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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 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 |
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| | [http://www.ncbi.nlm.nih.gov/protein/169237479 Aspartate Carbamoyltransferase] . . . [http://www.uniprot.org/jobs/A6GS.fasta Protein Sequence] and [http://www.uniprot.org/uniprot/B0R9W9 Information about Protein] | | [http://www.ncbi.nlm.nih.gov/protein/169237479 Aspartate Carbamoyltransferase] . . . [http://www.uniprot.org/jobs/A6GS.fasta Protein Sequence] and [http://www.uniprot.org/uniprot/B0R9W9 Information about Protein] |
| | | | |
| − | Comparison of Each Enzyme's Protein Sequences using blastp and clustalW. . .
| |
| − |
| |
| − | Citrate Synthase Sequences:
| |
| − |
| |
| − | [[Image:hccs.jpg]]
| |
| − | [[Image:hccscw.jpg]]
| |
| − |
| |
| − | Malic Enzyme Sequences: (Query=our species' malic enzyme protein sequence and Subject= ''H. salinarium'' malic enzyme sequence)
| |
| − | Malate Dehydrogenase:
| |
| − |
| |
| − | [[Image:hcme.jpg]]
| |
| − | [[Image:hcmecw.jpg]]
| |
| − |
| |
| − | Malate Dehydrogenase (oxaloacetate decarboxylating) / phosphate acetyltransferase:
| |
| − |
| |
| − | [[Image:hcbp1.jpg]]
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| − | [[Image:hcbp2.jpg]]
| |
| − |
| |
| − | [[Image:hccw1.jpg]]
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| − | [[Image:hccw2.jpg]]
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| − |
| |
| − | Aspartate Carbamoyltransferase Sequences: (Query= our species' and Subject=''H. salinarium'' aspartate carbamoyltranserase enzyme protein sequence)
| |
| − |
| |
| − | [[Image:hcac.jpg]]
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| − | [[Image:hcaccw.jpg]]
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| − |
| |
| − | The high conservation between the Aspartate Carbamoyltransferase and Citrate Synthase between our species' enzyme protein sequences and that of the halophile studied may prove to show that these enzymes in our species are also dependent on high salt concentrations.
| |
| − |
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| − |
| |
| − | '''5). Find these genes in the other 8 genomes of halophiles that have been annotated and the closely related halophiles as indicated by Dr. C's phylogenetic tree'''
| |
| − |
| |
| − | Citrate Synthase:
| |
| − |
| |
| − | Haloarcula californiae ATCC 33799:
| |
| − | MSDDLKKGLEGVIVAESELSVIDGDAGKLVYRGYTIEDLAKGASY
| |
| − | EEVLYLLWHGHLPNRDELSEFKQAMVDARGVDDDVISTVRQLAEADENPMAALRTAVSM
| |
| − | LSAFDPAPEDAEPTDEMVNLETGRRITAKIPTIIAAFTRIRDGKEPVEPHDDLDHAANF
| |
| − | LYMLNGEEPDDVLADVFDQALVLHADHGLNASTFSAITTASTLSDVHSAVTSAIGTLKG
| |
| − | PLHGGANQDVMEMLKEVDDAESDPLDWVKNALDEGRRVSGFGHRVYNVKDPRAKILGER
| |
| − | SKELGEAAGTLKWYEMSTTIEDYLMEEKGLAPNVDFYSASTYYQMGIPIDIYTPIFAMS
| |
| − | RVGGWVAHVFEYIEDNRLIRPRARYVGKNTDETEFVPLDER
| |
| − |
| |
| − | Haloarcula sinaiiensis ATCC 33800
| |
| − | MSDDLKKGLEGVIVAESELSVIDGDAGKLVYRGYTIEDLAKGASY
| |
| − | EEVLYLLWHGHLPNRDELSEFKQAMVDARGVDDDVISTVRQLAEADENPMAALRTAVSM
| |
| − | LSAFDPAPEDAEPTDEMVNLETGRRITAKIPTIIAAFTRIRDGKVPVEPRDDLDHAANF
| |
| − | LYMLNGEEPDDVLADVFDQALVLHADHGLNASTFSAITTASTLSDVHSAVTSAIGTLKG
| |
| − | PLHGGANQDVMEMLKEVDDAESDPLDWVKNALDEGRRVSGFGHRVYNVKDPRAKILGER
| |
| − | SKELGEAAGTLKWYEMSTTIEDYLMEEKGLAPNVDFYSASTYYQMGIPIDIYTPIFAMS
| |
| − | RVGGWVAHVFEYIEDNRLIRPRARYVGKNTDETEFVPLDER
| |
| − |
| |
| − | Haloarcula vallismortis ATCC 29715
| |
