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

DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) [Homo sapiens (Human)] 

>MLH1_HUMAN
MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVI
VKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFR
GEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQI
TVEDLFYNIATRRKALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGET
VADVRTLPNASTVDNIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISNAN
YSVKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISP
QNVDVNVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQTLLP
GLAGPSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPL
SKPLSSQPQAIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGD
TTKGTSEMSEKRGPTSSNPRKRHREDSDVEMVEDDSRKEMTAACTPRRRI
INLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQWALAQHQTKLYLL
NTTKLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEE
DGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGNLIGLPLLIDNYVPPL
EGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQ
QSEVPGSIPNSWKWTVEHIVYKALRSHILPPKHFTEDGNILQLANLPDLY
KVFERC

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

Fasta label (*)               Workbench label
 
MLH1_HUMAN          DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) 
                                     [Homo sapiens (Human)] 
GENPEPT:3880333     Caenorhabditis elegans cosmid T28A8, complete sequence_ 
GENPEPT:460627       Saccharomyces cerevisiae DNA mismatch repair (MLH1) gene, complete 
GENPEPT:3192877     Drosophila melanogaster mutL homolog (Mlh1) gene, complete cds_ 
GENPEPT:1724118     Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete 
GENPEPT:7595954     Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds. 

Sequence alignment
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_7595954          -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK
         GENPEPT_1724118           -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMTENCLDAK
         MLH1_HUMAN                -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK
         GENPEPT_3192877          ------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALKELLENSLDAQ
         GENPEPT_460627            --------------------MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDAN
         GENPEPT_3880333 MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIKELVENSLDAG
         *: * ***::****:: * **:**: **.:** 

GENPEPT_7595954 STNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLASISTYGFRGEA
         GENPEPT_1724118 STNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAMISTYGFRGEA
         MLH1_HUMAN STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEA
         GENPEPT_3192877 STHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQIATFGFRGEA
         GENPEPT_460627 ATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEA
         GENPEPT_3880333 ATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATSKLQKFEDLMHMKTYGFRGEA
         :* * : :: **:*::*: ***.**.: *: ::****:**** **** : *:******

GENPEPT_7595954 LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRR
         GENPEPT_1724118 LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRK
         MLH1_HUMAN LASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRR
         GENPEPT_3192877 LASISHVAHLSIQTKTAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIEDLFYNMPQRR
         GENPEPT_460627 LASISHVARVTVTTKVKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRL
         GENPEPT_3880333 LASLSHVAKVNIVSKRADAKCAYQANFLDGKMTADTKPAAGKNGTCITATDLFYNLPTRR
         ***:****::.: :* . :*.::..: :**: .** **::** * ***:*: * 

GENPEPT_7595954 KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA
         GENPEPT_1724118 KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA
         MLH1_HUMAN KALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNA
         GENPEPT_3192877 QALRSPAEEFQRLSEVLARYAVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAA
         GENPEPT_460627 RALRSHNDEYSKILDVVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKS
         GENPEPT_3880333 NKMTTHGEEAKMVNDTLLRFAIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRD
         . : . :* : :.: *:::* :.*: :: : . . . : : : . 

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_460627 VASNLITFHISKVEDLNLESVDGKVCNLNFISKKSIS---------LIFFINNRLVTCDL
         GENPEPT_3880333 VADTILPLS-LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI
         :: :: . . : : : . . : .*** * * . 

GENPEPT_7595954 LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILQRVQQHIE
         GENPEPT_1724118 LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE
         MLH1_HUMAN LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE
         GENPEPT_3192877 LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEEIVDSIKQQVE
         GENPEPT_460627 LRRALNSVYSNYLPKGFRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLH
         GENPEPT_3880333 LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEEIIEEIRAYFE
         *: .:: : . : * : : : :********..* ** ::.*:: : ..

GENPEPT_7595954 SKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTGVASSSTSGSGDKVYAYQMVR
         GENPEPT_1724118 SKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTGIASSSTSGSGDKVHAYQMVR
         MLH1_HUMAN SKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTSLTSSSTSGSSDKVYAHQMVR
         GENPEPT_3192877 ARLLGSNATRTFYKQLRLPGAP-----------------DLDETQLADKTQRIYPKEMVR
         GENPEPT_460627 AELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRK
         GENPEPT_3880333 KVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPMSQSLKSIEAIRKPDTKPEFK
         : . . . . . :

GENPEPT_7595954 TDSRDQKLDAFLQPVSSLVPSQPQDPAPVRGARTEGSPERATREDEEMLALPAPAEAAAE
         GENPEPT_1724118 TDSRDQKLDAFMQPVSRRLPSQPQD--PVPGNRTEGSPEKAMQKDQEISELPAPMEAAAD
         MLH1_HUMAN TDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK
         GENPEPT_3192877 TDSTEQKLDKFLAPLVK-------------------------------------------
         GENPEPT_460627 AKRQENKLVRIDASQAKITSFLSSS--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTL
         GENPEPT_3880333 SSPSAWKSDKKRVDYMEVRTDAKERKIDEFVTRGGAVGPTTSNDDIFGGSGILKRARTED
         :. * 

GENPEPT_7595954 SENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRII
         GENPEPT_1724118 SASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRII
         MLH1_HUMAN NQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRII
         GENPEPT_3192877 ----------------SDSGVSSSSSQEASRLPEES------------FRVTAAKKSREV
         GENPEPT_460627 NESEQPRDANTINDNDLKDQPKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNV
         GENPEPT_3880333 STGGEKEPEDLNTDFDDVSMVSLVSTADGRRLNESQD-----LGEDDDVDFEYGKTHREF
         : . .

GENPEPT_7595954 NLTSVLSLQEEISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
         GENPEPT_1724118 NLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
         MLH1_HUMAN NLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
         GENPEPT_3192877 RLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL
         GENPEPT_460627 NLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL
         GENPEPT_3880333 HFESIEVLRKEIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF
         .: *: :::.: * . : . :** :: . . *. *: : .. *:

GENPEPT_7595954 FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA-----EYIVEF
         GENPEPT_1724118 FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA-----EYIVEF
         MLH1_HUMAN FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA-----EYIVEF
         GENPEPT_3192877 FYQRMIYEFQNCSEITICPPLPLKELLILSLESRAAGWTPEDEDKAELA-----DGAADI
         GENPEPT_460627 FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK---------EKIISK
         GENPEPT_3880333 FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFANVENRFAAEKL
         *** : .* * . : : : * . : . 

GENPEPT_7595954 LKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW
         GENPEPT_1724118 LKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW
         MLH1_HUMAN LKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNYVPPLEGLPIFILRLATEVNW
         GENPEPT_3192877 LLKKAPIMREYFGLRISEDGM--------LESLPSLLHQHRPCVAHLPVYLLRLATEVDW
         GENPEPT_460627 IWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDW
         GENPEPT_3880333 LAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYFVPQLEKLPFLIATLVLNVDY
         : . : :: :*:.:.: : : :* *:. . * : **. : * :*::

GENPEPT_7595954 DEEKECFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSKPWKWT--VEHIIYKAF
         GENPEPT_1724118 DEE-ECFESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSKPWKWT--VEHIIYKAF
         MLH1_HUMAN DEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWT--VEHIVYKAL
         GENPEPT_3192877 EQETRCFETFCRETARFY--------------AQLDWREGATAVFSRWT--MEHVLFPAF
         GENPEPT_460627 EDEQECLDGILREIALLYIPDMVPKVDTLDASLSEDEKAQFINRKEHISSLLEHVLFPCI
         GENPEPT_3880333 DDEQNTFRTICRAIGDLFTLDTN---------FITLDKKISAFSATPWKTLIKEVLMPLV
         ::* . : : : . :: . ::.:: .

GENPEPT_7595954 RSHLLPPKHFTEDGNVLQLANLPDLYKVFERC--
         GENPEPT_1724118 RSHLLPPKHFTEDGNVLQLANLPDLCKVFERC--
         MLH1_HUMAN RSHILPPKHFTEDGNILQLANLPDLYKVFERC--
         GENPEPT_3192877 KKYLLPPR---IKDQIYELTNLPTLYKVFERC--
         GENPEPT_460627 KRRFLAPRHILKD--VVEIANLPDLYKVFERC--
         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.