(*) Clustalw cuts off Fasta labels after the first space (e.g. ">abc def" becomes ">abc").
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 MLH1_M._musculus -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIK MLH1_R._norvegicus -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK MLH1_Human -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK MLH1_D._melanogaster ---------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALK MLH1_S._cerevisiae --------------------MSLRIKALDASVVNKIAAGEIIISPVNALK MLH1_C._elegans MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIK *: * ***::****:: * **:* MLH1_M._musculus EMIENCLDAKSTNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTS MLH1_R._norvegicus EMTENCLDAKSTNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTS MLH1_Human EMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTS MLH1_D._melanogaster ELLENSLDAQSTHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTS MLH1_S._cerevisiae EMMENSIDANATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTS MLH1_C._elegans ELVENSLDAGATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATS *: **.:** :* * : :: **:*::*: ***.**.: *: ::****:** MLH1_M._musculus KLQTFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG MLH1_R._norvegicus KLQTFEDLAMISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG MLH1_Human KLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG MLH1_D._melanogaster KLTRFEDLSQIATFGFRGEALASISHVAHLSIQTKTAKEKCGYKATYADG MLH1_S._cerevisiae KLQKFEDLSQIQTYGFRGEALASISHVARVTVTTKVKEDRCAWRVSYAEG MLH1_C._elegans KLQKFEDLMHMKTYGFRGEALASLSHVAKVNIVSKRADAKCAYQANFLDG ** **** : *:*********:****::.: :* . :*.::..: :* MLH1_M._musculus KLQAPPKPCAGNQGTLITVEDLFYNIITRRKALKNPSEEYGKILEVVGRY MLH1_R._norvegicus KLQAPPKPCAGNQGTLITVEDLFYNIITRKKALKNPSEEYGKILEVVGRY MLH1_Human KLKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRY MLH1_D._melanogaster KLQGQPKPCAGNQGTIICIEDLFYNMPQRRQALRSPAEEFQRLSEVLARY MLH1_S._cerevisiae KMLESPKPVAGKDGTTILVEDLFFNIPSRLRALRSHNDEYSKILDVVGRY MLH1_C._elegans KMTADTKPAAGKNGTCITATDLFYNLPTRRNKMTTHGEEAKMVNDTLLRF *: .** **::** * ***:*: * . : . :* : :.: *: MLH1_M._musculus SIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG- MLH1_R._norvegicus SIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG- MLH1_Human SVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIG- MLH1_D._melanogaster AVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAAISKELLEFS- MLH1_S._cerevisiae AIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKSVASNLITFHI MLH1_C._elegans AIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRDVADTILPLS- ::* :.*: :: : . . . : : : . :: :: . MLH1_M._musculus CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA MLH1_R._norvegicus CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA MLH1_Human CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESTS MLH1_D._melanogaster HRDEVYKFE-AECLITQVNYSAKKCQ----------MLLFINQRLVESTA MLH1_S._cerevisiae SKVEDLNLESVDGKVCNLNFISKKSIS---------LIFFINNRLVTCDL MLH1_C._elegans LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI . : : : . . : .*** * * . MLH1_M._musculus LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEES MLH1_R._norvegicus LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEES MLH1_Human LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEES MLH1_D._melanogaster LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEE MLH1_S._cerevisiae LRRALNSVYSNYLPKGFRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDE MLH1_C._elegans LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEE *: .:: : . : * : : : :********..* ** ::. MLH1_M._musculus ILQRVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTG MLH1_R._norvegicus ILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTG MLH1_Human ILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTS MLH1_D._melanogaster IVDSIKQQVEARLLGSNATRTFYKQLRLPGAP-----------------D MLH1_S._cerevisiae IIEKIANQLHAELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKS MLH1_C._elegans IIEEIRAYFEKVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPM *:: : .. : . . . MLH1_M._musculus VASSSTSGSGDKVYAYQMVRTDSRDQKLDAFLQPVSSLVPSQPQDPAPVR MLH1_R._norvegicus IASSSTSGSGDKVHAYQMVRTDSRDQKLDAFMQPVSRRLPSQPQD--PVP MLH1_Human LTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQ--AIVT MLH1_D._melanogaster LDETQLADKTQRIYPKEMVRTDSTEQKLDKFLAPLVK------------- MLH1_S._cerevisiae LRQAQVVENSYTTANSQLRKAKRQENKLVRIDASQAKITSFLSSS--QQF MLH1_C._elegans SQSLKSIEAIRKPDTKPEFKSSPSAWKSDKKRVDYMEVRTDAKERKIDEF . . ::. * MLH1_M._musculus GARTEGSPERATREDEEMLALPAPAEAAAESENLERESLMETSDAAQKAA MLH1_R._norvegicus GNRTEGSPEKAMQKDQEISELPAPMEAAADSASLERESVIGASEVVAPQR MLH1_Human EDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRG MLH1_D._melanogaster ----------------------------------------------SDSG MLH1_S._cerevisiae NFEGSSTKRQLSEPKVTNVSHSQEAEKLTLNESEQPRDANTINDNDLKDQ MLH1_C._elegans VTRGGAVGPTTSNDDIFGGSGILKRARTEDSTGGEKEPEDLNTDFDDVSM MLH1_M._musculus PTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRIINLTSVLSLQE MLH1_R._norvegicus HPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRIINLTSVLSLQE MLH1_Human PTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRIINLTSVLSLQE MLH1_D._melanogaster