Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)
  • Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
  • Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
  • Drosophila melanogaster genomic scaffold 142000013386047 section 5
  • Caenorhabditis elegans cosmid T28A8, complete sequence_
  • Saccharomyces cerevisiae DNA mismatch repair (MLH1) gene, complete
  • DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) [Homo sapiens (Human)]

    Fasta label (*) Workbench label
    M. Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
    R. Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
    D. Drosophila melanogaster genomic scaffold 142000013386047 section 5
    C. Caenorhabditis elegans cosmid T28A8, complete sequence_
    S. Saccharomyces cerevisiae DNA mismatch repair (MLH1) gene, complete
    MLH1_HUMAN DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) [Homo sapiens (Human)]

    (*) Clustalw cuts off Fasta labels after the first space (e.g. ">abc def" becomes ">abc").

    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


R._norvegicus        -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMTENCLDAK
M._musculus          -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK
MLH1_HUMAN           -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAK
D._melanogaster      ---------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALKELLENSLDAQ
S._cerevisiae        --------------------MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDAN
C._elegans           MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIKELVENSLDAG
                                             *: *   ***::****::  * **:**: **.:** 

R._norvegicus        STNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAMISTYGFRGEA
M._musculus          STNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLASISTYGFRGEA
MLH1_HUMAN           STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEA
D._melanogaster      STHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQIATFGFRGEA
S._cerevisiae        ATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEA
C._elegans           ATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATSKLQKFEDLMHMKTYGFRGEA
                     :* * : :: **:*::*: ***.**.: *: ::****:****  ****  : *:******

R._norvegicus        LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRK
M._musculus          LASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRR
MLH1_HUMAN           LASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRR
D._melanogaster      LASISHVAHLSIQTKTAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIEDLFYNMPQRR
S._cerevisiae        LASISHVARVTVTTKVKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRL
C._elegans           LASLSHVAKVNIVSKRADAKCAYQANFLDGKMTADTKPAAGKNGTCITATDLFYNLPTRR
                     ***:****::.: :*  . :*.::..: :**:   .** **::** *   ***:*:  * 

R._norvegicus        KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA
M._musculus          KALKNPSEEYGKILEVVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNA
MLH1_HUMAN           KALKNPSEEYGKILEVVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNA
D._melanogaster      QALRSPAEEFQRLSEVLARYAVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAA
S._cerevisiae        RALRSHNDEYSKILDVVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKS
C._elegans           NKMTTHGEEAKMVNDTLLRFAIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRD
                     . : .  :*   : :.: *:::*   :.*: ::  :    . .    .  : :  : .  

R._norvegicus        VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA
M._musculus          VSRELIEVG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA
MLH1_HUMAN           VSRELIEIG-CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESTS
D._melanogaster      ISKELLEFS-HRDEVYKFE-AECLITQVNYSAKKCQ----------MLLFINQRLVESTA
S._cerevisiae        VASNLITFHISKVEDLNLESVDGKVCNLNFISKKSIS---------LIFFINNRLVTCDL
C._elegans           VADTILPLS-LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI
                     ::  :: .   .     :      : :     . .           : .*** * * .  

R._norvegicus        LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE
M._musculus          LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILQRVQQHIE
MLH1_HUMAN           LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIE
D._melanogaster      LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEEIVDSIKQQVE
S._cerevisiae        LRRALNSVYSNYLPKGFRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLH
C._elegans           LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEEIIEEIRAYFE
                     *: .:: : .    :    *  : : :    :********..* ** ::.*:: :   ..

R._norvegicus        SKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTGIASSSTSGSGDKVHAYQMVR
M._musculus          SKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTGVASSSTSGSGDKVYAYQMVR
MLH1_HUMAN           SKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTSLTSSSTSGSSDKVYAHQMVR
D._melanogaster      ARLLGSNATRTFYKQLRLPGAP-----------------DLDETQLADKTQRIYPKEMVR
S._cerevisiae        AELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRK
C._elegans           KVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPMSQSLKSIEAIRKPDTKPEFK
                       :      .    .      .                    . .              :

R._norvegicus        TDSRDQKLDAFMQPVSRRLPSQPQD--PVPGNRTEGSPEKAMQKDQEISELPAPMEAAAD
M._musculus          TDSRDQKLDAFLQPVSSLVPSQPQDPAPVRGARTEGSPERATREDEEMLALPAPAEAAAE
MLH1_HUMAN           TDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDISSGRARQQDEEMLELPAPAEVAAK
D._melanogaster      TDSTEQKLDKFLAPLVK-------------------------------------------
S._cerevisiae        AKRQENKLVRIDASQAKITSFLSSS--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTL
C._elegans           SSPSAWKSDKKRVDYMEVRTDAKERKIDEFVTRGGAVGPTTSNDDIFGGSGILKRARTED
                     :.    *                                                     

R._norvegicus        SASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRII
M._musculus          SENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRII
MLH1_HUMAN           NQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRII
D._melanogaster      ----------------SDSGVSSSSSQEASRLPEES------------FRVTAAKKSREV
S._cerevisiae        NESEQPRDANTINDNDLKDQPKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNV
C._elegans           STGGEKEPEDLNTDFDDVSMVSLVSTADGRRLNESQD-----LGEDDDVDFEYGKTHREF
                                                   :  .                         .