| − | MSDDLKKGLEGVIVAESELSVIDGDAGKLVYRGYTIEDLAKGASY
| |
| − | EEVLYLLWHGHLPNRDELSEFKQAMVEARDVDDDVISTVRQLAEADENPMAALRTAVSM
| |
| − | LSAFDPAPEDAEPTDETVNLETGRRITAKIPTIIAAFTRIRDGKEPVEPRDDLDHAANF
| |
| − | LYMLNGEAPDDVLADVFDQALVLHADHGLNASTFSAITTASTLSDVHSAVTSAIGTLKG
| |
| − | PLHGGANQDVMEMLKEVDDAESDPLEWVQNALDEGRRVSGFGHRVYNVKDPRAKILGER
| |
| − | SKELGEAAGTLKWYEMSTTIEDYLMEEKGLAPNVDFYSASTYYQMGIPIDIYTPIFAMS
| |
| − | RVGGWVAHVFEYIEDNRLIRPRARYVGKNPDETTFVPLDER
| |
| − |
| |
| − | Haloferax denitrificans ATCC 35960
| |
| − | MSGELKRGLEGVLVTESKLSFIDGDAGQLVYCGYDIEDLARDASY
| |
| − | EEVLYLLWHGELPTREELDAFSDELAAHRGLDDGVLDVARELAEQDESPMAALRTLVSA
| |
| − | MSAYDENADFEDVTDREVNLEKAKRITAKMPSVLAAYARFRRGDDYVEPDESLNHAANF
| |
| − | LYMLNGEEPNEVLAETFDMALVLHADHGLNASTFSAMVTSSTLSDLYSAVTSAIGTLSG
| |
| − | SLHGGANANVMRMLKDVDDSDMDPTEWVEDALDRGERVAGFGHRVYNVKDPRAKILGAK
| |
| − | SEALGEAAGDMKWYEMSVAIEEYIGEEKGLAPNVDFYSASTYYQMGIPIDLYTPIFAVS
| |
| − | RAGGWIAHVLEQYEDNRLIRPRARYTGEKGLEFPTVDER
| |
| − |
| |
| − | Haloferax mediteranei ATCC 33500
| |
| − | MSGELKRGLEGVLVTESELSFIDGDAGQLIYRGYDIEDLARDASY
| |
| − | EEVLYLLWHGELPNRTQLDEFSDELAAHRDIGDGILDVARELAEQDESPMAALRTLVSA
| |
| − | MSAYDENADFEDVTDREVNLEKAKRITAKMPSVLAAYARFRRGDDYVAPNDDLNHAANF
| |
| − | LYMLNGEEPNEVLAETFDMALVLHADHGLNASTFSAMVTSSTLSDMYSAVTSAIGTLSG
| |
| − | SLHGGANANVMRMLKDVDDSDMDPVDWVEDALDRGERVAGFGHRVYNVKDPRAKILGQK
| |
| − | SEALGEAAGDMKWYEMSVAIEEYISEEKGLAPNVDFYSASTYYQMDIPIDLYTPIFAVS
| |
| − | RSGGWIAHILEQYDDNRLIRPRARYTGDKDLDFPTLDER
| |
| − |
| |
| − | Haloferax mucosum ATCC BAA-1512
| |
| − | MDEVELNRGLAGVLVAETKLSFIDGEEGELIIGGFPLAELAANAT
| |
| − | YEESVFLLLNDRLPTAAELDEFRADLAARRDIGDEVRAVLRRAATERKPPMDALRMGVA
| |
| − | AATLGTDDQSNETAARRVVAVLPTLVATYWRYRAGDEPVAPRADLGHAANYHYMLNGEE
| |
| − | PTDAEVRGLETYLNTVIDHGLNASTFTARVVVSTESDVVSAATAAVGTLKGPLHGGAPG
| |
| − | PVLDMLREVADGDDPRAYVQAKLDAGERLMGFGHRVYRVRDPRAAVLSAAAKSFYEDSG
| |
| − | DTEFFDTVQTFEDVAVELLAEHKPGRRLETNVEFYTAALLHGVGIPKDLFTTTFAVARV
| |
| − | GGWIAHCLEQLADNRIIRPRSQYVGEKGRTWVPVEER
| |
| − |
| |
| − | MVSNLPGMSGELKRGLEGVLVTESELSFIDGDAGQLIYRGYAIED
| |
| − | LARDASYEEVLYLLWHGELPTSSELDEFSDELAAHRDLGDGILDVARELAEQDESPMAA
| |
| − | LRTLVSAMSAYDEHADFEDVTDREVNLEKAKRITAKMPSVLAAYARFRRGDDYVAPNSD
| |
| − | LNHAANFLYMLNGEEPNEVLAETFDMALVLHADHGLNASTFSAMVTASTLSDMYSAVTS
| |
| − | AVGTLSGSLHGGANANVMRMLKDVDDSDMDPVEWVKDALDRGERVAGFGHRVYNVKDPR
| |
| − | AKILGEKSEALGKAAGDMKWYEMSVAVEEYISGEKGLAPNVDFYSASTYYQMGIPIDLY
| |
| − | TPIFAVSRVGGWIAHVLEQYDDNRLIRPRARYTGDTDLDFPALDER
| |
| − |
| |
| − | Haloferax sulfurifontis ATCC BAA-897
| |
| − | MLYLLWHGELPTREELDAFSDELAAHRGLDDGVLDVARELAEQDE
| |
| − | SPMAALRTLVSAMSAYDENADFEDVTDREVNLEKAKRITAKMPSVLAAYARFRRGDDYV
| |
| − | EPEESLNHAANFLYMLNGEEPNEVLAETFDMALVLHADHGLNASTFSAMVTSSTLSDLY
| |
| − | SAVTSAIGTLSGSLHGGANANVMRMLKDVDDSDMDPTEWVEDALDRGERVAGFGHRVYN
| |
| − | VKDPRAKILGAKSEALGEAAGDMKWYEMSVAIEEYIGEEKGLAPNVDFYSASTYYQMGI
| |
| − | PIDLYTPIFAVSRAGGWIAHVLEQYEDNRLIRPRARYTGEKDLDFPSVDER
| |
| | | | |
| − | Haloferax volcanii ATCC 29605
| |
| − | MSGELKRGLEGVLVAESKLSFIDGDAGQLVYCGYDIEDLARDASY
| |
| − | EEVLYLLWHGALPTGEELDAFSDELAAHRDLDDGVLDVARELAEQDESPMAALRTLVSA
| |
| − | MSAYDESADFEDVTDREVNLEKAKRITAKMPSVLAAYARFRRGDDYVEPDESLNHAANF
| |
| − | LYMLNGEEPNEVLAETFDMALVLHADHGLNASTFSAMVTSSTLSDLYSAVTSAIGTLSG
| |
| − | SLHGGANANVMRMLKDVDDSDMDPTEWVKDALDRGERVAGFGHRVYNVKDPRAKILGAK
| |
| − | SEALGEAAGDMKWYEMSVAIEEYIGEEKGLAPNVDFYSASTYYQMGIPIDLYTPIFAVS
| |
| − | RAGGWIAHVLEQYEDNRLIRPRARYTGEKDLDFTPVDER
| |
| | | | |
| − | Halorhabdus utahensis
| + | [[Comparison of Each Enzyme's Protein Sequences using blastp and clustalW. . .]] |
| | | | |
| | | | |
| | | | |
| | | | |
| | + | '''[[5). Find these genes in the other 8 genomes of halophiles that have been annotated and the closely related halophiles as indicated by Dr. C's phylogenetic tree]] |
| | + | ''' |
| | | | |
| | + | Citrate Synthase ClustalW with all of the species listed above along with a dendogram and an N-J Tree |
| | | | |
| | + | [[Image:cwdata1.jpg]] |
| | | | |
| − | Malic Enzyme:
| + | [[Image:cs1.jpg]] |
| | + | [[Image:cs2.jpg]] |
| | + | [[Image:cs3.jpg]] |
| | + | [[Image:cs4.jpg]] |
| | | | |
| − | Haloarcula californiae ATCC 33799
| + | [[Image:csnj.jpg]] |
| − | MGLDEDALEYHRSKPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | EEIDKDPEKAFEYTAKGNLVGVVSDGSAVLGLGDIGPEAGKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDTDNAEAMIQTVEAMEPTFGGINLEDIAAPECFEVERRLSEKLDIPVFHDDQHG
| |
| − | TAIISGAALVNAADIADKELDELEVVFSGAGASAIASAKFYVSLGVSKDNITMCDSSGI
| |
| − | ITEERANHEELNRFKQEFARDIPEGGLADAMDGADVFVGLSVGGIVDQEMVRSMASDPI
| |
| − | IFAMANPDPEIAYEDAKAARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EEMKVAAARALADLARQDVPDEVVKAYGDQPLQFGPDYIIPKPLDPRVLFEVTPAVAEA
| |
| − | AIESGAARTELDTAAYVEELEARLGKSREMMRVVLNKAKSDPQRVVLAEGHDEKMIRAA
| |
| − | YQLVEQGIAEPILIGDADRIESTRRKFGLEFDPVVVDPETADVADYADRLYELRQRKGV
| |
| − | TRREADELIRDGNYLGSVMVEMGDADAMLTGLTHHYPSALRPPLQVIGTADDADYAAGV
| |
| − | YMLTFKNRVIFCADTTVNQDPDTDVLEEVTRHTGELARRFNVEPRAAMLSYSNFGSVDN
| |
| − | LGTKKIRRAVSRLQDDDRVDFPVDGEMQADTAVVEDILQDTYEFSELDDPANVLVFPNL
| |
| − | EAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQ
| |
| | | | |
| − | Haloarcula sinaiiensis ATCC 33800
| + | [[Image:csdendogram.jpg]] |
| − | MGLDEDALEYHRSKPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | EEIDKDPEKAFEYTAKGNLVGVVSDGSAVLGLGDIGPEAGKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDTDNAEAMIQTVEAMEPTFGGINLEDIAAPECFEVERRLSEKLDIPVFHDDQHG
| |
| − | TAIISGAALVNAADIADKELDELEVVFSGAGASAIASAKFYVSLGVSKDNITMCDSSGI
| |
| − | ITEERANHEELNRFKQEFARDIPEGGLADAMDGADVFVGLSVGGIVDQEMVRSMASDPI
| |
| − | IFAMANPDPEIAYEDAKAARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EEMKVAAARALADLARQDVPDEVVKAYGDQPLQFGPDYIIPKPLDPRVLFEVTPAVAEA
| |
| − | AIESGAARTELDTAAYVEELEARLGKSREMMRVVLNKAKSDPQRVVLAEGHDEKMIRAA
| |
| − | YQLVEQGIAEPILIGDADRIESTRRKFGLEFDPVVVDPETADVADYADRLYELRQRKGV
| |
| − | TRREADELIRDGNYLGSVMVEMGDADAMLTGLTHHYPSALRPPLQVIGTADDADYAAGV
| |
| − | YMLTFKNRVIFCADTTVNQDPDTDVLEEVTRHTGELARRFNVEPRAAMLSYSNFGSVDN
| |
| − | LGTKKIRRAVSRLQDDDRVDFPVDGEMQADTAVVEDILQDTYEFSELDDPANVLVFPNL
| |
| − | EAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQQE
| |
| | | | |
| − | Haloarcula vallismortis ATCC 29715
| |
| − | MGLDEDALEYHRSKPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | NEIDEDPERAFEYTAKGNLVGVVSDGSAVLGLGDIGPEAGKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDTDDAEAMIQTVAAMEPTFGGINLEDIAAPECFEVERRLSEKLDIPVFHDDQHG
| |
| − | TAIISGAALVNAADIAGKELEDLEVVFSGAGASAIASAKFYVSLGVSKDNITMCDSSGI
| |
| − | ITEERATHEDLNRFKQEFARDIPEGGLADAMDGADVFVGLSVGGIVDQEMVRSMASDPI
| |
| − | IFAMANPDPEIAYEDAKSARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EEMKVAAARALADLARQDVPDEVVKAYGDQPLQFGPDYIIPKPLDPRVLFEVTPAVAEA
| |
| − | AIESGAARTEIDTDAYVEQLEARLGKSREMMRVVLNKAKSDPQRVVLAEGHDEKMIRAA
| |
| − | YQLVEQGIAEPVLIGDADQIESTRRKFGLEFDPVVVDPETADVADYADRLYEIRQRKGI
| |
| − | TRREAEELVRDGNYLGSVMVEMGDADAMLTGLTHHYPSALRPPLQVIGTADDADYAAGV
| |
| − | YMLTFKNRVIFCADTTVNQAPDADVLEEVTRHTGELARRFNVEPRAAMLSYSNFGSVDN
| |
| − | PGTKKIRRAVSRLQDDDRVDFPVDGEMQADTAVVEDILQDTYEFSELDEPANVLVFPNL
