Difference between revisions of "Citrate Synthase"

Latest revision as of 23:58, 6 October 2009

I did a blastp search using our species' citrate synthase protein sequence.

The following halophillic Archaea were the top hits and are accompanied by their basltp results:

Haloarcula marismortui citrate synthase protein sequence:

        1 msddlkkgle gvivaesels vidgdagklv yrgytiedla kgasyeevly llwhghlpnr
      61 delsefkqam vdargvdddv istvrqlaea denpmaalrt avsmlsafdp apedaeptde
     121 mvnletgrri takiptiiaa ftrirdgkep vephddldha anflymlnge epddvladvf
     181 dqalvlhadh glnastfsai ttastlsdvh savtsaigtl kgplhgganq dvmemlkevd
     241 daesdpldwv knaldegrrv sgfghrvynv kdprakilge rskelgeaag tlkwyemstt
     301 iedylmeekg lapnvdfysa styyqmgipi diytpifams rvggwvahvf eyiednrlir
     361 praryvgknt detefvplde r

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:

       1 msdelkkgle gvlvaessls yidgdegklv yrgytiddla rnasfeevvy llwhgelpta
      61 delgsfkssm aeerhlddgv qqlvrelaea deepmaalrs ivsslsaydp dadaeptdea
     121 anlrkgrrit akiptalaaf sriregddpv epredldhaa nflymlngee pdevladtfd
     181 malvlhadhg lnastfsamv tsstladlha aitsavgals gslhgganqd vmeallelde
     241 sgkepvewve drldagervp gfghrvynvk dprakilsee sealgeaagt pqwhnystei
     301 eeylteekgl apnvdfysas tyyqmgipvd iytpifamsr vggwiahvle qyddnrlirp
     361 rgryvgpddr tvtpider

Halogeometricum borinquense citrate synthase protein sequence

       1 msddlkrgle gvlvaesels yidgdagqlv yrghtiedla rnasyeevvy llwhgelptr
      61 eqldefstam aeerelddav ldeiralaaa devpmaalrt ivsslsaydd dadhedvtdl
     121 ktnikkgcri takiptalaa fnrlrngedv vhprtdlsha anflymlnge epddvlaetf
     181 dmalvlhadh glnastfsam vtastlsdlh savtsaigtl agslhggana nvmrmlkeid
     241 esdkdptqwv edalesgrrv pgfghrvynv kdprakilge ksealgeaag dmkwydysva
     301 iedyigeekg lapnvdfysa styyqmgipv diytpifams rvggwiahvi eqfednrlir
     361 praryvgred qtftpider

Haloferax volcanii citrate synthase protein sequence

       1 msgelkrgle gvlvaeskls fidgdagqlv ycgydiedla rdasyeevly llwhgalptg
      61 eeldafsdel aahrdlddgv ldvarelaeq despmaalrt lvsamsayde sadfedvtdr
     121 evnlekakri takmpsvlaa yarfrrgddy vepdeslnha anflymlnge epnevlaetf
     181 dmalvlhadh glnastfsam vtsstlsdly savtsaigtl sgslhggana nvmrmlkdvd
     241 dsdmdptewv kdaldrgerv agfvhrvynv kdprakilga ksealgeaag dmkwyemsva
     301 ieeyigeekg lapnvdfysa styyqmgipi dlytpifavs raggwiahvl eqyednrlir
     361 prarytgekd ldftpvder

Haloquadratum walsbyi citrate synthase protein sequence

       1 msdevkrgle dvlvaesels cidgdagelv yrgysiedla qkasyeevvy llwhgrlptg
      61 delqsftdam ieertintgv yeqierlaaa despmaalrt ivstlsaydp dadaevidhe
     121 anarkarria aklptalaal qrcregndpv tprsdldhaa nflymlngse pdpvlaetfd
     181 malvlhadhg lnastfsakv tastlsdlhc aittavgtls gslhgganan vmrmlkevha
     241 sdadavtwie dalesgrrvp gfghrvynvk dprarilger skelaeaage mcwynysiti
     301 eeyiddhkgl apnvdfysas tyyqmgipid iytpifamar tagwiahtfe qydenrlirp
     361 raryvgneda tfksvekr

Halobacterium salinarum citrate synthase protein sequence:

       1 msdelkkgle dvlvaesdls fidgdagklv ycgyaiedla rtasyeevly llwhgdlptr
      61 seldafradm ashreidddv lalvenlaaa dadpmaalrt aasalsahdd taggsdpdda
     121 resgkritak lptivaaftr lrngddvvap rddlghaanf lymlngeapd dvladvfdqa
     181 lvlhadhgln astfsgmvta stladvhaav tsaigtlsgs lhggananvm rmlkevddsd
     241 kdplswvqda langervmgf ghrvynvkdp rahilserse elgaaagdtk wyemsvaied
     301 ymadekglap nvdfysasty yqmgipvdiy tpifamsrvg gwvghvleqy ddnrlirpra
     361 ryvgaedrds tplder

Halorhabdus utahensis

       1 mpdelrkgle gvlvaessls didgeegrlv yrgyaiedla rntsfeevly llweghlpte
      61 selepfeeqm aeeravreev lstvrelaaa eenpmaalrt avsmlsaydp ddstgeagdg
     121 eiaqrkgrri takmptivaa ykrlrdgeep vaprtdlsha enflymlnge epaqtladvf
     181 dmalvvhadh ginastfaam vtastlsdlh ssvtsaigal kgglhgganq nvmqmlleld
     241 esdltavewa reavesgdri pgfghrvydv kdprarilsa kskalgkaad elkwysysra
     301 ieefmaketg iapnvdfysa smyyemgipi dlytpifams rvggwvahvl eyqeenrlir
     361 praryvgped refvrieqr

Halorubrum lacusprofundi

>Halorubrum lacusprofundi ATCC 49239
MSDELKRGLEGVLVAESDLSYVDGEVGKLVYRGYDIEDLARGASYEEVLYLLWRGSLPTREELDAFTADL
AAERAVDDDALDAVRTLADAGERPMAALRTAVSMLSAYEPESDADPEDLDATLRQGRRITAKIPTLLAAF
ERARQGEDPVAPDPDLSHAANFLYMLTGTEPDDVSAETFDMALTLHADHGLNASTFTAIVIGSTMADVYS
GVTGGIGALSGPLHGGANQDVMEVLQEVDASDKDPVQWVKDAREEGRRIPGFGHRVYKVKDPRAKILEEK
LRDLSESSGDTKWLDYTTAIEEYLTEQGLLDKGIAPNVDFYSGSVYDSLGIPVDMYTPIFAMSRAGGWIA
HMVEYQEDNRLIRPRARYTGPKASEFVPVDER

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- 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

       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

ClustalW Alignment of Salt-Loving Organisms:

The following is a salt-tolerant bacteria:

Oceanobacillus iheyensis citrate synthase protein sequence:

       1 mtastkgleg ivatqssiss iiddqlsyvg yriddlaens sfeeiiyllw nqklpnksel
      61 delksqlaen mdipdaiinh lrsydlntvh pmaalrtais llglydnead vmdeqankrk
     121 avriqaqiat ivttfsrirk gqepvkpkkd lsyaenfiym lngkepedie veainkalvl
     181 hadhelnast ftarvcvatl sdiysgitaa igalkgplhg ganenvmkml teigeeenai
     241 pyikeklank dkimgmghrv yrtgdprakf lremskeltk ltgqekwynm svkiedyike
     301 nkglpanvdf ysasvyhslg ldhdiftplf avsrtsgwia hileqyennr lirpraeytg
     361 pelrdyvsie qrg

The following non-salt loving prokaryotes were the top hits among their domain

Alicyclobacillus acidocaldarius- thermoacidiphillic bacterium citrate synthase protein sequence:

       1 maaettfkag ledvvsntse icfldgkqgr llyygydihd lvdggasfee vvyllwhgel
      61 pnqselkaft eelaserala epvldllkrl pkdanamavl rtavsflgly dpddgdesle
     121 anyrkaarlv akiptivtsy erirqgldpv qpdpslsaaa nffyllrgtk psefeekafn
     181 talilhadhe lnastfsarv tagtlsdmys aitsaigtlk gplhgganeq vmrmlleigd
     241 pskaitwide alaqkkkimg fghrvyrted prathlrels kqagelkget kwfemsqaie
     301 khmlevkglh anvdfysasl yyslgipthl ytpifacsri sgwtahvleq yknnrlirpr
     361 aeyvgptdrk fvplser

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

Bacillus cereus-endemic, soil-dwelling citrate synthase protein sequence

       1 mgefsgkgen vmtvirgleg vvattssvss iiddtltyvg yniddlaena tfeevvyllw
      61 hrklpnekel aefkdtvsey ykvpgeilty lkqvdlkiah pmsvlrtais mlslydesae
     121 imdgksnylk avklqaqvgt liaayarirk gldvveprkd lslaanflym lndrepneve
     181 ieafdkalvl hadhelnast ftarvcvatl sdvysgitaa igalkgplhg ganenvmkml
     241 teigeeenve syihnalqnk vkimgfghrv yehgdprakh lremskrlcv llgedkwynm
     301 sikiedivtk ekglppnvdf ysasvyhclg idhdlftpif aisrmsgwla hileqyennr
     361 lirpradyng pthqvyvpia qr

Bacillus thuringiensis- soil-dwelling bacterium, commonly used as a pesticide citrate synthase protein sequence