R._norvegicus        NLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
M._musculus          NLTSVLSLQEEISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
MLH1_HUMAN           NLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
D._melanogaster      RLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL
S._cerevisiae        NLTSIKKLREKVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL
C._elegans           HFESIEVLRKEIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF
                     .: *:  :::.:       * . : .  :** :: .   .  *.   *:  :  ..  *:

R._norvegicus        FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA-----EYIVEF
M._musculus          FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA-----EYIVEF
MLH1_HUMAN           FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA-----EYIVEF
D._melanogaster      FYQRMIYEFQNCSEITISPPLPLKELLILSLESEAAGWTPEDGDKAELA-----DGAADI
S._cerevisiae        FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK---------EKIISK
C._elegans           FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFANVENRFAAEKL
                     ***  : .* * .   :        : :  * .       : .               . 

R._norvegicus        LKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW
M._musculus          LKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSYVPPLEGLPIFILRLATEVNW
MLH1_HUMAN           LKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNYVPPLEGLPIFILRLATEVNW
D._melanogaster      LLKKAPIMREYFGLRISEDGM--------LESLPSLLHQHRPCVAHLPVYLLRLATEVDW
S._cerevisiae        IWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGYIPSLVKLPFFIYRLGKEVDW
C._elegans           LAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYFVPQLEKLPFLIATLVLNVDY
                     : . : :: :*:.:.: :           :  :* *:. . * :  **. :  *  :*::

R._norvegicus        DEE-ECFESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSKPWKWT--VEHIIYKAF
M._musculus          DEEKECFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSKPWKWT--VEHIIYKAF
MLH1_HUMAN           DEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPNSWKWT--VEHIVYKAL
D._melanogaster      EQETRCFETFCRETARFY--------------AQLDWREGATAGFSRWT--MEHVLFPAF
S._cerevisiae        EDEQECLDGILREIALLYIPDMVPKVDTLDASLSEDEKAQFINRKEHISSLLEHVLFPCI
C._elegans           DDEQNTFRTICRAIGDLFTLDTN---------FITLDKKISAFSATPWKTLIKEVLMPLV
                     ::* . :  : :  . ::                              .  ::.::   .

R._norvegicus        RSHLLPPKHFTEDGNVLQLANLPDLCKVFERC--
M._musculus          RSHLLPPKHFTEDGNVLQLANLPDLYKVFERC--
MLH1_HUMAN           RSHILPPKHFTEDGNILQLANLPDLYKVFERC--
D._melanogaster      KKYLLPPPRIKD--QIYELTNLPTLYKVFERC--
S._cerevisiae        KRRFLAPRHILK--DVVEIANLPDLYKVFERC--
C._elegans           KRKFIPPEHFKQAGVIRQLADSHDLYKVFERCGT
                     :  ::.* :: .   : ::::   * ******

    Clustal W dendrogram



    Unrooted tree (generated by Phylip's Drawtree)

    Download a PostScript version of the output



    Phylip-format dendrogram

    (
(
MLH1_HUMAN:0.05571,
(
(
S._cerevisiae:0.33028,
C._elegans:0.37453)
:0.04951,
D._melanogaster:0.24191)
:0.19214)
:0.02570,
R._norvegicus:0.04837,
M._musculus:0.03486);

    Clustal W options and diagnostic messages

    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_HUMAN           756 aa
Sequence 2: S._cerevisiae        769 aa
Sequence 3: C._elegans           779 aa
Sequence 4: D._melanogaster      664 aa
Sequence 5: R._norvegicus        757 aa
Sequence 6: M._musculus          760 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  36
Sequences (1:3) Aligned. Score:  32
Sequences (1:4) Aligned. Score:  51
Sequences (1:5) Aligned. Score:  86
Sequences (1:6) Aligned. Score:  88
Sequences (2:3) Aligned. Score:  29
Sequences (2:4) Aligned. Score:  37
Sequences (2:5) Aligned. Score:  36
Sequences (2:6) Aligned. Score:  36
Sequences (3:4) Aligned. Score:  33
Sequences (3:5) Aligned. Score:  31
Sequences (3:6) Aligned. Score:  32
Sequences (4:5) Aligned. Score:  48
Sequences (4:6) Aligned. Score:  50
Sequences (5:6) Aligned. Score:  91
Time for pairwise alignment: 1.157255

Guide tree        file created:   [../tmp-dir/13848.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: 2.037239

Alignment Score 30185
CLUSTAL-Alignment file created  [../tmp-dir/13848.CLUSTALW.aln]

    Citation

      Algorithm 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.

    Copyright (C) 1999, Board of Trustees of the University of Illinois.