Multiple Sequence Alignment of MLH1 protein.
- To do Multiple Sequence Alignment in Biology Workbench
- To draw phylogenetic tree from alignment

1. Add MLH1_Human protein to the Biology Workbench. Predict its secondary structure by GOR4.

>MLH1_HUMAN

Sequence   MSFVAGVIRR LDETVVNRIA AGEVIQRPAN AIKEMIENCL DAKSTSIQVI

Structure  CCCCEEEEEE CCHHHHHHHH HCHHHHHHHH HHHHHHHHHC CCCCCCHHHH

Sequence   VKEGGLKLIQ IQDNGTGIRK EDLDIVCERF TTSKLQSFED LASISTYGFR

Structure  HHHCCCEEEE ECCCCCCCHH HHHHHHHCCC CCCCCCCCHH HHHHCCCCCC

Sequence   GEALASISHV AHVTITTKTA DGKCAYRASY SDGKLKAPPK PCAGNQGTQI

Structure  CCHHHHHHHE EEEEEEECCC CCCCEEEECC CCCCCCCCCC CCCCCCCCEE

Sequence   TVEDLFYNIA TRRKALKNPS EEYGKILEVV GRYSVHNAGI SFSVKKQGET

Structure  EEHHHHHHHH HHHHHHCCCC HHHHHEEEEE ECCCCCCCCE EEEECCCCCE

Sequence   VADVRTLPNA STVDNIRSIF GNAVSRELIE IGCEDKTLAF KMNGYISNAN

Structure  EEEEEECCCC CCCCCEEEEC CCCCCHHHHH HCCCHHHHHH CCCCCEECCC

Sequence   YSVKKCIFLL FINHRLVEST SLRKAIETVY AAYLPKNTHP FLYLSLEISP

Structure  CCCCCEEEEE ECCCCHHHHH HHHHHHHHHH HHCCCCCCCC EEEECCCCCC

Sequence   QNVDVNVHPT KHEVHFLHEE SILERVQQHI ESKLLGSNSS RMYFTQTLLP

Structure  CCCCEEECCC CCHHHHHHHH HHHHHHHHHH HHHHHCCCCC CEEEEEEECC

Sequence   GLAGPSGEMV KSTTSLTSSS TSGSSDKVYA HQMVRTDSRE QKLDAFLQPL

Structure  CCCCCCCCEE EEEEEEEEEC CCCCCCHHHH HHHHHHHHHH HHHHHHHCCC

Sequence   SKPLSSQPQA IVTEDKTDIS SGRARQQDEE MLELPAPAEV AAKNQSLEGD

Structure  CCCCCCCCCE EECCCCCCHH HHHHHHHHHH HHHCCCHHHH HHHHHCCCCC

Sequence   TTKGTSEMSE KRGPTSSNPR KRHREDSDVE MVEDDSRKEM TAACTPRRRI

Structure  CCCCCCHHHC CCCCCCCCCC CCCCCCCCHH HHHHHHHHHH HHHCCCCCEE

Sequence   INLTSVLSLQ EEINEQGHEV LREMLHNHSF VGCVNPQWAL AQHQTKLYLL

Structure  ECCCCHHHHH HHHHHHHHHH HHHHHCCCCE EEEECCCCHH HHHHHHHHHH

Sequence   NTTKLSEELF YQILIYDFAN FGVLRLSEPA PLFDLAMLAL DSPESGWTEE

Structure  HCCCCHHHHH HHHHHHCCCC CCEECCCCCC CHHHHHHHHC CCCCCCCCCC

Sequence   DGPKEGLAEY IVEFLKKKAE MLADYFSLEI DEEGNLIGLP LLIDNYVPPL

Structure  CCCCCCHHHH HHHHHHHHHH HHHHHHHHHH HHCCCCCCCC EEECCCCCCC

Sequence   EGLPIFILRL ATEVNWDEEK ECFESLSKEC AMFYSIRKQY ISEESTLSGQ

Structure  CCCCHHHHHH HHHHCHHHHH HCCCCCCCCC HHHHHCCCCC CCHHHHCCCC

Sequence   QSEVPGSIPN SWKWTVEHIV YKALRSHILP PKHFTEDGNI LQLANLPDLY

Structure  CCCCCCCCCC CCCEEEECHH HHHHHCCCCC CCCCCCCCHH HHHHCCCCCE

Sequence   KVFERC

Structure  EEEEEC

LEGEND:

Alpha Helix = H Beta Sheet = E Random Coil = C

2. Do a homology searching of MLH1_Human in Genpept Full Release Database. Import MLH1-like protein of C. elegans, S. cerevisiae, D. melanogaster, R. norvegicus and M. musculus to your workbench. Run CLUSTALW to get multiple sequence alignment for these six proteins.

Consensus key (see documentation for details)

* - single, fully conserved residue

: - conservation of strong groups

. - conservation of weak groups

  - no consensus

CLUSTAL W (1.81) multiple sequence alignment

GENPEPT_460627       --------------------MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDAN

GENPEPT_825572       --------------------MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDAN

GENPEPT_7595954      -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK

GENPEPT_1724118      -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMTENCLDAK

MLH1_HUMAN           -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK

GENPEPT_3192877      ---------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALKELLENSLDAQ

GENPEPT_3880333      MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIKELVENSLDAG

                                             *: *   ***::****::  * **:**: **.:** 

GENPEPT_460627       ATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEA

GENPEPT_825572       ATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEA

GENPEPT_7595954      STNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLASISTYGFRGEA

GENPEPT_1724118      STNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAMISTYGFRGEA

MLH1_HUMAN           STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEA

GENPEPT_3192877      STHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQIATFGFRGEA

GENPEPT_3880333      ATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATSKLQKFEDLMHMKTYGFRGEA

                     :* * : :: **:*::*: ***.**.: *: ::****:****  ****  : *:******

GENPEPT_460627       LASISHVARVTVTTKVKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRL

GENPEPT_825572       LASISHVARVTVTTKVKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRL

GENPEPT_7595954      LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRR

GENPEPT_1724118      LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRK

MLH1_HUMAN           LASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRR

GENPEPT_3192877      LASISHVAHLSIQTKTAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIEDLFYNMPQRR

GENPEPT_3880333      LASLSHVAKVNIVSKRADAKCAYQANFLDGKMTADTKPAAGKNGTCITATDLFYNLPTRR

                     ***:****::.: :*  . :*.::..: :**:   .** **::** *   ***:*:  * 

GENPEPT_460627       RALRSHNDEYSKILDVVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKS

GENPEPT_825572       RALRSHNDEYSKILDVVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKS

GENPEPT_7595954      KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA

GENPEPT_1724118      KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA

MLH1_HUMAN           KALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNA

GENPEPT_3192877      QALRSPAEEFQRLSEVLARYAVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAA

GENPEPT_3880333      NKMTTHGEEAKMVNDTLLRFAIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRD

                     . : .  :*   : :.: *:::*   :.*: ::  :    . .    .  : :  : .  

GENPEPT_460627       VASNLITFHISKVEDLNLESVDGKVCNLNFISKKSIS---------LIFFINNRLVTCDL

GENPEPT_825572       VASNLITFHISKVEDLNLESVDGKVCNLNFISKKSIS---------PIFFINNRLVTCDL

GENPEPT_7595954      VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA

GENPEPT_1724118      VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA

MLH1_HUMAN           VSRELIEIG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESTS

GENPEPT_3192877      ISKELLEFS-HRDEVYKFE-AECLITQVNYSAKKCQ----------MLLFINQRLVESTA

GENPEPT_3880333      VADTILPLS-LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI

                     ::  :: .   .     :      : :     . .             .*** * * .  

GENPEPT_460627       LRRALNSVYSNYLPKGFRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLH

GENPEPT_825572       LRRALNSVYSNYLPKGNRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLH

GENPEPT_7595954      LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILQRVQQHIE

GENPEPT_1724118      LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE

MLH1_HUMAN           LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE

GENPEPT_3192877      LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEEIVDSIKQQVE

GENPEPT_3880333      LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEEIIEEIRAYFE

                     *: .:: : .    :    *  : : :    :********..* ** ::.*:: :   ..

GENPEPT_460627       AELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRK

GENPEPT_825572       AELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRK

GENPEPT_7595954      SKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTGVASSSTSGSGDKVYAYQMVR

GENPEPT_1724118      SKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTGIASSSTSGSGDKVHAYQMVR

MLH1_HUMAN           SKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTSLTSSSTSGSSDKVYAHQMVR

GENPEPT_3192877      ARLLGSNATRTFYKQLRLPGAP-----------------DLDETQLADKTQRIYPKEMVR

GENPEPT_3880333      KVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPMSQSLKSIEAIRKPDTKPEFK

                       :      .    .      .                    . .              :

GENPEPT_460627       AKRQENKLVRIDASQAKITSFLSSS--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTL

GENPEPT_825572       AKRQENKLVRIDASQAKITSFLSSS--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTL

GENPEPT_7595954      TDSRDQKLDAFLQPVSSLVPSQPQDPAPVRGARTEGSPERATREDEEMLALPAPAEAAAE

GENPEPT_1724118      TDSRDQKLDAFMQPVSRRLPSQPQD--PVPGNRTEGSPEKAMQKDQEISELPAPMEAAAD

MLH1_HUMAN           TDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK

GENPEPT_3192877      TDSTEQKLDKFLAPLVK-------------------------------------------

GENPEPT_3880333      SSPSAWKSDKKRVDYMEVRTDAKERKIDEFVTRGGAVGPTTSNDDIFGGSGILKRARTED

                     :.    *                                                     

GENPEPT_460627       NESEQPRDANTINDNDLKDQPKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNV

GENPEPT_825572       NESEQPRDANTINDNDLKDQPKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNV

GENPEPT_7595954      SENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRII

GENPEPT_1724118      SASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRII

MLH1_HUMAN           NQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRII

GENPEPT_3192877      ----------------SDSGVSSSSSQEASRLPEES------------FRVTAAKKSREV

GENPEPT_3880333      STGGEKEPEDLNTDFDDVSMVSLVSTADGRRLNES-----QDLGEDDDVDFEYGKTHREF

                                                   :  .                         .

GENPEPT_460627       NLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL

GENPEPT_825572       NLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL

GENPEPT_7595954      NLTSVLSLQEEISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL

GENPEPT_1724118      NLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL

MLH1_HUMAN           NLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL

GENPEPT_3192877      RLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL

GENPEPT_3880333      HFESIEVLRKEIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF

                     .: *:  :::.:       * . : .  :** :: .   .  *.   *:  :  ..  *:

GENPEPT_460627       FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK---------EKIISK

GENPEPT_825572       FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK---------EKIISK

GENPEPT_7595954      FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA-----EYIVEF

GENPEPT_1724118      FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA-----EYIVEF

MLH1_HUMAN           FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA-----EYIVEF

GENPEPT_3192877      FYQRMIYEFQNCSEITICPPLPLKELLILSLESRAAGWTPEDEDKAELA-----DGAADI

GENPEPT_3880333      FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFANVENRFAAEKL

                     ***  : .* * .   :        : :  * .       :                 . 

GENPEPT_460627       IWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDW

GENPEPT_825572       IWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDW

GENPEPT_7595954      LKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW

GENPEPT_1724118      LKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW

MLH1_HUMAN           LKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNYVPPLEGLPIFILRLATEVNW

GENPEPT_3192877      LLKKAPIMREYFGLRISEDGM--------LESLPSLLHQHRPCVAHLPVYLLRLATEVDW

GENPEPT_3880333      LAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYFVPQLEKLPFLIATLVLNVDY

                     : . : :: :*:.:.: :           :  :* *:. . * :  **. :  *  :*::

GENPEPT_460627       EDEQECLDGILREIALLYIPDMVPKVDTLDASLSEDEKAQFINRKEHISSLLEHVLFPCI

GENPEPT_825572       EDEQECLDGILREIALLYIPDMVPKVDTSDASLSEDEKAQFINRKEHISSLLEHVLFPCI

GENPEPT_7595954      DEEKECFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSKPWKWT--VEHIIYKAF

GENPEPT_1724118      DEE-ECFESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSKPWKWT--VEHIIYKAF

MLH1_HUMAN           DEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWT--VEHIVYKAL

GENPEPT_3192877      EQETRCFETFCRETARFY--------------AQLDWREGATAVFSRWT--MEHVLFPAF

GENPEPT_3880333      DDEQNTFRTICRAIGDLFTLDTN---------FITLDKKISAFSATPWKTLIKEVLMPLV

                     ::* . :  : :  . ::                              .  ::.::   .

GENPEPT_460627       KRRFLAPRHILKD--VVEIANLPDLYKVFERC--

GENPEPT_825572       KRRFLAPRHILKD--VVEIANLPDLYKVFERC--

GENPEPT_7595954      RSHLLPPKHFTEDGNVLQLANLPDLYKVFERC--

GENPEPT_1724118      RSHLLPPKHFTEDGNVLQLANLPDLCKVFERC--

MLH1_HUMAN           RSHILPPKHFTEDGNILQLANLPDLYKVFERC--

GENPEPT_3192877      KKYLLPPR---IKDQIYELTNLPTLYKVFERC--

GENPEPT_3880333      KRKFIPPEHFKQAGVIRQLADSHDLYKVFERCGT

                     :  ::.*.       : ::::   * ******  

3. Perform BOXSHADE program to get a color-coded plot for the results of question 2.

4. Draw rooted phylogenetic tree for these proteins.