| |
| − | EAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQQE
| |
| | | | |
| − | Haloferax denitrificans ATCC 35960
| |
| − | MGLDDDSREYHRQDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | LDIADDEDAAYEYTAKGNLVGVVSNGSAVLGLGNIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDITNVDEFVAATKAMEPTFGGINLEDIKAPECFEIERQLREQMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADVTDKDLDDLDIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
| |
| − | ITESRVEEGDVNKYKAEFAQPVDEGSLSDAIEGADVFAGLSVGGIVSQEMVRSMADDPI
| |
| − | IFAMANPDPEITYEDAKDAREDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYVIPKPLDPRVLFEVAPAVAQA
| |
| − | AMTSGAARERLDMNAYRERLEARLGKSREMMRVVLNKAKSNPKRVALAEGEDEKMIRAA
| |
| − | YQMQEEGIAEPILVGKTTTILRKAEELGLDFDPTIANPRDGEWDHYVDRLYELRQRKGV
| |
| − | TKSEAEELVRRDSNYFASVMVEVGDADAMLTGLTHHYPSALRPPLQIIGTAADANYAAG
| |
| − | VYMMTFKNRVVFCADTTVNLDPDEEILAEITKHTADLARQFNVEPRAALLSYSNFGSVT
| |
| − | NEGTRKPRDAAALLQGDPEVDFPVDGEMQADTALVEDILEGTYDFAELDGPANVLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQEEE
| |
| | | | |
| − | Haloferax mediteranei ATCC 33500
| + | Malic Enzyme |
| − | MTLEDDARDYHRRPPSGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | LDIADDETVAYDYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELGLDDPESFVQAVAAMEPTFGGINLEDIKAPECFEIEAGLRDEMSIPVFHDDQHG
| |
| − | TAIISGAALLNAVDIADKDRSSLQVTFAGAGAAATATARFYVSLGIPRENITMCDIDGI
| |
| − | LSERRADAGDLNEYTEPFARGVDDGELEDAMEGADVFVGLSVGGIVSQDMVRSMADNPI
| |
| − | IFAMANPDPEITYEDAKNARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALANLARQDVPDAVVKAYGDEPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
| |
| − | AMESGAARRERDLDAYREELEARLGKSREMMRVVLNKAKSDPKRVALAEGEDEKMIRAA
| |
| − | SQLVEDGIAEPILIGRTTEILRTAEELGLDFDPTIANPHDGEWNHYVDHLYEQRQRKGL
| |
| − | TRTEAAELVQQDSNHFASVMVDIGDADAMLTGLTHHYSSALRPPLQLIGTAEDATYAAG
| |
| − | VYMLTFRNRVIFCADATVNLDPDEEVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVN
| |
| − | NAGTAKPQNAVKRLHDDPDVDFPVDGEMQADTALVEEMLTDTYDFTELDGPANVLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGIAVVDAQE
| |
| | | | |
| − | MGLDDDSREYHRRDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| + | [[Image:cwdata3.jpg]] |
| − | RDIDEDEDAAYEYTAKGNLVGVVSNGTAVLGLGDIGSQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDITDVDDFVAATKAMEPTFGGINLEDIKAPECFEIERQLRETMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADVLGKDLEDLEIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
| |
| − | ITESRVSAGDVNKYKAEFAQDVEEGSLAHAMEGADVFAGLSVGGIVSQDMVRSMADNPI
| |
| − | IFAMANPDPEITYEDAKNARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDPRVLFEVAPAVAQA
| |
| − | AMTSGAARERLDMNEYRERLEARLGKSREMMRVVLNKAKSDPKRVALAEGSNEKMIRAA
| |
| − | YQMQEEGIAEPILVGDTTTILRKAEELGLEFDPTIANPHDGEWNHYVDHLYERRRRKGL
| |
| − | TRTEAAELVQQDSNYFASVMVSMDDADAMLTGLTHHYPSALRPPLQLIGTAEDANYAAG
| |
| − | VYMMTFKNRVVFCADTTVNLDPDEEILAEITKHTAELARRFNVEPRAALLSYSNFGSVR
| |
| − | NEGTAKPRDAARLLQNDPEVDFPVDGEMQADTALVEDILEGTYDFAELDDPANVLIFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQQE
| |
| | | | |
| − | Haloferax mucosum ATCC BAA-151
| + | [[Image:cs9.jpg]] |
| − | MGLDDDSREYHRRDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| + | [[Image:cs10.jpg]] |
| − | LDIDEDDDAAYEYTAKGNLVGVVSNGTAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| + | [[Image:cs11.jpg]] |
| − | FDVELDITDVDEFVAATKAMEPTFGGINLEDIKAPECFEIEHQLREQMDIPVFHDDQHG
| + | [[Image:cs12.jpg]] |
| − | TAIISGAALLNAADIVKKDLDDLEIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
| + | [[Image:cs13.jpg]] |
