Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)
  • DNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) [Homo sapiens (Human)]
  • S.cerevisiae genes RHO2, TOP2, MKT1, END2, PMS1 AND ORFs N2250,
  • Caenorhabditis elegans cosmid T28A8, complete sequence_
  • Drosophila melanogaster genomic scaffold 142000013386047 section 5
  • Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
  • Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.

    Fasta label (*)Workbench label
    MLH1_HUMANDNA MISMATCH REPAIR PROTEIN MLH1 (MUTL PROTEIN HOMOLOG 1) [Homo sapiens (Human)]
    GENPEPT:887629S.cerevisiae genes RHO2, TOP2, MKT1, END2, PMS1 AND ORFs N2250,
    GENPEPT:3880333Caenorhabditis elegans cosmid T28A8, complete sequence_
    GENPEPT:7304079Drosophila melanogaster genomic scaffold 142000013386047 section 5
    GENPEPT:1724118Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
    GENPEPT:7595954Mus musculus MutL homolog 1 protein (MLH1) 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      ---------------------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
GENPEPT_1724118      ---------------------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
MLH1_HUMAN           ---------------------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
GENPEPT_7304079      -------------------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALK
GENPEPT_3880333      ----------MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIK
GENPEPT_887629       MFHHIENLLIETEKRCKQKEQRYIPVKYLFSMTQIHQINDIDVHRITSGQVITDLTTAVK
                                                       *::: :  *:*:::*:::    .*:*

GENPEPT_7595954      EMIENCLDAKSTNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAS
GENPEPT_1724118      EMTENCLDAKSTNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAM
MLH1_HUMAN           EMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLAS
GENPEPT_7304079      ELLENSLDAQSTHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQ
GENPEPT_3880333      ELVENSLDAGATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATSKLQKFEDLMH
GENPEPT_887629       ELVDNSIDANANQIEIIFKDYGLESIECSDNGDGIDPSNYEFLALKHYTSKIAKFQDVAK
                     *: :*.:** :. * : .:  **: :: .*** **  .:  ::. :. ***:  *:*:  

GENPEPT_7595954      ISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVE
GENPEPT_1724118      ISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVE
MLH1_HUMAN           ISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVE
GENPEPT_7304079      IATFGFRGEALASISHVAHLSIQTKTAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIE
GENPEPT_3880333      MKTYGFRGEALASLSHVAKVNIVSKRADAKCAYQANFLDGKMTADTKPAAGKNGTCITAT
GENPEPT_887629       VQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSR-NKGTTVLVS
                     : * *******:*:. :*::.: :. :  *.        *:: . ....  ::** :   

GENPEPT_7595954      DLFYNIITRRKALKNPSE-EYGKILEVVGRYSIHNSGISFSVK---KQGETVSDVRTLPN
GENPEPT_1724118      DLFYNIITRKKALKNPSE-EYGKILEVVGRYSIHNSGISFSVK---KQGETVSDVRTLPN
MLH1_HUMAN           DLFYNIATRRKALKNPSE-EYGKILEVVGRYSVHNAGISFSVK---KQGETVADVRTLPN
GENPEPT_7304079      DLFYNMPQRRQALRSPAE-EFQRLSEVLARYAVHNPRVGFTLR---KQGDAQPALRTPVA
GENPEPT_3880333      DLFYNLPTRRNKMTTHGE-EAKMVNDTLLRFAIHRPDVSFALR---Q--NQAGDFRTKGD
GENPEPT_887629       QLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWNITPKGKKNLILSTMRN
                     :**:*:  *:: : .  : :      .:  ::: .. : *::       .    . *   

GENPEPT_7595954      ATTVDNIRSIFGNAVSRELIEVGCEDKTLAFKMNGYISN----------ANYSVKKCIFL
GENPEPT_1724118      ATTVDNIRSIFGNAVSRELIEVGCEDKTLAFKMNGYISN----------ANYSVKKCIFL
MLH1_HUMAN           ASTVDNIRSIFGNAVSRELIEIGCEDKTLAFKMNGYISN----------ANYSVKKCIFL
GENPEPT_7304079      SSRSENIRIIYGAAISKELLEFSHRDEVYKFEAECLITQ----------VNYSAKKCQML
GENPEPT_3880333      GNFRDVVCNLLGRDVADTILPLSLNSTRLKFTFTGHISKPIASATAAIAQNRKTSRSFFS
GENPEPT_887629       SSMRKNISSVFGAGGMR-------------------------------------------
                     ..  . :  : *                                                

GENPEPT_7595954      LFINHRLVESAALRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHE
GENPEPT_1724118      LFINHRLVESAALKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHE
MLH1_HUMAN           LFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHE
GENPEPT_7304079      LFINQRLVESTALRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQ
GENPEPT_3880333      VFINGRSVRCDILKHPIDEVLGARQLH--AQFCALHLQIDETRIDVNVHPTKNSVIFLEK
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      ESILQRVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEAARPTTG--------------
GENPEPT_1724118      ESILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEAVKSTTG--------------
MLH1_HUMAN           ESILERVQQHIESKLLGSNSSRMYFTQTLLPGLAGPSGEMVKSTTS--------------
GENPEPT_7304079      EEIVDSIKQQVEARLLGSNATRTFYKQLRLPGAP-----------D--------------
GENPEPT_3880333      EEIIEEIRAYFEKVIGEIFGFEALDVEKPEEEQPDIENLVMIPMSQSLKSIEAIRKPDTK
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      ---VASSSTSGSGDKVYAYQMVRTDSRDQKLDAFLQPVSSLVPSQPQDPAPVRGARTEGS
GENPEPT_1724118      ---IASSSTSGSGDKVHAYQMVRTDSRDQKLDAFMQPVSRRLPSQPQD--PVPGNRTEGS
MLH1_HUMAN           ---LTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQ--AIVTEDKTDIS
GENPEPT_7304079      ---LDETQLADKTQRIYPKEMVRTDSTEQKLDKFLAPLVK--------------------
GENPEPT_3880333      PEFKSSPSAWKSDKKRVDYMEVRTDAKERKIDEFVTRGGAVGPTTSND------------
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      PERATREDEEMLALPAPAEAAAESENLERESLMETSDAAQKAAPTSSPGSSRKRHREDSD
GENPEPT_1724118      PEKAMQKDQEISELPAPMEAAADSASLERESVIGASEVVAPQRHPSSPGSSRKRHPEDSD
MLH1_HUMAN           SGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSS--NPRKRHREDSD
GENPEPT_7304079      ---------------------------------------SDSGVSSSSSQEASRLPEES-
GENPEPT_3880333      -------DIFGGSGILKRARTEDSTGGEKEPEDLNTDFDDVSMVSLVSTADGRRLNESQD
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      VEMVENASGKEMTAACYPRRRIINLTSVLSLQEEISERCHETLREILRNHSFVGCVNPQW
GENPEPT_1724118      VEMMENDSRKEMTAACYPRRRIINLTSVLSLQEEINDRGHETLREMLRNHTFVGCVNPQW
MLH1_HUMAN           VEMVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREMLHNHSFVGCVNPQW
GENPEPT_7304079      -----------FRVTAAKKSREVRLSSVLDMRKRVERQCSVQLRSTLKNLVYVGCVDERR
GENPEPT_3880333      LG-----EDDDVDFEYGKTHREFHFESIEVLRKEIIANSSQSLREMFKTSTFVGSINVKQ
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESG--
GENPEPT_1724118      ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESG--
MLH1_HUMAN           ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESG--
GENPEPT_7304079      ALFQHETRLYMCNTRSFSEELFYQRMIYEFQNCSEITISPPLPLKELLILSLESEAAG--
GENPEPT_3880333      VLIQFGTSLYHLDFSTVLREFFYQISVFSFGNYGSYRLDEEPPAIIEILELLGELSTREP
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      --WTEDDGPKEGLAEYIVEFLKKKAEMLADYFSVEIDEEGN----LIGLPLLIDSYVPPL
GENPEPT_1724118      --WTEEDGPKEGLAEYIVEFLKKKAKMLADYFSVEIDEEGN----LIGLPLLIDSYVPPL
MLH1_HUMAN           --WTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGN----LIGLPLLIDNYVPPL
GENPEPT_7304079      --WTPEDGDKAELADGAADILLKKAPIMREYFGLRISEDGM----LESLPSLLHQHRPCV
GENPEPT_3880333      NYAAFEVFANVENRFAAEKLLAEHADLLHDYFAIKLDQLENGRLHITEIPSLVHYFVPQL
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      EGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYILEESTLSGQQSDMPGSTSK
GENPEPT_1724118      EGLPIFILRLATEVNWDEE-ECFESLSKECAVFYSIRKQYILEESALSGQQSDMPGSPSK
MLH1_HUMAN           EGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEESTLSGQQSEVPGSIPN
GENPEPT_7304079      AHLPVYLLRLATEVDWEQETRCFETFCRETARFY--------------AQLDWREGATAG
GENPEPT_3880333      EKLPFLIATLVLNVDYDDEQNTFRTICRAIGDLFTLDTN-------FITLDKKISAFSAT
GENPEPT_887629       ------------------------------------------------------------


