Olivia's Assignment - Revision history

Olhoshing at 16:48, 22 September 2009

2009-09-22T16:48:36Z

Olhoshing at 16:41, 22 September 2009

2009-09-22T16:41:36Z

Olhoshing at 16:15, 22 September 2009

2009-09-22T16:15:52Z

Olhoshing at 16:40, 15 September 2009

2009-09-15T16:40:58Z

Olhoshing at 16:40, 15 September 2009

2009-09-15T16:40:08Z

New page

I want to explore the question Does high salinity affect the proton pump? So I'd like to compare the rhodopsin hydrogen pump gene(s) found in H. mukohataei to those found in other halophiles and non-halophiles.

Using JGI, I found these known protein sequences predicted to be the proton pump in H. mukohataei:
*[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030941 644030941] bacteriorhodopsin
*[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032376 644032376] bacteriorhodopsin
*[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032569 644032569] Bacteriorhodopsin
*[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032598 644032598] bacteriorhodopsin<br>
[[Image:Mukohataei-rhodopsin.png|thumb|center|500px]]<br>

@@ Line 14: / Line 14: @@
 [[Image:Mukohataei-rhodopsin.png|thumb|center|500px]]<br>
-[[http://temp.geobio.uib.no/uploads/documents/species_in_haloarchaea.pdf]]
+[[http://temp.geobio.uib.no/uploads/documents/species_in_haloarchaea.pdf Species in Haloarchaea]] - may or may not be useful.
 == Other Species found to have Bacteriorhodopsin ==
 *Natronomonas pharaonis
 *H. vallismortis (ATCC 29715) sopII and htrII genes for sensory rhodopsin II apoprotein and sensory rhodopsin II transducer ACCESSION Z35308
+*Haloarcula marismortui ATCC 43049 chromosome I, complete sequence
+*Halorhabdus utahensis DSM 12940, complete genome
+*Pseudomonas syringae pv. tomato str. DC3000, complete genome
-I searched the [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=110065 Conserved Domains Database for pFam01036] bacteriorhodopsin. I aligned all 14 rows to compare the bacteriorhodopsin sequences. From this information, I can see the generall diversity within the bacteriorhodopsin gene and identify the species that have the gene. I can then BLAST our genome's bacteriorhodopsin genes to find more dissimilar species - non-halophiles - to compare in a phylogenetic tree.
+*Bradyrhizobiu sp. BTAi1, complete genome
-[[Image:pFam1.png|600px]]
+[[Image:644030941-dissimilar1.png|600px]]
-[[Image:pFam2.png|600px]]
+[[Image:644030941-dissimilar2.png|600px]]

← Older revision		Revision as of 16:41, 22 September 2009
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−	I searched the [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=110065 Conserved Domains Database for pFam01036] bacteriorhodopsin.	+	I searched the [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=110065 Conserved Domains Database for pFam01036] bacteriorhodopsin. I aligned all 14 rows to compare the bacteriorhodopsin sequences. From this information, I can see the generall diversity within the bacteriorhodopsin gene and identify the species that have the gene. I can then BLAST our genome's bacteriorhodopsin genes to find more dissimilar species - non-halophiles - to compare in a phylogenetic tree.
		+
		+
		+	[[Image:pFam1.png\|600px]]
		+	[[Image:pFam2.png\|600px]]

← Older revision		Revision as of 16:40, 15 September 2009
Line 1:		Line 1:
−	I want to explore the question Does high salinity affect the proton pump? So I'd like to compare the rhodopsin hydrogen pump gene(s) found in H. mukohataei to those found in other halophiles and non-halophiles.	+	I want to explore the question '''Does high salinity affect the proton pump?''' So I'd like to compare the rhodopsin hydrogen pump gene(s) found in H. mukohataei to those found in other halophiles and non-halophiles.

	Using JGI, I found these known protein sequences predicted to be the proton pump in H. mukohataei:		Using JGI, I found these known protein sequences predicted to be the proton pump in H. mukohataei:

@@ Line 1: / Line 1: @@
 I want to explore the question '''Does high salinity affect the proton pump?''' So I'd like to compare the rhodopsin hydrogen pump gene(s) found in H. mukohataei to those found in other halophiles and non-halophiles.
 Using JGI, I found these known protein sequences predicted to be the proton pump in H. mukohataei:
@@ Line 7: / Line 13: @@
 *[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032598 644032598]	 bacteriorhodopsin<br>
 [[Image:Mukohataei-rhodopsin.png|thumb|center|500px]]<br>