| − | ITQSRVEAGDVNTYKAEFAQPVDDGSLEDAMAGADVFVGLSVGGIVSQEMVRSMADNPI
| + | [[Image:cs14.jpg]] |
| − | IFAMANPDPEITYEDAKDARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| + | [[Image:cs15.jpg]] |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDPRVLFEVAPAVAQA
| + | [[Image:cs16.jpg]] |
| − | AMTSGAARERLDMNEYRERLEARLGKSREMMRVVLNKAKSDPKRVALAEGSNEKMIRAA
| |
| − | YQMQEEGIAEPILVGNTTSILRKAEELGLDFDPTIANPRDGEWDHYVDRLYELRKRKGI
| |
| − | TESEASELIRRDSNYFASIMVEIGDADAMLTGLTHHYPGGLRPPLQVIGTAEDANYAAG
| |
| − | VYMMTFKNRVVFCADTTVNLDPDEEVLAEITKHTAELARRFNVEPRAALLSYSNFGSVR
| |
| − | NEGTAKPRAAADILQNDPDVDFPVDGEMQADTALVEDILEGTYDFAELDDPANVLIFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQQE
| |
| | | | |
| − | MTLEDDARDYHREPPSGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | LDIDEDDDAAYDYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDIADVDEFVAATKAMEPTFGGINLEDIKAPECFEIEHQLREQMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADIADKELSSLNVVFAGAGAAATATARFYVSLGIPRENITMCDIDGV
| |
| − | LSEHRADTGDLNEYTEPFAQGVDDGSLEDAMVGADVFVGLSVGGIVSQEMVRSMADNPI
| |
| − | IFAMANPDPEITYEDAKDARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
| |
| − | AMESGAARRERDLDTYREELEARLGKSREMMRVVLNKAKSDPKRVVLAEGEDEKMIRAA
| |
| − | SQLVEDGIAEPILVGRTKEILRTAEELGLDFDPTIANPHEGEWNHYVEYLYEQRRRKGL
| |
| − | TRSEAAELVTQDSNYFASVMVAMDDADAMLTGLTHHYPSALRPPLQLIGTADDADYAAG
| |
| − | VYMLTFRNRVIFCADATVNLDPDENVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVS
| |
| − | NEGAAKPQNAVARLHDDPDVDFPVDGEMQSDTALVEEMLTDTYDFTELDGPANVLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGIAVVDAQ
| |
| | | | |
| | + | Aspartate Carbamoyltransferase ClustalW with all of the species listed above: |
| | | | |
| − | Haloferax sulfurifontis ATCC BAA-897
| + | [[Image:cwdata2.jpg]] |
| − | MGLDDDSREYHRQDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | LDIAEDEDAAYEYTAKGNLVGVVSNGSAVLGLGNIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDITNVDDFVAATKAMEPTFGGINLEDIKAPECFEIERQLREQMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADVTDKDLDDLDIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
| |
| − | ITESRVEAGDVNKYKAEFAQPVDEGSLSDAMEGADVFAGLSVGGIVSQEMVRSMADDPI
| |
| − | IFAMANPDPEITYEDAKAAREDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYVIPKPLDPRVLFEVAPAVAQA
| |
| − | AMTSGAARERLDMNAYRERLEARLGKSREMMRVVLNKAKSNPKRVALAEGEDEKMIRAA
| |
| − | YQMQEEGIAEPILVGKTTTILRKAEELGLDFDPTIANPRDGEWDHYVDRLYELRQRKGV
| |
| − | TKSEAEELVRRDSNYFASVMVEVGDADAMLTGLTHHYPSALRPPLQIIGTAADANYAAG
| |
| − | VYMMTFKNRVVFCADTTVNLDPDEEILAEITKHTADLARQFNVEPRAALLSYSNFGSVT
| |
| − | NEGTRKPRDAAALLQDDPDVDFPVDGEMQADTALVEDILEGTYDFAELDEPANLLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQEE
| |
| | | | |
| − | MTLEDDARDYHRRPPAGKVEIATTKPTNTQRDLSLAYSPGVAAPC
| + | [[Image:cs5.jpg]] |
| − | LDIADDENAAYEYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| + | [[Image:cs6.jpg]] |
| − | FDVEFDHDDPQAFVESVAAMEPTFGGINLEDIKAPECFEIEESLRDRMDIPVFHDDQHG
| + | [[Image:cs7.jpg]] |
| − | TAIISGAALLNAADIADKELSSLNVTFSGAGAAATATARFYVSLGIPHENITLCDIDGV
| + | [[Image:cs8.jpg]] |
| − | LSESRAEAGGLDEYAEPFARGVDDGDLEDAIEGADVLVGLSVGGIVSQEMVRSMADDPI
| |
| − | IFAMANPEPEIAYEDAKEARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EEMKRAAAEALANLARQDVPDAVVKAYGDGPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
| |
| − | AMESGAARRVRDLDAYREELEARLGKSREMMRVVLNKAASNPKRVVLAEGEDEKMIRAA
| |
| − | SQLVEEGIAEPILVGRTKEILRTAEELGLDFDPTIADPESGEWNHYVDHLYERRQRKGL
| |
| − | TRTEAAELVRSDSNYFASVMVAMGDADAMLTGLTHHYPSALRPPLQIIGTADDADYAAG
| |
