Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)
  • Human DNA mismatch repair protein homolog (hMLH1) mRNA, complete
  • Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
  • S.cerevisiae chromosome XIII cosmid 8520_
  • Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
  • Drosophila melanogaster mutL homolog (Mlh1) gene, complete cds_

    Fasta label (*)Workbench label
    GENPEPT:463989Human DNA mismatch repair protein homolog (hMLH1) mRNA, complete
    GENPEPT:7595954Mus musculus MutL homolog 1 protein (MLH1) mRNA, complete cds.
    GENPEPT:825572S.cerevisiae chromosome XIII cosmid 8520_
    GENPEPT:1724118Rattus norvegicus mismatch repair protein (MLH1) mRNA, complete
    GENPEPT:3192877Drosophila melanogaster mutL homolog (Mlh1) gene, 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_1724118      --MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMTENCLDAKSTNIQVIVREGGLKL
GENPEPT_7595954      --MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTNIQVVVKEGGLKL
GENPEPT_463989       --MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKL
GENPEPT_3192877      MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALKELLENSLDAQSTHIQVQVKAGGLKL
GENPEPT_825572       -----MSLRIKALDASVVNKIAAGEIIISPVNALKEMMENSIDANATMIDILVKEGGIKV
                           .  *: **  ***:*****:*  *.**:**: **.:**::* *:: *: **:*:

GENPEPT_1724118      IQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLAMISTYGFRGEALASISHVAHVTITTK
GENPEPT_7595954      IQIQDNGTGIRKEDLDIVCERFTTSKLQTFEDLASISTYGFRGEALASISHVAHVTITTK
GENPEPT_463989       IQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTK
GENPEPT_3192877      LQIQDNGTGIRREDLAIVCERFTTSKLTRFEDLSQIATFGFRGEALASISHVAHLSIQTK
GENPEPT_825572       LQITDNGSGINKADLPILCERFTTSKLQKFEDLSQIQTYGFRGEALASISHVARVTVTTK
                     :** ***:**.: ** *:*********  ****: * *:**************:::: **

GENPEPT_1724118      TADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRKKALKNPSEEYGKILE
GENPEPT_7595954      TADGKCAYRASYSDGKLQAPPKPCAGNQGTLITVEDLFYNIITRRKALKNPSEEYGKILE
GENPEPT_463989       TADGKCAYRASYSDGKLKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILE
GENPEPT_3192877      TAKEKCGYKATYADGKLQGQPKPCAGNQGTIICIEDLFYNMPQRRQALRSPAEEFQRLSE
GENPEPT_825572       VKEDRCAWRVSYAEGKMLESPKPVAGKDGTTILVEDLFFNIPSRLRALRSHNDEYSKILD
                     . . :*.::.:*::**:   *** **::** * :****:*:  * :**:.  :*: :: :

GENPEPT_1724118      VVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG-CEDKT
GENPEPT_7595954      VVGRYSIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG-CEDKT
GENPEPT_463989       VVGRYSVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIG-CEDKT
GENPEPT_3192877      VLARYAVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAAISKELLEFS-HRDEV
GENPEPT_825572       VVGRYAIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKSVASNLITFHISKVED
                     *:.**::*.  :.*: :* *::   : .    :  :.** ::. ::: :*: .   . : 

GENPEPT_1724118      LAFK-MNGYISNANYSVKKCIF-LLFINHRLVESAALKKAIEAVYAAYLPKNTHPFLYLI
GENPEPT_7595954      LAFK-MNGYISNANYSVKKCIF-LLFINHRLVESAALRKAIETVYAAYLPKNTHPFLYLS
GENPEPT_463989       LAFK-MNGYISNANYSVKKCIF-LLFINHRLVESTSLRKAIETVYAAYLPKNTHPFLYLS
GENPEPT_3192877      YKFE-AECLITQVNYSAKKCQM-LLFINQRLVESTALRTSVDSIYATYLPRGHHPFVYMS
GENPEPT_825572       LNLESVDGKVCNLNFISKKSISPIFFINNRLVTCDLLRRALNSVYSNYLPKGNRPFIYLG
                       ::  :  : : *:  **.   ::***:*** .  *: :::::*: ***:. :**:*: 

GENPEPT_1724118      LEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG-
GENPEPT_7595954      LEISPQNVDVNVHPTKHEVHFLHEESILQRVQQHIESKLLGSNSSRMYFTQTLLPGLAG-
GENPEPT_463989       LEISPQNVDVNVHPTKHEVHFLHEESILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG-
GENPEPT_3192877      LTLPPQNLDVNVHPTKHEVHFLYQEEIVDSIKQQVEARLLGSNATRTFYKQLRLPGAP--
GENPEPT_825572       IVIDPAAVDVNVHPTKREVRFLSQDEIIEKIANQLHAELSAIDTSRTFKASSISTNKPES
                     : : *  :********:**:** ::.*:: : :::.:.* . :::* :  .   .. .  

GENPEPT_1724118      -----PSGEAVKSTTGIASSSTSGSGDKVHAYQMVRTDSRDQKLDAFMQPVSRRLPSQPQ
GENPEPT_7595954      -----PSGEAARPTTGVASSSTSGSGDKVYAYQMVRTDSRDQKLDAFLQPVSSLVPSQPQ
GENPEPT_463989       -----PSGEMVKSTTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQ
GENPEPT_3192877      ---------------DLDETQLADKTQRIYPKEMVRTDSTEQKLDKFLAPLVK-------
GENPEPT_825572       LIPFNDTIESDRNRKSLRQAQVVENSYTTANSQLRKAKRQENKLVRIDASQAKITSFLSS
                                    .: .:.   .       :: ::.  ::**  :  .          

GENPEPT_1724118      D--PVPGNRTEGSPEKAMQKDQEISELPAPMEAAADSASLERESVIGASEVVAPQRHPSS
GENPEPT_7595954      DPAPVRGARTEGSPERATREDEEMLALPAPAEAAAESENLERESLMETSDAAQKAAPTSS
GENPEPT_463989       --AIVTEDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRGPTSS
GENPEPT_3192877      ----------------------------------------------------SDSGVSSS
GENPEPT_825572       S--QQFNFEGSSTKRQLSEPKVTNVSHSQEAEKLTLNESEQPRDANTINDNDLKDQPKKK
                                                                               ..

GENPEPT_1724118      PGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRIINLTSVLSLQEEINDRGHETLREML
GENPEPT_7595954      PGSSRKRHREDSDVEMVENASGKEMTAACYPRRRIINLTSVLSLQEEISERCHETLREIL
GENPEPT_463989       --NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRIINLTSVLSLQEEINEQGHEVLREML
GENPEPT_3192877      SSQEASRLPEES------------FRVTAAKKSREVRLSSVLDMRKRVERQCSVQLRSTL
GENPEPT_825572       QKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNVNLTSIKKLREKVDDSIHRELTDIF
                           :  . :                   .   :.*:*: .:::.:.      * . :

GENPEPT_1724118      RNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLPEPAPLF
GENPEPT_7595954      RNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLSEPAPLF
GENPEPT_463989       HNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEELFYQILIYDFANFGVLRLSEPAPLF
GENPEPT_3192877      KNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEELFYQRMIYEFQNCSEITICPPLPLK
GENPEPT_825572       ANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYELFYQIGLTDFANFGKINLQSTNVSD
                      *  :** *: .   *  **: :*:: :  ... *****  : :* * . : :  .    

GENPEPT_1724118      DFAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAKMLADYFSVEIDEEGN--------
GENPEPT_7595954      DLAMLALDSPESGWTEDDGPKEGLAEYIVEFLKKKAEMLADYFSVEIDEEGN--------
GENPEPT_463989       DLAMLALDSPESGWTEEDGPKEGLAEYIVEFLKKKAEMLADYFSLEIDEEGN--------
GENPEPT_3192877      ELLILSLESRAAGWTPEDEDKAELADGAADILLKKAPIMREYFGLRISEDGM--------
GENPEPT_825572       DIVLYNLLSEFDELN-DDASK----EKIISKIWDMSSMLNEYYSIELVNDGLDNDLKSVK
                     :: :  * *     . :*  *    :   . : . : :: :*:.:.: ::*         

GENPEPT_1724118      LIGLPLLIDSYVPPLEGLPIFILRLATEVNWDEE-ECFESLSKECAVFYSIRKQYILEES
GENPEPT_7595954      LIGLPLLIDSYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYILEES
GENPEPT_463989       LIGLPLLIDNYVPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEES
GENPEPT_3192877      LESLPSLLHQHRPCVAHLPVYLLRLATEVDWEQETRCFETFCRETARFY-----------
GENPEPT_825572       LKSLPLLLKGYIPSLVKLPFFIYRLGKEVDWEDEQECLDGILREIALLYIPDMVPKVDTS
                     * .** *:. : * :  **.:: **..**:*::* .*:: : :* * :*           

GENPEPT_1724118      ALSGQQSDMPGSPSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLANLPDLCKVF
GENPEPT_7595954      TLSGQQSDMPGSTSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLANLPDLYKVF
GENPEPT_463989       TLSGQQSEVPGSIPNSWKWT--VEHIVYKALRSHILPPKHFTEDGNILQLANLPDLYKVF
GENPEPT_3192877      ---AQLDWREGATAVFSRWT--MEHVLFPAFKKYLLPPR---IKDQIYELTNLPTLYKVF
GENPEPT_825572       DASLSEDEKAQFINRKEHISSLLEHVLFPCIKRRFLAPRHILKD--VVEIANLPDLYKVF
                         . .          : :  :**::: .::  :*.*:    .  : :::*** * ***

GENPEPT_1724118      ERC
GENPEPT_7595954      ERC
GENPEPT_463989       ERC
GENPEPT_3192877      ERC
GENPEPT_825572       ERC
                     ***

    Clustal W dendrogram



    Unrooted tree (generated by Phylip's Drawtree)

    Download a PostScript version of the output



    Phylip-format dendrogram

    (
(
(
GENPEPT_3192877:0.24219,
GENPEPT_825572:0.37772)
:0.19411,
GENPEPT_463989:0.05567)
:0.02574,
GENPEPT_1724118:0.04825,
GENPEPT_7595954:0.03497);

    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_3192877      663 aa
Sequence 2: GENPEPT_1724118      757 aa
Sequence 3: GENPEPT_825572       769 aa
Sequence 4: GENPEPT_7595954      760 aa
Sequence 5: GENPEPT_463989       756 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  48
Sequences (1:3) Aligned. Score:  38
Sequences (1:4) Aligned. Score:  50
Sequences (1:5) Aligned. Score:  51
Sequences (2:3) Aligned. Score:  36
Sequences (2:4) Aligned. Score:  91
Sequences (2:5) Aligned. Score:  86
Sequences (3:4) Aligned. Score:  36
Sequences (3:5) Aligned. Score:  36
Sequences (4:5) Aligned. Score:  88
Time for pairwise alignment: 2.186492

Guide tree        file created:   [../tmp-dir/17104.CLUSTALW.dnd]
Start of Multiple Alignment
There are 4 groups
Aligning...
Group 1: Sequences:   2      Score:15727
Group 2: Sequences:   3      Score:15398
Group 3: Sequences:   4      Score:10921
Group 4: Sequences:   5      Score:10151
Time for multiple alignment: 4.390420

Alignment Score 24505
CLUSTAL-Alignment file created  [../tmp-dir/17104.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.