VSSSSSQEASRLPEES------------FRVTAAKKSREVRLSSVLDMRK MLH1_S._cerevisiae PKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNVNLTSIKKLRE MLH1_C._elegans VSLVSTADGRRLNESQD-----LGEDDDVDFEYGKTHREFHFESIEVLRK : . ..: *: ::: MLH1_M._musculus EISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL MLH1_R._norvegicus EINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL MLH1_Human EINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL MLH1_D._melanogaster RVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL MLH1_S._cerevisiae KVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL MLH1_C._elegans EIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF .: * . : . :** :: . . *. *: : .. *: MLH1_M._musculus FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA- MLH1_R._norvegicus FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA- MLH1_Human FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA- MLH1_D._melanogaster FYQRMIYEFQNCSEITISPPLPLKELLILSLESEAAGWTPEDGDKAELA- MLH1_S._cerevisiae FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK----- MLH1_C._elegans FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFAN *** : .* * . : : : * . : . MLH1_M._musculus ----EYIVEFLKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSY MLH1_R._norvegicus ----EYIVEFLKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSY MLH1_Human ----EYIVEFLKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNY MLH1_D._melanogaster ----DGAADILLKKAPIMREYFGLRISEDGM--------LESLPSLLHQH MLH1_S._cerevisiae ----EKIISKIWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGY MLH1_C._elegans VENRFAAEKLLAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYF . : . : :: :*:.:.: : : :* *:. . MLH1_M._musculus VPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYILEEST MLH1_R._norvegicus VPPLEGLPIFILRLATEVNWDEE-ECFESLSKECAVFYSIRKQYILEESA MLH1_Human VPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEEST MLH1_D._melanogaster RPCVAHLPVYLLRLATEVDWEQETRCFETFCRETARFY------------ MLH1_S._cerevisiae IPSLVKLPFFIYRLGKEVDWEDEQECLDGILREIALLYIPDMVPKVDTLD MLH1_C._elegans VPQLEKLPFLIATLVLNVDYDDEQNTFRTICRAIGDLFTLDTN------- * : **. : * :*::::* . : : : . :: MLH1_M._musculus LSGQQSDMPGSTSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLA MLH1_R._norvegicus LSGQQSDMPGSPSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLA MLH1_Human LSGQQSEVPGSIPNSWKWT--VEHIVYKALRSHILPPKHFTEDGNILQLA MLH1_D._melanogaster --AQLDWREGATAGFSRWT--MEHVLFPAFKKYLLPPPRIKD--QIYELT MLH1_S._cerevisiae ASLSEDEKAQFINRKEHISSLLEHVLFPCIKRRFLAPRHILK--DVVEIA MLH1_C._elegans --FITLDKKISAFSATPWKTLIKEVLMPLVKRKFIPPEHFKQAGVIRQLA . ::.:: .: ::.* :: . : ::: MLH1_M._musculus NLPDLYKVFERC-- MLH1_R._norvegicus NLPDLCKVFERC-- MLH1_Human NLPDLYKVFERC-- MLH1_D._melanogaster NLPTLYKVFERC-- MLH1_S._cerevisiae NLPDLYKVFERC-- MLH1_C._elegans DSHDLYKVFERCGT : * ******
( ( MLH1_M._musculus:0.03502, MLH1_R._norvegicus:0.04820) :0.02520, ( MLH1_D._melanogaster:0.24257, ( MLH1_S._cerevisiae:0.33127, MLH1_C._elegans:0.37354) :0.04885) :0.19165, MLH1_Human:0.05620);
Alignment type: Protein Alignment order: aligned Pairwise alignment parameters Method: accurate Matrix: Gonnet Gap open penalty: 10.00 Gap extension penalty: 0.10 Multiple alignment parameters Matrix: Gonnet Negative matrix?: no Gap open penalty: 10.00 Gap extension penalty: 0.20 % identity for delay: 30 Residue-specific gap penalties: on Penalize end gaps: on Hydrophilic gap penalties: on Gap separation distance: 0 Hydrophilic residues: GPSNDQEKR CLUSTAL W (1.81) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson Sequence 1: MLH1_M._musculus 760 aa Sequence 2: MLH1_R._norvegicus 757 aa Sequence 3: MLH1_D._melanogaster 664 aa Sequence 4: MLH1_S._cerevisiae 769 aa Sequence 5: MLH1_C._elegans 779 aa Sequence 6: MLH1_Human 756 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 91 Sequences (1:3) Aligned. Score: 50 Sequences (1:4) Aligned. Score: 36 Sequences (1:5) Aligned. Score: 32 Sequences (1:6) Aligned. Score: 88 Sequences (2:3) Aligned. Score: 48 Sequences (2:4) Aligned. Score: 36 Sequences (2:5) Aligned. Score: 32 Sequences (2:6) Aligned. Score: 86 Sequences (3:4) Aligned. Score: 37 Sequences (3:5) Aligned. Score: 33 Sequences (3:6) Aligned. Score: 51 Sequences (4:5) Aligned. Score: 29 Sequences (4:6) Aligned. Score: 36 Sequences (5:6) Aligned. Score: 32 Time for pairwise alignment: 1.122501 Guide tree file created: [../tmp-dir/5807.CLUSTALW.dnd] Start of Multiple Alignment There are 5 groups Aligning... Group 1: Sequences: 2 Score:15725 Group 2: Sequences: 3 Score:15401 Group 3: Sequences: 4 Score:10965 Group 4: Sequences: 5 Score:10162 Group 5: Sequences: 6 Score:7702 Time for multiple alignment: 1.980457 Alignment Score 30185 CLUSTAL-Alignment file created [../tmp-dir/5807.CLUSTALW.aln]
Citation
Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Computer Applications in the Biosciences (CABIOS), 8(2):189-191.
Thompson J.D., Higgins D.G., Gibson T.J. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 22:4673-4680(1994).
Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Program Citation:
CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications.
PHYLIP: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.