| − | VYMLTFRNRVVFCADATVNLDPDQNVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVT
| |
| − | NEGTRKPRNAVEQLHADPDVDFPVDGEMQADTALVEEMLTDTYDFAELDEPANLLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPILVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQAE
| |
| | | | |
| − | Haloferax volcanii ATCC 29605
| |
| − | MGLDDDSRKYHRQDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
| |
| − | LDIAEDEDAAYEYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVELDIADVDDFVAATKAMEPTFGGINLEDIKAPECFEIERQLREQMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADIVDKDLDELDIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
| |
| − | ITESRVEDGDVNKYKAEFAKPVDEGSLSDAMEGADVLAGLSVGGIVSQEMVRSMADNPV
| |
| − | IFAMANPDPEITYEDAKDARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGADYVIPKPLDPRVLFEVAPAVAQA
| |
| − | AMTSGAARERLDMNAYREELEARLGKSREMMRVVLNKAKSNPKRVALAEGEDEKMIRAA
| |
| − | YQMQEEGIAEPILVGETTTILRKAEELGLDFDPTIANPRDGEWDHYVDRLYELRQRKGV
| |
| − | TNSEAEELVRRDSNYFASVMVEVGDADAMLTGLTHHYPSALRPPLQIIGTADDADYAAG
| |
| − | VYMMTFKNRVVFCADTTVNLDPDEEVLAEITKHTADLARQFNVEPRAALLSYSNFGSVT
| |
| − | NEGTRKPRDAAALLQDDPEVDFPVDGEMQADTALVEDILEGTYDFAELDGPANVLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQEE
| |
| | | | |
| − | MTLGDDARDYHRRPPAGKVEIATTKPTNTQRDLSLAYSPGVAAPC
| + | '''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)''' |
| − | RDIAEDENAAYEYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
| |
| − | FDVEFDHDDPQAFVESVAAMEPTFGGINLEDIRAPECFEIEESLRERMDIPVFHDDQHG
| |
| − | TAIISGAALLNAADIADKELSSLNVTFSGAGAAATATARFYVSLGIPHENITLCDIDGV
| |
| − | LSESRAEAGELDEYAEPFARGVDDGDLEDAMEGADVLVGLSVGGIVSQETVRSMADDPI
| |
| − | IFAMANPEPEIAYEDAKEARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
| |
| − | EEMKRAAAEALANLARQDVPDAVVKAYGDGPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
| |
| − | AMKSGAARRERDLDDYREELEARLGKSREMMRVVLNKAASNPKRVVLAEGEDEKMIRAA
| |
| − | SQLVEEGIAEPILVGRTKEILRTAEDLGLDFDPTIADPESGEWNHYVDHLYERRQRKGL
| |
| − | TRTEAAELVRGDSNYFASVMVEVGDADAMLTGLTHHYPSALRPPLQIIGTADDADYAAG
| |
| − | VYMLTFRNRVIFCADATVNLDPDENVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVT
| |
| − | NEGTRKPRNAVEQLHADPDVDFPVDGEMQADTALVEEMLTDTYDFAELDDPANVLVFPN
| |
| − | LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQSE
| |
| | | | |
| − | Halorhabdus utahensis
| + | Is there any section of the salt-loving protein sequences that coincide as compared to non-salt-loving organisms. |
| | | | |
| − | Aspartate Carbamoyltransferase:
| + | [[Citrate Synthase]] |
| | | | |
| − | Haloarcula californiae ATCC 33799
| + | 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. |
| − | MRHDHIISAKQLSRGDIETVLDHAADIAADPGAFADRHSDTLLGL
| |
| − | LFFEPSTRTKMSFTTAMKRLGGDIVDMGSVESSSVKKGESLADTVRVVEGYTDALVLRH
| |
| − | PMEGSAKMASEFVDVPLVNAGDGAGQHPTQTLLDLYTIRENAGFDDLTIGIMGDLKYGR
| |
| − | TVHSLAHALTTVDASQHFISPESLQLPRSVRYDLHEAGAGIREHTELDDILPELDVLYV
| |
| − | TRIQAERFPDESEYREVAGQYQIDGD
| |
| | | | |
| − | Haloarcula sinaiiensis ATCC 33800
| + | [[Aspartate Carbamoyltransferase]] |
| − | MRHDHIISAKQLSRGDIETVLDHAADIAADPGAFADRHSDTLLGL
| |
| − | LFFEPSTRTKMSFTTAMKRLGGDIVDMGSVESSSVKKGESLADTVRVVEGYTDALVLRH
| |
| − | PMEGSAKMASEFVDVPLVNAGDGAGQHPTQTLLDLYTIRENAGFDDLTIGIMGDLKYGR
| |
| − | TVHSLAHALTTVDASQHFISPESLQLPRSVRYDLHEAGAGIREHTELDDILPELDVLYV
| |
| − | TRIQAERFPDESEYREVAGQYQIDGDTLAAAKDDLTVMHPLPRVDEIAHDVDETTHAQY
| |
| − | FQQAHNGVPVRMALLDLMLGGDQ
| |
| | | | |
| − | Haloarcula vallismortis ATCC 29715
| |
| − | MRHDHIISAKQLSRGDIETVLDHAADIAADPGAFANRHSDTLLGL
| |
| − | LFFEPSTRTKMSFTTAMKRLGGDIVDMGSVESSSVKKGESLADTVRVVEGYTDTLVLRH