       1 mgefsgkgen vmtvirgleg vvattssvss iiddtltyvg yniddlaena tfeevvyllw
      61 hrklpnekel aefneivsey ykvpgeilty lkqvdlkvah pmsvlrtais mlslydesae
     121 imdeksnylk avklqaqvgt lvaayarirk gldiveprkd lslaanflym lnnrepneve
     181 ieafdkalvl hadhelnast ftarvcvatl sdvysgitaa igalkgplhg ganenvmkml
     241 teigeeenve syihnalqnk vkimgfghrv yeqgdprakh lremskrlcv llgedkwynm
     301 sikiedivtk ekglppnvdf ysasvyhclg idhdlftpif aisrmsgwla hileqyennr
     361 lirpradyng pthqvyvpia qr

Bacillus weihenstephanensis-non-pathogenic, Gram-positive, typical facultative psychrophile generally found in soil citrate synthase protein sequence:

       1 mtvirglegv vattssvssi iddtltyvgy niddlaenat feevvyllwh rklpnekela
      61 efsgtvseyy kvpgevltyl kqvdlkiahp msvlrtaism lslydesaei mdgksnylka
     121 vklqaqvgtl iaayarirkg ldvveprkdl slaanflyml ndrepnevei eafdkalvlh
     181 adhelnastf tarvcvatls dvysgitaai galkgplhgg anenvmkmlt eigeeenves
     241 yihnalqnkv kimgfghrvy ehgdprakhl remskrlcvl lgedkwynms ikiedivtke
     301 kglppnvdfy sasvyhclgi dhdlftpifa isrmsgwlah ileqyennrl irpradydgp
     361 thqvyvplaq r

Bacillus mycoides- soil dwelling citrate synthase protein sequence:

       1 mgefsgkgen vmtvirgleg vvattssvss iiddtltyvg yniddlaena tfeevvyllw
      61 hrklpnekel aefsgtvsey ykvpgevlty lkqvdlkiah pmsvlrtais mlslydesae
     121 imdgksnylk avklqaqvgt liaayarirk gldvveprkd lslaanflym lndrepneve
     181 ieafdkalvl hadhelnast ftarvcvatl sdvysgitaa igalkgplhg ganenvmkml
     241 teigeeenve syihnalqnk vkimgfghrv yehgdprakh lremskrlcv llgedkwynm
     301 sikiedivtk ekglppnvdf ysasvyhclg idhdlftpif aisrmsgwla hileqyennr
     361 lirpradydg pthqvyvpla qr

Geobacillus sp.- thermophilic bacterium citrate synthase protein sequence:

Bacillus anthracis citrate synthase protein sequence:

       1 mtvirglegv vattssvssi iddtltyagy niddlaenat feevvyllwh rklpneqela
      61 kfneivseyy kvpgeilayl kqvdlkiahp msvlrtaism lslydesaei mdeksnylka
     121 vklqaqvgtl vaayarirkg ldvveprndl slaanflyml ndrepnevei eafdkalvlh
     181 adhelnastf tarvcvatls dvysgitaai galkgplhgg anenvmkmlt eigeeenves
     241 yihnalqnkv kimgfghrvy eqgdprakhl remskrlcvl lgeekwynms ikiedivtke
     301 kglppnvdfy sasvyhclgi dhdlftpifa isrmsgwlah ileqyennrl irpradyngp
     361 thqvyvpiaq r

Bacillus methanolicus citrate synthase protein sequence:

Bacillus subtilis citrate synthase protein sequence:

       1 mtatrglegv vattssvssi iddtltyvgy diddltenas feeiiyllwh lrlpnkkele
      61 elkqqlakea avpqeiiehf ksyslenvhp maalrtaisl lglldseadt mnpeanyrka
     121 irlqakvpgl vaafsrirkg lepvepredy giaenflytl ngeepspiev eafnkalilh
     181 adhelnastf tarvcvatls diysgitaai galkgplhgg anegvmkmlt eigevenaep
     241 yiraklekke kimgfghrvy khgdprakhl kemskrltnl tgeskwyems iriedivtse
     301 kklppnvdfy sasvyhslgi dhdlftpifa vsrmsgwlah ileqydnnrl irpradytgp
     361 dkqkfvpiee ra

Exiguobacterium

>Exiguobacterium sp. AT1b]
MSTTKGLEGIVAAASKVSSIIDGQLTYGGYTIDDLADNATFEEVVFLLWNDRLPNAEELTALSEALVKEA
TLPEEVIDTLKRAPKSANAMATIRTALSQLALYDEESEDMSDEANMRKAIRLQAQVATIVTAFARLRKGE
QPVAPKPGLSYAANFLYMLNGEEPSDVAEKTIDKALILHADHELNASTFTARVCVATLSDMYSGVTAAMG
ALKGPLHGGANEAVMKMLHEIDSVDRVEEYVRGKFERKEKIMGFGHRVYKDGDPRAKHLKEMSRQLTAQI
GEPKWYEMSEKIDHLVETEKGLKPNVDFYSASTYYALGLEEDLFTPIFAVSRMSGWIAHILEQYADNRLI
RPRAEYVGETSRKYVPVNER

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.