Citrate Synthase - Revision history

Karicheson at 23:58, 6 October 2009

2009-10-06T23:58:47Z

Karicheson at 23:52, 6 October 2009

2009-10-06T23:52:41Z

Karicheson at 23:44, 6 October 2009

2009-10-06T23:44:14Z

Karicheson at 04:05, 1 October 2009

2009-10-01T04:05:50Z

Karicheson at 04:05, 1 October 2009

2009-10-01T04:05:13Z

Karicheson at 03:27, 1 October 2009

2009-10-01T03:27:41Z

Karicheson at 03:25, 1 October 2009

2009-10-01T03:25:37Z

Karicheson at 03:01, 1 October 2009

2009-10-01T03:01:45Z

Karicheson at 02:34, 1 October 2009

2009-10-01T02:34:24Z

Karicheson at 02:25, 1 October 2009

2009-10-01T02:25:52Z

@@ Line 14: / Line 14: @@
 [[Image:csh1.jpg]]
-''Natronomonas pharaonis'' - halophillic archaean
+''Natronomonas pharaonis'' - halophillic archaean - got rid of because is not just a salt-loving organism but can also survive high salinity
 citrate synthase protein sequence:
 msdelkkgle gvlvaessls yidgdegklv yrgytiddla rnasfeevvy llwhgelpta
@@ Line 23: / Line 23: @@
 eeylteekgl apnvdfysas tyyqmgipvd iytpifamsr vggwiahvle qyddnrlirp
 rgryvgpddr tvtpider
 ''Halogeometricum borinquense''
@@ Line 69: / Line 67: @@
 ryvgaedrds tplder
 [[Image:csh6.jpg]]

← Older revision		Revision as of 23:52, 6 October 2009
Line 208:		Line 208:
	301 kklppnvdfy sasvyhslgi dhdlftpifa vsrmsgwlah ileqydnnrl irpradytgp		301 kklppnvdfy sasvyhslgi dhdlftpifa vsrmsgwlah ileqydnnrl irpradytgp
	361 dkqkfvpiee ra		361 dkqkfvpiee ra
		+
		+	''Exiguobacterium''
		+	>Exiguobacterium sp. AT1b]
		+	MSTTKGLEGIVAAASKVSSIIDGQLTYGGYTIDDLADNATFEEVVFLLWNDRLPNAEELTALSEALVKEA
		+	TLPEEVIDTLKRAPKSANAMATIRTALSQLALYDEESEDMSDEANMRKAIRLQAQVATIVTAFARLRKGE
		+	QPVAPKPGLSYAANFLYMLNGEEPSDVAEKTIDKALILHADHELNASTFTARVCVATLSDMYSGVTAAMG
		+	ALKGPLHGGANEAVMKMLHEIDSVDRVEEYVRGKFERKEKIMGFGHRVYKDGDPRAKHLKEMSRQLTAQI
		+	GEPKWYEMSEKIDHLVETEKGLKPNVDFYSASTYYALGLEEDLFTPIFAVSRMSGWIAHILEQYADNRLI
		+	RPRAEYVGETSRKYVPVNER
		+

@@ Line 84: / Line 84: @@
 lleqwadnrl irpraqyvga rdrtvapiae r
-''Bacillus selenitireducens''- halophilic bacerium
+''Bacillus selenitireducens''- haloalkaliphilic bacerium- throwing this out because i want to focus in on salt-loving specifically and do not want to have other extreme natured organisms in the salt-loving category
 citrate protein sequence
 msttkglegv vattssvssi iddvltyrgy niddladhas feevvyllwn eklptkqeld
@@ Line 93: / Line 93: @@
 kgllpnvdfy sasvyhslgi dhdlftpifa vsrvsgwiah ileqysnnrl irpraeyvgp
 dkqswipiek r

← Older revision		Revision as of 04:05, 1 October 2009
Line 209:		Line 209:

	I next did a ClustalW Multiple Alignment with the salt-loving and non-salt loving organisms. I was looking for areas of commonality in the salt-loving alignment that had disappeared in the combined alignment. If the conserved region disappeared than it would signal that some aspect of the citrate synthase protein sequence that is unique to halophilic organisms is not seen in non-salt loving organisms. I found common sequences in all 7 strains according to the ClustalW multiple alignment of the salt-loving organisms and then went in search for the same sequences in the overall alignment. The picture below shows a highly conserved sequence among salt loving and non salt loving organisms BUT there is one amino acid difference, a change from glycine (salt loving) to glutamic acid (non salt loving). These amino acids are highly different: glutamic acid is hydrophilic and charged whereas glycine is nonpolar and hydrophobic. This change may indicate that there is a genetic and primary protein sequence reason behind why citrate synthase needs salt to work properly.		I next did a ClustalW Multiple Alignment with the salt-loving and non-salt loving organisms. I was looking for areas of commonality in the salt-loving alignment that had disappeared in the combined alignment. If the conserved region disappeared than it would signal that some aspect of the citrate synthase protein sequence that is unique to halophilic organisms is not seen in non-salt loving organisms. I found common sequences in all 7 strains according to the ClustalW multiple alignment of the salt-loving organisms and then went in search for the same sequences in the overall alignment. The picture below shows a highly conserved sequence among salt loving and non salt loving organisms BUT there is one amino acid difference, a change from glycine (salt loving) to glutamic acid (non salt loving). These amino acids are highly different: glutamic acid is hydrophilic and charged whereas glycine is nonpolar and hydrophobic. This change may indicate that there is a genetic and primary protein sequence reason behind why citrate synthase needs salt to work properly.
		+
		+	[[Image:csfinal.jpg]]

← Older revision		Revision as of 04:05, 1 October 2009
Line 206:		Line 206:
	301 kklppnvdfy sasvyhslgi dhdlftpifa vsrmsgwlah ileqydnnrl irpradytgp		301 kklppnvdfy sasvyhslgi dhdlftpifa vsrmsgwlah ileqydnnrl irpradytgp
	361 dkqkfvpiee ra		361 dkqkfvpiee ra
		+
		+
		+	I next did a ClustalW Multiple Alignment with the salt-loving and non-salt loving organisms. I was looking for areas of commonality in the salt-loving alignment that had disappeared in the combined alignment. If the conserved region disappeared than it would signal that some aspect of the citrate synthase protein sequence that is unique to halophilic organisms is not seen in non-salt loving organisms. I found common sequences in all 7 strains according to the ClustalW multiple alignment of the salt-loving organisms and then went in search for the same sequences in the overall alignment. The picture below shows a highly conserved sequence among salt loving and non salt loving organisms BUT there is one amino acid difference, a change from glycine (salt loving) to glutamic acid (non salt loving). These amino acids are highly different: glutamic acid is hydrophilic and charged whereas glycine is nonpolar and hydrophobic. This change may indicate that there is a genetic and primary protein sequence reason behind why citrate synthase needs salt to work properly.

@@ Line 100: / Line 100: @@
 [[Image:slcw2.jpg]]
 [[Image:slcw3.jpg]]
 [[Image:slcw4.jpg]]

← Older revision		Revision as of 03:25, 1 October 2009
Line 93:		Line 93:
	301 kgllpnvdfy sasvyhslgi dhdlftpifa vsrvsgwiah ileqysnnrl irpraeyvgp		301 kgllpnvdfy sasvyhslgi dhdlftpifa vsrvsgwiah ileqysnnrl irpraeyvgp
	361 dkqswipiek r		361 dkqswipiek r
		+
		+
		+	ClustalW Alignment of Salt-Loving Organisms:
		+
		+	[[Image:slcw.jpg]]
		+	[[Image:slcw2.jpg]]
		+	[[Image:slcw3.jpg]]
		+	[[Image:slcw4.jpg]]
		+

@@ Line 1: / Line 1: @@
 I did a blastp search using our species' citrate synthase protein sequence.
-'''The following halophiles were the tops hits and are accompanied by their basltp results:'''
+'''The following halophillic Archaea were the top hits and are accompanied by their basltp results:'''
 ''Haloarcula marismortui''
@@ Line 14: / Line 14: @@
 [[Image:csh1.jpg]]
-''Natronomonas pharaonis''
+''Natronomonas pharaonis'' - halophillic archaean
 citrate synthase protein sequence:
 msdelkkgle gvlvaessls yidgdegklv yrgytiddla rnasfeevvy llwhgelpta
@@ Line 93: / Line 93: @@
 kgllpnvdfy sasvyhslgi dhdlftpifa vsrvsgwiah ileqysnnrl irpraeyvgp
 dkqswipiek r
 '''The following non-salt loving prokaryotes were the top hits among their domain'''
 ''Alicyclobacillus acidocaldarius''- thermoacidiphillic bacterium
 ''Acidobacterium capsulatum''- aerobic, mesophilic, chemo-organotroph bacterium
@@ Line 107: / Line 130: @@
 yinqekklna nvdfysasty ttlgididlf tpifaisria gwsahvieql ddnrlirpra
 eyigpeypsk yipvaer