| |
| − | PMEGSAKMASEFVDVPLVNAGDGAGQHPTQTLLDLYTIRENAGFEDLTIGIMGDLKYGR
| |
| − | TVHSLAHALTTVDARQHFISPESLQLPRSVRYDLHEAGAGIREHTDLDEILPDLDVLYV
| |
| − | TRIQAERFPDESEYREVAGQYQIDADTLAAAKDDLTVMHPLPRVDEIAHDVDETTHAQY
| |
| − | FQQAHNGVPVRMALLDLMLGGDQ
| |
| | | | |
| − | Haloferax denitrificans ATCC 35960
| |
| − | MRQDHLISASHLSREDIEAVLDRAADIDADPAAFRQRHAGKVLGL
| |
| − | CFFEPSTRTRMSFDSAMKRLGGQTVDMGPVESSSVKKGETLADTVRVVEGYADALVLRH
| |
| − | PSEGAATMAAEFVDVPLVNAGDGAGQHPSQTLLDLYTIRENAGLDDLTIGIMGDLKYGR
| |
| − | TVHSLAEALTNFDASQHFISPESLRLPRNVRYDLHASGAQVREHTELDEVLPELDVLYV
| |
| − | TRIQRERFPDENEYRKVAGQYQIDSETLDAASDDLTIMHPLPRVDEISPDIDDTDHATY
| |
| − | FEQAHNGIPVRMALLDILLSQDR
| |
| | | | |
| − | Haloferax mediteranei ATCC 33500
| |
| − | MRQDHLISAAHLSREDIEAVLDRAAEIDDDTAAFRQRHAGKVLGL
| |
| − | CFFEPSTRTRMSFDTAMKRLGGQTVDMGPVESSSVKKGETLADTVRVVEGYADALVLRH
| |
| − | PSEGAATMAAEFVDVPLVNAGDGAGQHPSQTLLDLYTIRENAGLDDLTIGIMGDLKYGR
| |
| − | TVHSLAEALTNFDASQHFISPESLRLPRNVRYDLHASGAQVKEHTELDEVLPELDVLYV
| |
| − | TRIQRERFPDENEYRKVAGQYQIDAETLKAASDDLTVMHPLPRVDEISPDIDDTDHATY
| |
| − | FEQAHNGIPVRMALLDILLSQADD
| |
| | | | |
| − | Haloferax mucosum ATCC BAA-1512
| |
| − | MRQDHLISAAHLSREDIEAVLDRAAEIDDDTAAFRQRHAGKVLGL
| |
| − | CFFEPSTRTRMSFDTAMKRLGGQTVDMGPVESSSVKKGETLADTVRVVEGYADALVLRH
| |
| − | PSEGAATMAAEFVDIPLVNAGDGAGQHPSQTLLDLYTIRENAGLDDLTIGIMGDLKYGR
| |
| − | TVHSLAGALTNFDVSQHFISPESLRLPRNVRYDLHAAGAQVKEHTQLDDVLPELDVLYV
| |
| − | TRIQRERFPDENEYRKVAGQYQIDAETLEAATDDLTVMHPLPRVDEISPDIDDTDHATY
| |
| − | FEQAHNGIPVRMALLDILLSQADD
| |
| | | | |
| − | Haloferax sulfurifontis ATCC BAA-897
| + | '''7). Look for similarities between the genes for these 3 enzymes that are salt dependent.''' |
| − | MPGDSSRCRSRHSSMRQDHLISASHLSREDIEAVLDRAADIDADP
| |
| − | AAFRQRHAGKVLGLCFFEPSTRTRMSFDSAMKRLGGQTVDMGPVESSSVKKGETLADTV
| |
| − | RVVEGYADALVLRHPSEGAATMASEFVDVPLVNAGDGAGQHPSQTLLDLYTIRENAGLD
| |
| − | DLTIGIMGDLKYGRTVHSLAEALTNFDASQHFISPESLRLPRNVRYDLHASGAQVREHT
| |
| − | ELDEVLPELDVLYVTRIQRERFPDENEYRKVAGQYQIDSETLEAASDDLTIMHPLPRVD
| |
| − | EISPDIDDTDHATYFEQAHNGIPVRMALLDILLSQDDD
| |
| | | | |
| − | Haloferax volcanii ATCC 29605
| + | ClustalW Multiple Alignment between all three enzyme protein sequences for our species: |
| − | MRQDHLISASHLSREDIEAVLDRAADIDADPAAFRQRHAGKVLGL
| |
| − | CFFEPSTRTRMSFDSAMKRLGGQTVDMGPVESSSVKKGETLADTVRVVEGYADALVLRH
| |
| − | PSEGAATMAAEFVDVPLVNAGDGAGQHPSQTLLDLYTIRENAGLDDLTIGIMGDLKYGR
| |
| − | TVHSLAEALTNFDASQHFISPESLRLPRNVRYDLHASGAQVREHTELDEVLPELDVLYV
| |
| − | TRIQRERFPDENEYRKVAGQYQIDSETLDAAADDLTIMHPLPRVDEISPDIDDTDHATY
| |
| − | FEQAHNGIPVRMALLDILLSQDR
| |
| | | | |
| − | Halorhabdus utahensis
| + | [[Image:cwdata4.jpg]] |
| | + | [[Image:cwdata5.jpg]] |
| | + | [[Image:cwdata6.jpg]] |
| | | | |
| − | 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)
| |
| | | | |
| − | 7). Look for differences in predicted protein structure and potential amino acid bias. (ClustalW)
| + | ClustalW Multiple Alignment between all three enzyme protein sequences in the species studied in the paper (H. salinarium) |
| | | | |
| − | 8). Look for similarities between the genes for these 3 enzymes that are salt dependent.
| + | [[Image:cwdata10.jpg]] |
| | + | [[Image:cwdata11.jpg]] |
| | + | [[Image:cwdata12.jpg]] |
I am interested in exploring the genetic make up of enzymes that have been previously identified as being "salt dependent" for activity- such as citrate synthase, malic enzyme and aspartae transcarbamylase (which are all found in our species' genome).
