Biology WorkBench 3.2

Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)

MutL homolog 1 protein [Mus musculus]

hMlh1 proein

Mlh1 gene product [Drosophila melanogaster]

Mlh1p Saccharomyces cerevisiae

mismatch repair protein [Rattus norvegicus]

hypothetical protein T28A8.7 - Caenorhabditis elegans

Fasta label (*) Workbench label
gi_7595954_gb_AAF64514.1_AF250844_1 MutL homolog 1 protein [Mus musculus]

gi_463989_gb_AAC50285.1_ hMlh1 proein

gi_7304079_gb_AAF59117.1_ Mlh1 gene product [Drosophila melanogaster]

gi_460627_gb_AAA16835.1_ Mlh1p Saccharomyces cerevisiae

gi_13591989_ref_NP_112315.1_ mismatch repair protein [Rattus norvegicus]

gi_7508639_pir__T25389 hypothetical protein T28A8.7 - Caenorhabditis elegans

Fasta label (*)	Workbench label
gi_7595954_gb_AAF64514.1_AF250844_1	MutL homolog 1 protein [Mus musculus]
gi_463989_gb_AAC50285.1_	hMlh1 proein
gi_7304079_gb_AAF59117.1_	Mlh1 gene product [Drosophila melanogaster]
gi_460627_gb_AAA16835.1_	Mlh1p Saccharomyces cerevisiae
gi_13591989_ref_NP_112315.1_	mismatch repair protein [Rattus norvegicus]
gi_7508639_pir__T25389	hypothetical protein T28A8.7 - Caenorhabditis elegans

(*) 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


gi_13591989_ref_NP_112315.1_      -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
gi_7595954_gb_AAF64514.1_AF2      -----------------MAFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
gi_463989_gb_AAC50285.1__hML      -----------------MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIK
gi_7304079_gb_AAF59117.1__Ml      ---------------MAEYLQPGVIRKLDEVVVNRIAAGEIIQRPANALK
gi_460627_gb_AAA16835.1__Mlh      --------------------MSLRIKALDASVVNKIAAGEIIISPVNALK
gi_7508639_pir__T25389_hypot      MWHCGYRTRNCDEFSKIEFSLMGLIQRLPQDVVNRMAAGEVLARPCNAIK
                                                          *: *   ***::****::  * **:*

gi_13591989_ref_NP_112315.1_      EMTENCLDAKSTNIQVIVREGGLKLIQIQDNGTGIRKEDLDIVCERFTTS
gi_7595954_gb_AAF64514.1_AF2      EMIENCLDAKSTNIQVVVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTS
gi_463989_gb_AAC50285.1__hML      EMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTS
gi_7304079_gb_AAF59117.1__Ml      ELLENSLDAQSTHIQVQVKAGGLKLLQIQDNGTGIRREDLAIVCERFTTS
gi_460627_gb_AAA16835.1__Mlh      EMMENSIDANATMIDILVKEGGIKVLQITDNGSGINKADLPILCERFTTS
gi_7508639_pir__T25389_hypot      ELVENSLDAGATEIMVNMQNGGLKLLQVSDNGKGIEREDFALVCERFATS
                                  *: **.:** :* * : :: **:*::*: ***.**.: *: ::****:**

gi_13591989_ref_NP_112315.1_      KLQTFEDLAMISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG
gi_7595954_gb_AAF64514.1_AF2      KLQTFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG
gi_463989_gb_AAC50285.1__hML      KLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDG
gi_7304079_gb_AAF59117.1__Ml      KLTRFEDLSQIATFGFRGEALASISHVAHLSIQTKTAKEKCGYKATYADG
gi_460627_gb_AAA16835.1__Mlh      KLQKFEDLSQIQTYGFRGEALASISHVARVTVTTKVKEDRCAWRVSYAEG
gi_7508639_pir__T25389_hypot      KLQKFEDLMHMKTYGFRGEALASLSHVAKVNIVSKRADAKCAYQANFLDG
                                  **  ****  : *:*********:****::.: :*  . :*.::..: :*

gi_13591989_ref_NP_112315.1_      KLQAPPKPCAGNQGTLITVEDLFYNIITRKKALKNPSEEYGKILEVVGRY
gi_7595954_gb_AAF64514.1_AF2      KLQAPPKPCAGNQGTLITVEDLFYNIITRRKALKNPSEEYGKILEVVGRY
gi_463989_gb_AAC50285.1__hML      KLKAPPKPCAGNQGTQITVEDLFYNIATRRKALKNPSEEYGKILEVVGRY
gi_7304079_gb_AAF59117.1__Ml      KLQGQPKPCAGNQGTIICIEDLFYNMPQRRQALRSPAEEFQRLSEVLARY
gi_460627_gb_AAA16835.1__Mlh      KMLESPKPVAGKDGTTILVEDLFFNIPSRLRALRSHNDEYSKILDVVGRY
gi_7508639_pir__T25389_hypot      KMTADTKPAAGKNGTCITATDLFYNLPTRRNKMTTHGEEAKMVNDTLLRF
                                  *:   .** **::** *   ***:*:  * . : .  :*   : :.: *:

gi_13591989_ref_NP_112315.1_      SIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG-
gi_7595954_gb_AAF64514.1_AF2      SIHNSGISFSVKKQGETVSDVRTLPNATTVDNIRSIFGNAVSRELIEVG-
gi_463989_gb_AAC50285.1__hML      SVHNAGISFSVKKQGETVADVRTLPNASTVDNIRSIFGNAVSRELIEIG-
gi_7304079_gb_AAF59117.1__Ml      AVHNPRVGFTLRKQGDAQPALRTPVASSRSENIRIIYGAAISKELLEFS-
gi_460627_gb_AAA16835.1__Mlh      AIHSKDIGFSCKKFGDSNYSLSVKPSYTVQDRIRTVFNKSVASNLITFHI
gi_7508639_pir__T25389_hypot      AIHRPDVSFALRQ--NQAGDFRTKGDGNFRDVVCNLLGRDVADTILPLS-
                                  ::*   :.*: ::  :    . .    .  : :  : .  ::  :: .  

gi_13591989_ref_NP_112315.1_      CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA
gi_7595954_gb_AAF64514.1_AF2      CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESAA
gi_463989_gb_AAC50285.1__hML      CEDKTLAFK-MNGYISNANYSVKKCI----------FLLFINHRLVESTS
gi_7304079_gb_AAF59117.1__Ml      HRDEVYKFE-AECLITQVNYSAKKCQ----------MLLFINQRLVESTA
gi_460627_gb_AAA16835.1__Mlh      SKVEDLNLESVDGKVCNLNFISKKSIS---------LIFFINNRLVTCDL
gi_7508639_pir__T25389_hypot      LNSTRLKFT-FTGHISKPIASATAAIAQNRKTSRSFFSVFINGRSVRCDI
                                   .     :      : :     . .           : .*** * * .  

gi_13591989_ref_NP_112315.1_      LKKAIEAVYAAYLPKNTHPFLYLILEISPQNVDVNVHPTKHEVHFLHEES
gi_7595954_gb_AAF64514.1_AF2      LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEES
gi_463989_gb_AAC50285.1__hML      LRKAIETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEES
gi_7304079_gb_AAF59117.1__Ml      LRTSVDSIYATYLPRGHHPFVYMSLTLPPQNLDVNVHPTKHEVHFLYQEE
gi_460627_gb_AAA16835.1__Mlh      LRRALNSVYSNYLPKGFRPFIYLGIVIDPAAVDVNVHPTKREVRFLSQDE
gi_7508639_pir__T25389_hypot      LKHPIDEVLG--ARQLHAQFCALHLQIDETRIDVNVHPTKNSVIFLEKEE
                                  *: .:: : .    :    *  : : :    :********..* ** ::.

gi_13591989_ref_NP_112315.1_      ILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEAVKSTTG
gi_7595954_gb_AAF64514.1_AF2      ILQRVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEAARPTTG
gi_463989_gb_AAC50285.1__hML      ILERVQQHIESKLLGSNSSRMYFTQTLLPGLAG------PSGEMVKSTTS
gi_7304079_gb_AAF59117.1__Ml      IVDSIKQQVEARLLGSNATRTFYKQLRLPGAP-----------------D
gi_460627_gb_AAA16835.1__Mlh      IIEKIANQLHAELSAIDTSRTFKASSISTNKPESLIPFNDTIESDRNRKS
gi_7508639_pir__T25389_hypot      IIEEIRAYFEKVIGEIFGFEALDVEKPEEEQPD--------IENLVMIPM
                                  *:: :   ..  :      .    .      .                  

gi_13591989_ref_NP_112315.1_      IASSSTSGSGDKVHAYQMVRTDSRDQKLDAFMQPVSRRLPSQPQD--PVP
gi_7595954_gb_AAF64514.1_AF2      VASSSTSGSGDKVYAYQMVRTDSRDQKLDAFLQPVSSLVPSQPQDPAPVR
gi_463989_gb_AAC50285.1__hML      LTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQ--AIVT
gi_7304079_gb_AAF59117.1__Ml      LDETQLADKTQRIYPKEMVRTDSTEQKLDKFLAPLVK-------------
gi_460627_gb_AAA16835.1__Mlh      LRQAQVVENSYTTANSQLRKAKRQENKLVRIDASQAKITSFLSSS--QQF
gi_7508639_pir__T25389_hypot      SQSLKSIEAIRKPDTKPEFKSSPSAWKSDKKRVDYMEVRTDAKERKIDEF
                                    . .              ::.    *                       

