Katie's Assignment

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).

Why/How did I pick these three enzymes?

JGI Genes:

Citrate Synthase JGI: 2916896..2918032 (+) (1137bp). . . nucleotide sequence

Allosteric NADP-dependent Malic Enzyme 2055313..2057565 (+) (2253bp) . . . nucleotide sequence

Aspartate carbamoyltransferase regulatory subunit: 1503175..1503639 (-) (465bp). . . sequence

carbamoyltransferase: 1503636..1504550 (-) (915bp) . . . sequence

RAST Genes:

Citrate Synthase TCA Cycle. . . sequence . . . protein sequence

>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

Citrate Synthase Glyoxylate Synthesis . . . protein sequence

NADP-dependent malic enzyme. . . protein sequence

>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

Aspartate carbamoyltransferase

>fig|485914.5.peg.1562 [Halomicrobium mukohataei DSM 12286] [Aspartate carbamoyltransferase (EC 2.1.3.2)] MRQDHIISAKQLSRRDIEAVLDRAAEIAADPSAYADRHEGSLLGLLFFEP STRTKMSFSAAMKRLGGDIVDMGTVESSSVKKGESLADTVRVVEGYADAL VLRHPSEGAAQMASEFVDAPLINAGDGAGQHPTQTLLDLYTIRENAGFDD LSIGIMGDLKYGRTVHSLAHALTVFDARQHFVSPESLQLPRSVRYDLHES GAEVREHTDLDDVLSELDVLYVTRIQKERFPDESEYHEVAGEYQIDAATI REHNEDLTVMHPLPRVDEIDHDVDELDGAQYFQQAHNGVPVRMALLDMVL EESR

Aspartate carbamoyltransferase regulatory chain

Main Tasks

1). Are the genes different between the annotation services?

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.

2). Look for other genes in our species' genome that are similar and may have been missed during annotation

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.

Malic Enzyme blasted against our species' genome using Genome Portal: Three hits shown below:

Aspartate carbamoyltransferase blasted against our species' genome using Genome Portal, results are below: (no 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)

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

4). Look at the sequences from the halophile studied in the article as compared to these gene sequences Lanyi in his paper, "Salt- Dependent Properties of Proteins from Extremely Halophilic Bacteria ," explores multiple enzymes that require salt to function properly. The three I have choosen to study: citrate synthase, malic enzyme and asparatate transcarbamylase, were isolated from H. cutirubrum. I had difficulty finding H. cutirubrum sequences in NCBI so I did some background research and discovered that H. cutirubrum is a specific strain of the H. salinarium species. According to Ventoso and Oren, there is no difference between this strain and the H. salinarium species.

The H. salinarium genome webpage outlines the three genes and below are the gene sequences:

Citrate Synthase . . . Protein Sequence and Information about the Protein

Found two possible sequences in H. salinarium's genome for malic enzyme: 1). malate dehydrogenase and 2).malate dehydrogenase (oxaloacetate decarboxylating) / phosphate acetyltransferase:

Malate Dehydrogenase (malic enzyme) . . .Protein Sequence and Information about the Protein

Malate Dehydrogenase (oxaloacetate decarboxylating) / phosphate acetyltransferase. . .Protein Sequence and Information about the Protein

The second malic enzyme sequence is most similar to our species' in length but both comparisons are shown below.

Aspartate Carbamoyltransferase . . . Protein Sequence and Information about Protein

Comparison of Each Enzyme's Protein Sequences using blastp and clustalW. . .

Citrate Synthase Sequences:

Malic Enzyme Sequences: (Query=our species' malic enzyme protein sequence and Subject= H. salinarium malic enzyme sequence) Malate Dehydrogenase:

Malate Dehydrogenase (oxaloacetate decarboxylating) / phosphate acetyltransferase:

Aspartate Carbamoyltransferase Sequences: (Query= our species' and Subject=H. salinarium aspartate carbamoyltranserase enzyme protein sequence)

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.

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 Haloferax volcanii ATCC 29605 Halorhabdus utahensis

Malic Enzyme:

Haloarcula californiae ATCC 33799

                  MGLDEDALEYHRSKPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
                  EEIDKDPEKAFEYTAKGNLVGVVSDGSAVLGLGDIGPEAGKPVMEGKGVLFKRFADIDV
                  FDVELDTDNAEAMIQTVEAMEPTFGGINLEDIAAPECFEVERRLSEKLDIPVFHDDQHG
                  TAIISGAALVNAADIADKELDELEVVFSGAGASAIASAKFYVSLGVSKDNITMCDSSGI
                  ITEERANHEELNRFKQEFARDIPEGGLADAMDGADVFVGLSVGGIVDQEMVRSMASDPI
                  IFAMANPDPEIAYEDAKAARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
                  EEMKVAAARALADLARQDVPDEVVKAYGDQPLQFGPDYIIPKPLDPRVLFEVTPAVAEA
                  AIESGAARTELDTAAYVEELEARLGKSREMMRVVLNKAKSDPQRVVLAEGHDEKMIRAA
                  YQLVEQGIAEPILIGDADRIESTRRKFGLEFDPVVVDPETADVADYADRLYELRQRKGV
                  TRREADELIRDGNYLGSVMVEMGDADAMLTGLTHHYPSALRPPLQVIGTADDADYAAGV
                  YMLTFKNRVIFCADTTVNQDPDTDVLEEVTRHTGELARRFNVEPRAAMLSYSNFGSVDN
                  LGTKKIRRAVSRLQDDDRVDFPVDGEMQADTAVVEDILQDTYEFSELDDPANVLVFPNL
                  EAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGVAVVDAQ

Haloarcula sinaiiensis ATCC 33800

                  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

                  MTLEDDARDYHRRPPSGKIEIATTKPTNTQRDLSLAYSPGVAAPC
                  LDIADDETVAYDYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
                  FDVELGLDDPESFVQAVAAMEPTFGGINLEDIKAPECFEIEAGLRDEMSIPVFHDDQHG
                  TAIISGAALLNAVDIADKDRSSLQVTFAGAGAAATATARFYVSLGIPRENITMCDIDGI
                  LSERRADAGDLNEYTEPFARGVDDGELEDAMEGADVFVGLSVGGIVSQDMVRSMADNPI
                  IFAMANPDPEITYEDAKNARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
                  EAMKRAAAEALANLARQDVPDAVVKAYGDEPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
                  AMESGAARRERDLDAYREELEARLGKSREMMRVVLNKAKSDPKRVALAEGEDEKMIRAA
                  SQLVEDGIAEPILIGRTTEILRTAEELGLDFDPTIANPHDGEWNHYVDHLYEQRQRKGL
                  TRTEAAELVQQDSNHFASVMVDIGDADAMLTGLTHHYSSALRPPLQLIGTAEDATYAAG
                  VYMLTFRNRVIFCADATVNLDPDEEVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVN
                  NAGTAKPQNAVKRLHDDPDVDFPVDGEMQADTALVEEMLTDTYDFTELDGPANVLVFPN
                  LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGIAVVDAQE

                  MGLDDDSREYHRRDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
                  RDIDEDEDAAYEYTAKGNLVGVVSNGTAVLGLGDIGSQASKPVMEGKGVLFKRFADIDV
                  FDVELDITDVDDFVAATKAMEPTFGGINLEDIKAPECFEIERQLRETMDIPVFHDDQHG
                  TAIISGAALLNAADVLGKDLEDLEIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
                  ITESRVSAGDVNKYKAEFAQDVEEGSLAHAMEGADVFAGLSVGGIVSQDMVRSMADNPI
                  IFAMANPDPEITYEDAKNARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
                  EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDPRVLFEVAPAVAQA
                  AMTSGAARERLDMNEYRERLEARLGKSREMMRVVLNKAKSDPKRVALAEGSNEKMIRAA
                  YQMQEEGIAEPILVGDTTTILRKAEELGLEFDPTIANPHDGEWNHYVDHLYERRRRKGL
                  TRTEAAELVQQDSNYFASVMVSMDDADAMLTGLTHHYPSALRPPLQLIGTAEDANYAAG
                  VYMMTFKNRVVFCADTTVNLDPDEEILAEITKHTAELARRFNVEPRAALLSYSNFGSVR
                  NEGTAKPRDAARLLQNDPEVDFPVDGEMQADTALVEDILEGTYDFAELDDPANVLIFPN
                  LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQQE

Haloferax mucosum ATCC BAA-151

                  MGLDDDSREYHRRDPPGKIEIATTKPTNTQRDLSLAYSPGVAAPC
                  LDIDEDDDAAYEYTAKGNLVGVVSNGTAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
                  FDVELDITDVDEFVAATKAMEPTFGGINLEDIKAPECFEIEHQLREQMDIPVFHDDQHG
                  TAIISGAALLNAADIVKKDLDDLEIVFSGAGASALATARFYVSLGAKKENITMCDSSGI
                  ITQSRVEAGDVNTYKAEFAQPVDDGSLEDAMAGADVFVGLSVGGIVSQEMVRSMADNPI
                  IFAMANPDPEITYEDAKDARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
                  EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDPRVLFEVAPAVAQA
                  AMTSGAARERLDMNEYRERLEARLGKSREMMRVVLNKAKSDPKRVALAEGSNEKMIRAA
                  YQMQEEGIAEPILVGNTTSILRKAEELGLDFDPTIANPRDGEWDHYVDRLYELRKRKGI
                  TESEASELIRRDSNYFASIMVEIGDADAMLTGLTHHYPGGLRPPLQVIGTAEDANYAAG
                  VYMMTFKNRVVFCADTTVNLDPDEEVLAEITKHTAELARRFNVEPRAALLSYSNFGSVR
                  NEGTAKPRAAADILQNDPDVDFPVDGEMQADTALVEDILEGTYDFAELDDPANVLIFPN
                  LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAATAVVDAQQE

                  MTLEDDARDYHREPPSGKIEIATTKPTNTQRDLSLAYSPGVAAPC
                  LDIDEDDDAAYDYTAKGNLVGVVSNGSAVLGLGDIGAQASKPVMEGKGVLFKRFADIDV
                  FDVELDIADVDEFVAATKAMEPTFGGINLEDIKAPECFEIEHQLREQMDIPVFHDDQHG
                  TAIISGAALLNAADIADKELSSLNVVFAGAGAAATATARFYVSLGIPRENITMCDIDGV
                  LSEHRADTGDLNEYTEPFAQGVDDGSLEDAMVGADVFVGLSVGGIVSQEMVRSMADNPI
                  IFAMANPDPEITYEDAKDARDDTVIMATGRSDYPNQVNNVLGFPFIFRGALDVRATEIN
                  EAMKRAAAEALAELARQDVPDAVVKAYGDHPLQFGPDYLIPKPLDQRVLYEVTPAVAEA
                  AMESGAARRERDLDTYREELEARLGKSREMMRVVLNKAKSDPKRVVLAEGEDEKMIRAA
                  SQLVEDGIAEPILVGRTKEILRTAEELGLDFDPTIANPHEGEWNHYVEYLYEQRRRKGL
                  TRSEAAELVTQDSNYFASVMVAMDDADAMLTGLTHHYPSALRPPLQLIGTADDADYAAG
                  VYMLTFRNRVIFCADATVNLDPDENVLAEVTKHTAELARRFNVEPRAALLSYSDFGSVS
                  NEGAAKPQNAVARLHDDPDVDFPVDGEMQSDTALVEEMLTDTYDFTELDGPANVLVFPN
                  LEAGNIGYKLLQRLGGAEAIGPMLVGMDKPVHVLQRGDEVKDIVNLAGIAVVDAQ

Haloferax sulfurifontis ATCC BAA-897 Haloferax volcanii ATCC 29605 Halorhabdus utahensis

Aspartate Carbamoyltransferase:

Haloarcula californiae ATCC 33799

                  MRHDHIISAKQLSRGDIETVLDHAADIAADPGAFADRHSDTLLGL
                  LFFEPSTRTKMSFTTAMKRLGGDIVDMGSVESSSVKKGESLADTVRVVEGYTDALVLRH
                  PMEGSAKMASEFVDVPLVNAGDGAGQHPTQTLLDLYTIRENAGFDDLTIGIMGDLKYGR
                  TVHSLAHALTTVDASQHFISPESLQLPRSVRYDLHEAGAGIREHTELDDILPELDVLYV
                  TRIQAERFPDESEYREVAGQYQIDGD

Haloarcula sinaiiensis ATCC 33800

                  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 Haloferax volcanii ATCC 29605 Halorhabdus utahensis

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)

8). Look for similarities between the genes for these 3 enzymes that are salt dependent.

Katie's Assignment

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