>fig|485914.5.peg.3029 [Halomicrobium mukohataei DSM 12286] [Citrate synthase (si) (EC 2.3.3.1)]
MSDDLKQGLEGVLVTESELSKIDGDAGKLVYRGYTIEDLATGASFEEVLY
LLWHGHLPNAAELDEFTDAMVEERHVDDDVMQTVEQLADADENPMAALRT
AVSMLSSHDPDAETDPTDLDANLRKGRRITAKIPTVLAAFARFRDGQDAV
EPREDLSHAANFLYMLNGEAPDEVLAETFDMALVLHADHGINASTFSAMV
TASTLSDLHSAITSAIGTLKGSLHGGANQDVMEMLKEVDDAQQDPIDWVK
TALDEGRRVSGFGHRVYNVKDPRAKILSQRSKELGEAAGSLKWYEMSTAI
EDYLKAEKGLAPNVDFYSASTYYQMGIPIDIYTPIFAMSRVGGWTAHVLE
QYENNRLIRPRARYVGPTDQTFVPLDER
>fig|485914.5.peg.2113 [Halomicrobium mukohataei DSM 12286] [NADP-dependent malic enzyme (EC 1.1.1.40)]
MGLDEDALDYHGRAPPGKIEIATTKPTNTQRDLSLAYSPGVAAPCEAIHE
TPEDAFKYTARGNLVAVVSDGSAVLGLGDIGPEASKPVMEGKGVLFKRFA
DIDVFDLELDTDDPDAMIEAVDAMGPTFGGINLEDIAAPACFEIERELRE
RMDVPVFHDDQHGTAIISGAALLNAADIVDKELEEMEIVFSGAGASAIAS
ARFYVSLGVRKENITMCDSSGIITADRVENDGLNRYKAEFASEGTGGDLA
DALAGADAFVGLSVGGVVDEAMVRSMASEPIIFAMANPDPEIDYETAKAA
RDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEINEEMKVAAARA
LARLARQDVPDAVVKAYGDQPLQFGPEYIIPKPLDPRVLFEVTPAVAEAA
MDSGAARKSIDLDDYVERLEARLGKSREMMRVVLNKAKSDPKRVVLAEGD
DEKMIRAAYQLIEQGIAEPVLLGDRDRISAITDTLGLAFEPEIVDPDEGG
LDEYADRLYELRQRKGVTRREADELVTDGNYLGSVMVEMGDADAMLTGLT
HHYPSALRPPLQIVGTAPEAEYAAGVYMLTFRNRVVFCADTTVNTDPDAD
VLTEVTRHTAELARRFNVEPRAAMLSYSNFGSVDSPSTRAPRRAAERLRE
DPATDFPVDGEMQADTAVVEDILQGTYEFSELDDPANVLVFPSLEAGNIG
YKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNMAGVAVVDAQDD
>fig|485914.5.peg.1562 [Halomicrobium mukohataei DSM 12286] [Aspartate carbamoyltransferase (EC 2.1.3.2)]
MRQDHIISAKQLSRRDIEAVLDRAAEIAADPSAYADRHEGSLLGLLFFEP
STRTKMSFSAAMKRLGGDIVDMGTVESSSVKKGESLADTVRVVEGYADAL
VLRHPSEGAAQMASEFVDAPLINAGDGAGQHPTQTLLDLYTIRENAGFDD
LSIGIMGDLKYGRTVHSLAHALTVFDARQHFVSPESLQLPRSVRYDLHES
GAEVREHTDLDDVLSELDVLYVTRIQKERFPDESEYHEVAGEYQIDAATI
REHNEDLTVMHPLPRVDEIDHDVDELDGAQYFQQAHNGVPVRMALLDMVL
EESR
The two citrate synthase genes annotated from RAST are the same gene. . . below are the nucleotide blast alignment results:
The citrate synthase gene from JGI matches the citrate synthase genes from RAST, nucleotide blast alignment dot plot is below:
The aspartate carbamoyltransferase regulatory gene sequences are a 100% match between the two annotation services.
The aspartate carbamoyltransferase gene sequences are the same between both annotation services as well.
The malic enzyme genes are 100% the same between the two annotation services as well.
I also checked to see if the aspartate carbamoyltransferase regulatory subunit was part of the aspartate carbamoyltransferase gene but it was not as confirmed by blastn with alignment and the nucleotide base regions where the gene occurs.
Citrate Synthase blasted against our genome using Genome Portal: Two hits that are small but maybe a conserved region between the three enzymes that makes them salt dependent. Note that the subject alignments do not fall within any of the other two genes we are studying and thus this correlated sequence within our species' genome is not from one of the other salt dependent enzyme genes.
Aspartate carbamoyltransferase regulatory unit blasted against out species' genome using Genome Portal, results are below: (no other hits besides the original gene)
3). Note the pathways and systems that these genes play a role in
Found two possible sequences in H. salinarium's genome for malic enzyme: 1). malate dehydrogenase and 2).malate dehydrogenase (oxaloacetate decarboxylating) / phosphate acetyltransferase:
The second malic enzyme sequence is most similar to our species' in length but both comparisons are shown below.
Citrate Synthase ClustalW with all of the species listed above along with a dendogram and an N-J Tree
Is there any section of the salt-loving protein sequences that coincide as compared to non-salt-loving organisms.
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.
ClustalW Multiple Alignment between all three enzyme protein sequences for our species:
