Multiple Sequence Alignment of MLH1 protein.

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

Ans: add MLH1_Human protein to the Biology Workbench

        predict its secondary structure by GOR4

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.

Ans: result

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

Ans: 

GENPEPT_7595954 -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK GENPEPT_1724118 -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMTENCLDAK GENPEPT_466462 -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK GENPEPT_3192877 ---------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALKELLENSLDAQ GENPEPT_825572 --------------------MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDAN GENPEPT_3880333 MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIKELVENSLDAG *: * ***::****:: * **:**: **.:** GENPEPT_7595954 STNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLASISTYGFRGEA GENPEPT_1724118 STNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAMISTYGFRGEA GENPEPT_466462 STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEA GENPEPT_3192877 STHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQIATFGFRGEA GENPEPT_825572 ATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEA GENPEPT_3880333 ATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATSKLQKFEDLMHMKTYGFRGEA :* * : :: **:*::*: ***.**.: *: ::****:**** **** : *:****** GENPEPT_7595954 LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRR GENPEPT_1724118 LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRK GENPEPT_466462 LASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRR GENPEPT_3192877 LASISHVAHLSIQTKTAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIEDLFYNMPQRR GENPEPT_825572 LASISHVARVTVTTKVKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRL GENPEPT_3880333 LASLSHVAKVNIVSKRADAKCAYQANFLDGKMTADTKPAAGKNGTCITATDLFYNLPTRR ***:****::.: :* . :*.::..: :**: .** **::** * ***:*: * GENPEPT_7595954 KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA GENPEPT_1724118 KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA GENPEPT_466462 KALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSVFGNA GENPEPT_3192877 QALRSPAEEFQRLSEVLARYAVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAA GENPEPT_825572 RALRSHNDEYSKILDVVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKS GENPEPT_3880333 NKMTTHGEEAKMVNDTLLRFAIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRD . : . :* : :.: *:::* :.*: :: : . . . : : : . GENPEPT_7595954 VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCIF----------LLFINHRLVESAA GENPEPT_1724118 VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCIF----------LLFINHRLVESAA GENPEPT_466462 VSRELIEIG-CEDKTLAFK-MNGYISNANYSVKKCIF----------LLFINHRLVESTS GENPEPT_3192877 ISKELLEFS-HRDEVYKFE-AECLITQVNYSAKKCQM----------LLFINQRLVESTA GENPEPT_825572 VASNLITFHISKVEDLNLESVDGKVCNLNFISKKSISP---------IFFINNRLVTCDL GENPEPT_3880333 VADTILPLS-LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI :: :: . . : : : . . .*** * * . GENPEPT_7595954 LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILQRVQQHIE GENPEPT_1724118 LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE GENPEPT_466462 LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE GENPEPT_3192877 LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEEIVDSIKQQVE GENPEPT_825572 LRRALNSVYSNYLPKGNRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLH GENPEPT_3880333 LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEEIIEEIRAYFE *: .:: : . : * : : : :********..* ** ::.*:: : .. GENPEPT_7595954 SKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTGVASSSTSGSGDKVYAYQMVR GENPEPT_1724118 SKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTGIASSSTSGSGDKVHAYQMVR GENPEPT_466462 SKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTSLTSSSTSGSSDKVYAHQMVR GENPEPT_3192877 ARLLGSNATRTFYKQLRLPGAP-----------------DLDETQLADKTQRIYPKEMVR GENPEPT_825572 AELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRK GENPEPT_3880333 KVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPMSQSLKSIEAIRKPDTKPEFK : . . . . . : GENPEPT_7595954 TDSRDQKLDAFLQPVSSLVPSQPQDPAPVRGARTEGSPERATREDEEMLALPAPAEAAAE GENPEPT_1724118 TDSRDQKLDAFMQPVSRRLPSQPQD--PVPGNRTEGSPEKAMQKDQEISELPAPMEAAAD GENPEPT_466462 TDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK GENPEPT_3192877 TDSTEQKLDKFLAPLVK------------------------------------------- GENPEPT_825572 AKRQENKLVRIDASQAKITSFLSSS--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTL GENPEPT_3880333 SSPSAWKSDKKRVDYMEVRTDAKERKIDEFVTRGGAVGPTTSNDDIFGGSGILKRARTED :. * GENPEPT_7595954 SENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRII GENPEPT_1724118 SASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRII GENPEPT_466462 NQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRII GENPEPT_3192877 ----------------SDSGVSSSSSQEASRLPEES------------FRVTAAKKSREV GENPEPT_825572 NESEQPRDANTINDNDLKDQPKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNV GENPEPT_3880333 STGGEKEPEDLNTDFDDVSMVSLVSTADGRRLNESQD-----LGEDDDVDFEYGKTHREF : . . GENPEPT_7595954 NLTSVLSLQEEISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL GENPEPT_1724118 NLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL GENPEPT_466462 NLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL GENPEPT_3192877 RLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL GENPEPT_825572 NLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL GENPEPT_3880333 HFESIEVLRKEIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF .: *: :::.: * . : . :** :: . . *. *: : .. *: GENPEPT_7595954 FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA-----EYIVEF GENPEPT_1724118 FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA-----EYIVEF GENPEPT_466462 FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA-----EYIVEF GENPEPT_3192877 FYQRMIYEFQNCSEITICPPLPLKELLILSLESRAAGWTPEDEDKAELA-----DGAADI GENPEPT_825572 FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK---------EKIISK GENPEPT_3880333 FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFANVENRFAAEKL *** : .* * . : : : * . : . GENPEPT_7595954 LKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW GENPEPT_1724118 LKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW GENPEPT_466462 LKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNYVPPLEGLPIFILRLATEVNW GENPEPT_3192877 LLKKAPIMREYFGLRISEDGM--------LESLPSLLHQHRPCVAHLPVYLLRLATEVDW GENPEPT_825572 IWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDW GENPEPT_3880333 LAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYFVPQLEKLPFLIATLVLNVDY : . : :: :*:.:.: : : :* *:. . * : **. : * :*:: GENPEPT_7595954 DEEKECFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSKPWKWT--VEHIIYKAF GENPEPT_1724118 DEE-ECFESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSKPWKWT--VEHIIYKAF GENPEPT_466462 DEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWT--VEHIVYKAL GENPEPT_3192877 EQETRCFETFCRETARFY--------------AQLDWREGATAVFSRWT--MEHVLFPAF GENPEPT_825572 EDEQECLDGILREIALLYIPDMVPKVDTSDASLSEDEKAQFINRKEHISSLLEHVLFPCI GENPEPT_3880333 DDEQNTFRTICRAIGDLFTLDTN---------FITLDKKISAFSATPWKTLIKEVLMPLV ::* . : : : . :: . ::.:: . GENPEPT_7595954 RSHLLPPKHFTEDGNVLQLANLPDLYKVFERC-- GENPEPT_1724118 RSHLLPPKHFTEDGNVLQLANLPDLCKVFERC-- GENPEPT_466462 RSHILPPKHFTEDGNILQLANLPDLYKVFERC-- GENPEPT_3192877 KKYLLPPR---IKDQIYELTNLPTLYKVFERC-- GENPEPT_825572 KRRFLAPRHILKD--VVEIANLPDLYKVFERC-- GENPEPT_3880333 KRKFIPPEHFKQAGVIRQLADSHDLYKVFERCGT : ::.*. : :::: * ******

4. Draw rooted phylogenetic tree for these proteins.

Ans: