genes that encoded adaptations to the high-salinity environment, specifically ion (cation) pumps. Of the proteins with known functions, our organism appears to encode 21 different proteins functioning as ion or ion-dependent pumps. I wanted to investigate these pumps, and their roles within the organism's metabolic pathways.
 ==Cation Pumps==

← Older revision		Revision as of 05:10, 1 October 2009
Line 126:		Line 126:
	[[Image:Pic18.png]]<br>		[[Image:Pic18.png]]<br>
	[[Image:Pic19.png]]<br>		[[Image:Pic19.png]]<br>
−
−	~~[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033168 AAA+ family ATPase 644033168]<br>~~
−	~~A BLAST using megablast produced no results other than our own species.<br>~~
−	~~A BLAST using blastn produced the following results:<br>~~
−	~~[[Image:Pic20.png]]<br>~~
−	~~[[Image:Pic21.png]]<br>~~
−	~~[[Image:Pic22.png]]<br>~~
−	~~[[Image:Pic23.png]]<br>~~

@@ Line 2: / Line 2: @@
 From the background information on our species, ''Halomicrobium mukohataei'', we know that our organism is not only a halophile, or salt-loving, but also that the organism in fact requires a high salinity environment to survive. This trait is unique and compelling because of the harsh environment and the many pumps and mechanisms that must be present for an living organism to survive. However, our organism is not the only one to have such adaptations. There are a number of halophile species as well as a number of salt-tolerant organisms, including a number of bacteria and a few yeasts.<br>
 Originally, I wanted to look into the genes that encoded adaptations to the high-salinity environment, specifically ion (cation) pumps. Of the proteins with known functions, our organism appears to encode 22 different proteins functioning as ion or ion-dependent pumps. I wanted to investigate these pumps, and their roles within the organism's metabolic pathways.
 ==Cation Pumps==
@@ Line 73: / Line 75: @@
 A BLAST using megablast produced no results other than our own species.<br>
 A BLAST using blast n produced the following results:<br>
-[Image:Picture 27.png]<br>
+[[Image:Picture 27.png]]<br>
 [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component 644032689]<br>

← Older revision		Revision as of 03:12, 1 October 2009
Line 69:		Line 69:
	A BLAST using blastn produced the following results:<br>		A BLAST using blastn produced the following results:<br>
	[[Image:Picture 24.png]]		[[Image:Picture 24.png]]
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032648 ABC-type Mn2+/Zn2+ transport system, permease component 644032648]<br>
		+	A BLAST using megablast produced no results other than our own species.<br>
		+	A BLAST using blast n produced the following results:<br>
		+	[Image:Picture 27.png]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component 644032689]<br>
		+	A BLAST using megablast produced the following results:<br>
		+	[[Image:Picture 28.png]]<br>
		+	[[Image:Picture 29.png]]<br>
		+	Trk active potassium channel<br>
		+	Potassium channel protein<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Picture 30.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032725 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/multisubunit Na+/H+ antiporter, MnhA subunit ( EC:1.6.5.3 ) 644032725]<br>
		+	A BLAST using megablast produced no results other than our own species.<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic3.png]]<br>
		+	[[Image:Pic1.png]]<br>
		+	[[Image:Pic2.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032854Kef-type K+ transport system, membrane component 644032854]<br>
		+	A BLAST using megablast produced no results other than our own species.<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic4.png]]<br>
		+	[[Image:Pic5.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032916 NhaP-type Na+(K+)/H+ antiporter 644032916]<br>
		+	A BLAST using megablast produced the following results:<br>
		+	[[Image:Pic6.png]]<br>
		+	[[Image:Pic7.png]]<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic8.png]]<br>
		+	[[Image:Pic9.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032920 AAA+ family ATPase 644032920]<br>
		+	A BLAST using megablast produced the following results:<br>
		+	[[Image:Pic10.png]]<br>
		+	[[Image:Pic11.png]]<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic12.png]]<br>
		+	[[Image:Pic13.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033032 ABC-type Fe3+ transport system, periplasmic component 644033032]<br>
		+	A BLAST using megablast produced no results other than our own species.<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic14.png]]<br>
		+	[[Image:Pic15.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033110 ABC-type Mn2+/Zn2+ transport system, permease component 644033110]<br>
		+	A BLAST using megablast produced the following results:<br>
		+	[[Image:Pic16.png]]<br>
		+	[[Image:Pic17.png]]<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic18.png]]<br>
		+	[[Image:Pic19.png]]<br>
		+
		+	[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644033168 AAA+ family ATPase 644033168]<br>
		+	A BLAST using megablast produced no results other than our own species.<br>
		+	A BLAST using blastn produced the following results:<br>
		+	[[Image:Pic20.png]]<br>
		+	[[Image:Pic21.png]]<br>
		+	[[Image:Pic22.png]]<br>
		+	[[Image:Pic23.png]]<br>