gi_13591989_ref_NP_112315.1_      GNRTEGSPEKAMQKDQEISELPAPMEAAADSASLERESVIGASEVVAPQR
gi_7595954_gb_AAF64514.1_AF2      GARTEGSPERATREDEEMLALPAPAEAAAESENLERESLMETSDAAQKAA
gi_463989_gb_AAC50285.1__hML      EDKTDISSGRARQQDEEMLELPAPAEVAAKNQSLEGDTTKGTSEMSEKRG
gi_7304079_gb_AAF59117.1__Ml      ----------------------------------------------SDSG
gi_460627_gb_AAA16835.1__Mlh      NFEGSSTKRQLSEPKVTNVSHSQEAEKLTLNESEQPRDANTINDNDLKDQ
gi_7508639_pir__T25389_hypot      VTRGGAVGPTTSNDDIFGGSGILKRARTEDSTGGEKEPEDLNTDFDDVSM


gi_13591989_ref_NP_112315.1_      HPSSPGSSRKRHPEDSDVEMMENDSRKEMTAACYPRRRIINLTSVLSLQE
gi_7595954_gb_AAF64514.1_AF2      PTSSPGSSRKRHREDSDVEMVENASGKEMTAACYPRRRIINLTSVLSLQE
gi_463989_gb_AAC50285.1__hML      PTSS--NPRKRHREDSDVEMVEDDSRKEMTAACTPRRRIINLTSVLSLQE
gi_7304079_gb_AAF59117.1__Ml      VSSSSSQEASRLPEES------------FRVTAAKKSREVRLSSVLDMRK
gi_460627_gb_AAA16835.1__Mlh      PKKKQKLGDYKVPSIADDEKNALPISKDGYIRVPKERVNVNLTSIKKLRE
gi_7508639_pir__T25389_hypot      VSLVSTADGRRLNESQD-----LGEDDDVDFEYGKTHREFHFESIEVLRK
                                            :  .                         ..: *:  :::

gi_13591989_ref_NP_112315.1_      EINDRGHETLREMLRNHTFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
gi_7595954_gb_AAF64514.1_AF2      EISERCHETLREILRNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
gi_463989_gb_AAC50285.1__hML      EINEQGHEVLREMLHNHSFVGCVNPQW--ALAQHQTKLYLLNTTKLSEEL
gi_7304079_gb_AAF59117.1__Ml      RVERQCSVQLRSTLKNLVYVGCVDERR--ALFQHETRLYMCNTRSFSEEL
gi_460627_gb_AAA16835.1__Mlh      KVDDSIHRELTDIFANLNYVGVVDEERRLAAIQHDLKLFLIDYGSVCYEL
gi_7508639_pir__T25389_hypot      EIIANSSQSLREMFKTSTFVGSINVKQ--VLIQFGTSLYHLDFSTVLREF
                                  .:       * . : .  :** :: .   .  *.   *:  :  ..  *:

gi_13591989_ref_NP_112315.1_      FYQILIYDFANFGVLRLPEPAPLFDFAMLALDSPESGWTEEDGPKEGLA-
gi_7595954_gb_AAF64514.1_AF2      FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEDDGPKEGLA-
gi_463989_gb_AAC50285.1__hML      FYQILIYDFANFGVLRLSEPAPLFDLAMLALDSPESGWTEEDGPKEGLA-
gi_7304079_gb_AAF59117.1__Ml      FYQRMIYEFQNCSEITISPPLPLKELLILSLESEAAGWTPEDGDKAELA-
gi_460627_gb_AAA16835.1__Mlh      FYQIGLTDFANFGKINLQSTNVSDDIVLYNLLSEFDELN-DDASK-----
gi_7508639_pir__T25389_hypot      FYQISVFSFGNYGSYRLDE-EPPAIIEILELLGELSTREPNYAAFEVFAN
                                  ***  : .* * .   :        : :  * .       : .       

gi_13591989_ref_NP_112315.1_      ----EYIVEFLKKKAKMLADYFSVEIDEEGN--------LIGLPLLIDSY
gi_7595954_gb_AAF64514.1_AF2      ----EYIVEFLKKKAEMLADYFSVEIDEEGN--------LIGLPLLIDSY
gi_463989_gb_AAC50285.1__hML      ----EYIVEFLKKKAEMLADYFSLEIDEEGN--------LIGLPLLIDNY
gi_7304079_gb_AAF59117.1__Ml      ----DGAADILLKKAPIMREYFGLRISEDGM--------LESLPSLLHQH
gi_460627_gb_AAA16835.1__Mlh      ----EKIISKIWDMSSMLNEYYSIELVNDGLDNDLKSVKLKSLPLLLKGY
gi_7508639_pir__T25389_hypot      VENRFAAEKLLAEHADLLHDYFAIKLDQLENGR----LHITEIPSLVHYF
                                          . : . : :: :*:.:.: :           :  :* *:. .