GENPEPT_7595954      PWKWTVEHIIYKAFRSHLLPPKHFTEDGNVLQLANLPDLYKVFERC--
GENPEPT_1724118      PWKWTVEHIIYKAFRSHLLPPKHFTEDGNVLQLANLPDLCKVFERC--
MLH1_HUMAN           SWKWTVEHIVYKALRSHILPPKHFTEDGNILQLANLPDLYKVFERC--
GENPEPT_7304079      FSRWTMEHVLFPAFKKYLLPPPRIKD--QIYELTNLPTLYKVFERC--
GENPEPT_3880333      PWKTLIKEVLMPLVKRKFIPPEHFKQAGVIRQLADSHDLYKVFERCGT
GENPEPT_887629       ------------------------------------------------

    Clustal W dendrogram



    Unrooted tree (generated by Phylip's Drawtree)

    Download a PostScript version of the output



    Phylip-format dendrogram

    (
(
GENPEPT_7595954:0.03542,
GENPEPT_1724118:0.04780)
:0.02879,
(
GENPEPT_7304079:0.24622,
(
GENPEPT_3880333:0.35127,
GENPEPT_887629:0.41435)
:0.07294)
:0.18680,
MLH1_HUMAN:0.05261);

    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_7595954      760 aa
Sequence 2: GENPEPT_1724118      757 aa
Sequence 3: GENPEPT_7304079      664 aa
Sequence 4: GENPEPT_3880333      779 aa
Sequence 5: GENPEPT_887629       256 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:  32
Sequences (1:5) Aligned. Score:  25
Sequences (1:6) Aligned. Score:  88
Sequences (2:3) Aligned. Score:  48
Sequences (2:4) Aligned. Score:  32
Sequences (2:5) Aligned. Score:  25
Sequences (2:6) Aligned. Score:  86
Sequences (3:4) Aligned. Score:  33
Sequences (3:5) Aligned. Score:  26
Sequences (3:6) Aligned. Score:  51
Sequences (4:5) Aligned. Score:  23
Sequences (4:6) Aligned. Score:  32
Sequences (5:6) Aligned. Score:  28
Time for pairwise alignment: 2.196014

Guide tree        file created:   [../tmp-dir/21345.CLUSTALW.dnd]
Start of Multiple Alignment
There are 5 groups
Aligning...
Group 1: Sequences:   2      Score:15727
Group 2: Sequences:   3      Score:15399
Group 3: Sequences:   4      Score:10965
Group 4: Sequences:   5      Score:7757
Group 5:                     Delayed
Sequence:5     Score:2556
Time for multiple alignment: 3.586259

Alignment Score 25187
CLUSTAL-Alignment file created  [../tmp-dir/21345.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.