Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)
  • Caenorhabditis elegans cosmid T28A8, complete sequence_
  • S.cerevisiae chromosome XIII cosmid 8520_
  • Drosophila melanogaster mutL homolog (Mlh1) gene, complete cds_
  • Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
  • Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
  • Human DNA mismatch repair (hmlh1) mRNA, complete cds_

    Fasta label (*)Workbench label
    GENPEPT:3880333Caenorhabditis elegans cosmid T28A8, complete sequence_
    GENPEPT:825572S.cerevisiae chromosome XIII cosmid 8520_
    GENPEPT:3192877Drosophila melanogaster mutL homolog (Mlh1) gene, complete cds_
    GENPEPT:1724118Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
    GENPEPT:7595954Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
    GENPEPT:466462Human DNA mismatch repair (hmlh1) mRNA, complete cds_

    (*) 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


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

    Clustal W dendrogram



    Unrooted tree (generated by Phylip's Drawtree)

    Download a PostScript version of the output



    Phylip-format dendrogram

    (
GENPEPT_466462:0.05763,
(
GENPEPT_7595954:0.03521,
GENPEPT_1724118:0.04802)
:0.02510,
(
GENPEPT_3192877:0.24567,
(
GENPEPT_825572:0.33043,
GENPEPT_3880333:0.37568)
:0.04833)
:0.19089);

    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: GENPEPT_466462       756 aa
Sequence 2: GENPEPT_7595954      760 aa
Sequence 3: GENPEPT_1724118      757 aa
Sequence 4: GENPEPT_3192877      663 aa
Sequence 5: GENPEPT_825572       769 aa
Sequence 6: GENPEPT_3880333      779 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  88
Sequences (1:3) Aligned. Score:  86
Sequences (1:4) Aligned. Score:  51
Sequences (1:5) Aligned. Score:  36
Sequences (1:6) Aligned. Score:  32
Sequences (2:3) Aligned. Score:  91
Sequences (2:4) Aligned. Score:  50
Sequences (2:5) Aligned. Score:  36
Sequences (2:6) Aligned. Score:  32
Sequences (3:4) Aligned. Score:  48
Sequences (3:5) Aligned. Score:  36
Sequences (3:6) Aligned. Score:  32
Sequences (4:5) Aligned. Score:  38
Sequences (4:6) Aligned. Score:  32
Sequences (5:6) Aligned. Score:  29
Time for pairwise alignment: 2.274260

Guide tree        file created:   [../tmp-dir/20758.CLUSTALW.dnd]
Start of Multiple Alignment
There are 5 groups
Aligning...
Group 1: Sequences:   2      Score:15725
Group 2: Sequences:   3      Score:15397
Group 3: Sequences:   4      Score:10921
Group 4: Sequences:   5      Score:10155
Group 5: Sequences:   6      Score:7685
Time for multiple alignment: 5.505672

Alignment Score 30082
CLUSTAL-Alignment file created  [../tmp-dir/20758.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.