gi_13591989_ref_NP_112315.1_      VPPLEGLPIFILRLATEVNWDEE-ECFESLSKECAVFYSIRKQYILEESA
gi_7595954_gb_AAF64514.1_AF2      VPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYILEEST
gi_463989_gb_AAC50285.1__hML      VPPLEGLPIFILRLATEVNWDEEKECFESLSKECAMFYSIRKQYISEEST
gi_7304079_gb_AAF59117.1__Ml      RPCVAHLPVYLLRLATEVDWEQETRCFETFCRETARFY------------
gi_460627_gb_AAA16835.1__Mlh      IPSLVKLPFFIYRLGKEVDWEDEQECLDGILREIALLYIPDMVPKVDTLD
gi_7508639_pir__T25389_hypot      VPQLEKLPFLIATLVLNVDYDDEQNTFRTICRAIGDLFTLDTN-------
                                   * :  **. :  *  :*::::* . :  : :  . ::            

gi_13591989_ref_NP_112315.1_      LSGQQSDMPGSPSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLA
gi_7595954_gb_AAF64514.1_AF2      LSGQQSDMPGSTSKPWKWT--VEHIIYKAFRSHLLPPKHFTEDGNVLQLA
gi_463989_gb_AAC50285.1__hML      LSGQQSEVPGSIPNSWKWT--VEHIVYKALRSHILPPKHFTEDGNILQLA
gi_7304079_gb_AAF59117.1__Ml      --AQLDWREGATAGFSRWT--MEHVLFPAFKKYLLPPPRIKD--QIYELT
gi_460627_gb_AAA16835.1__Mlh      ASLSEDEKAQFINRKEHISSLLEHVLFPCIKRRFLAPRHILK--DVVEIA
gi_7508639_pir__T25389_hypot      --FITLDKKISAFSATPWKTLIKEVLMPLVKRKFIPPEHFKQAGVIRQLA
                                                    .  ::.::   .:  ::.* :: .   : :::

gi_13591989_ref_NP_112315.1_      NLPDLCKVFERC--
gi_7595954_gb_AAF64514.1_AF2      NLPDLYKVFERC--
gi_463989_gb_AAC50285.1__hML      NLPDLYKVFERC--
gi_7304079_gb_AAF59117.1__Ml      NLPTLYKVFERC--
gi_460627_gb_AAA16835.1__Mlh      NLPDLYKVFERC--
gi_7508639_pir__T25389_hypot      DSHDLYKVFERCGT
                                  :   * ******

Clustal W dendrogram

Unrooted tree (generated by Phylip's Drawtree)

Download a PostScript version of the output

Phylip-format dendrogram

(
(
(
(
gi_7508639_pir__T25389_hypot:0.37453,
gi_460627_gb_AAA16835.1__Mlh:0.33028)
:0.04951,
gi_7304079_gb_AAF59117.1__Ml:0.24191)
:0.19214,
gi_463989_gb_AAC50285.1__hML:0.05571)
:0.02570,
gi_13591989_ref_NP_112315.1_:0.04837,
gi_7595954_gb_AAF64514.1_AF2:0.03486);

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: gi_7508639_pir__T25389_hypot      779 aa
Sequence 2: gi_13591989_ref_NP_112315.1_      757 aa
Sequence 3: gi_460627_gb_AAA16835.1__Mlh      769 aa
Sequence 4: gi_7304079_gb_AAF59117.1__Ml      664 aa
Sequence 5: gi_463989_gb_AAC50285.1__hML      756 aa
Sequence 6: gi_7595954_gb_AAF64514.1_AF2      760 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  31
Sequences (1:3) Aligned. Score:  29
Sequences (1:4) Aligned. Score:  33
Sequences (1:5) Aligned. Score:  32
Sequences (1:6) Aligned. Score:  32
Sequences (2:3) Aligned. Score:  36
Sequences (2:4) Aligned. Score:  48
Sequences (2:5) Aligned. Score:  86
Sequences (2:6) Aligned. Score:  91
Sequences (3:4) Aligned. Score:  37
Sequences (3:5) Aligned. Score:  36
Sequences (3:6) Aligned. Score:  36
Sequences (4:5) Aligned. Score:  51
Sequences (4:6) Aligned. Score:  50
Sequences (5:6) Aligned. Score:  88
Time for pairwise alignment: 1.150650

Guide tree        file created:   [../tmp-dir/21027.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: 2.021060

Alignment Score 30185
CLUSTAL-Alignment file created  [../tmp-dir/21027.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.