← Older revision		Revision as of 02:34, 1 October 2009
Line 70:		Line 70:
	[[Image:csh6.jpg]]		[[Image:csh6.jpg]]

−	'''The following prokaryotes were the top hits among their domain'''	+
		+	'''The following are salt-loving bacertia with top hits'''
		+
		+	''Salinibacter ruber''- Extremely halophilic, strictly aerobic, red-pigmented bacterium
		+	citrate synthase protein sequence
		+	1 mllcsektpa wagprgllqk rsradslnag lsqrpaclrp cpfgrdghav siplrlspht
		+	61 ffdmadqesv telttdkapi karglegvia leselssidg dkgqliyrgy dihdladhas
		+	121 feevvyllrh gelptqseld dfsshlrser alpapilnll retpadahpm avlrtavsal
		+	181 alydeeadtm eeaanhrkad rilaqiptii aafdrlrkdk epvapldhgs mahnflymln
		+	241 gekpgaaaed tfdvclvlha dhglnastft srvigstlsd mysavsgsvg alkgrlhgga
		+	301 nqevmrmlld idekgadpts yirdrldade rvmgfghrvy ntmdpraail rtmvkelsee
		+	361 agdmkwykyt tkihetmtee tgidpnvdff sgptyyqlgl dpdlfttifa lsrtagwtah
		+	421 lleqwadnrl irpraqyvga rdrtvapiae r
		+
		+	''Bacillus selenitireducens''- halophilic bacerium
		+	citrate protein sequence
		+	1 msttkglegv vattssvssi iddvltyrgy niddladhas feevvyllwn eklptkqeld
		+	61 tfkkelaevs avpdevinqm rtypidqvhp maalrtavsn lalfdeeads hdedanrrka
		+	121 lklqaqlpti vaafarvrqg kdpvapkqel syaanflyml ngeepdetsv kaidkalvlh
		+	181 adhelnastf tsrvcvatls dmysgitaai galkgplhgg anervmamls eietvenaep
		+	241 yikealankv kimgfghrvy kngdprakhl kemsrqmtei tgeskwydms vkvdeivtge
		+	301 kgllpnvdfy sasvyhslgi dhdlftpifa vsrvsgwiah ileqysnnrl irpraeyvgp
		+	361 dkqswipiek r
		+
		+	'''The following non-salt loving prokaryotes were the top hits among their domain'''
		+
		+	''Alicyclobacillus acidocaldarius''- thermoacidiphillic bacterium
		+
		+	''Acidobacterium capsulatum''- aerobic, mesophilic, chemo-organotroph bacterium
		+	citrate synthase protein sequence
		+	1 mstavatkgl egivaansgi cwidgdagvl ayrgidihel athsnfeett yllwhgklpt
		+	61 qaeladfskk laaarridpk iydllrslpk tgtpmealrt avsalsffdp neravdhdsn
		+	121 vrkafdltaq iamivaafdr irkgkaivep dpslshagnf lymlngekps etatkafdia
		+	181 lilhadheln astfaarvia atlsdihsai tgaigalkgp lhgganeavm rmlfeiekag
		+	241 adpvehvkkm laekkkvsgf ghrvyhtedp rathlrrmse dlgrsannak wfemsrkiel
		+	301 yinqekklna nvdfysasty ttlgididlf tpifaisria gwsahvieql ddnrlirpra
		+	361 eyigpeypsk yipvaer

← Older revision		Revision as of 02:25, 1 October 2009
Line 69:		Line 69:
	361 ryvgaedrds tplder		361 ryvgaedrds tplder
	[[Image:csh6.jpg]]		[[Image:csh6.jpg]]
		+
		+	'''The following prokaryotes were the top hits among their domain'''