Biology WorkBench 3.2

Version 3.2

CLUSTALW
Multiple Sequence Alignment

Selected Sequence(s)

hp9

HIV-1 isolate 2B-POL3 from Australia reverse transcriptase (pol)

Mycoplasma gallisepticum strain A5969var.B ribosomal proteins S10

HIV-1 isolate 4B-POL5 from Australia reverse transcriptase (pol)

Mesocricetus auratus cholesterol side-chain cleavage enzyme

Arabidopsis thaliana mRNA for dynamin-like protein ADLP3b (dlp3b

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


AY011100_11992579      ------------------------------------------------------------
AY011043_11992470      ------------------------------------------------------------
_11991512              -MESLIVLINTIQRACTVVGDHGGDSNALSSLWEALPSVAVVGGQSSGKSSVLESIVGRD
_11991512              -MESLIVLINTIQRACTVVGDHGGDSNALSSLWEALPSVAVVGGQSSGKSSVLESIVGRD
_11991512              -MESLIVLINTIQRACTVVGDHGGDSNALSSLWEALPSVAVVGGQSSGKSSVLESIVGRD
AF323965_11991654      MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANISTNSPRPFNEIPSPGDNGWLNLY
hp9                    ------------------------------------------------------------
AF036708_2766514       ------------------------------------------------------------


AY011100_11992579      ------------------------------------------------------------
AY011043_11992470      ------------------------------------------------------------
_11991512              FLPRGSGIVTRRPLVLQLHKTEN----GTEDNAEFLHLTNKKFTNFSLVRKEIEDETDRI
_11991512              FLPRGSGIVTRRPLVLQLHKTEN----GTEDNAEFLHLTNKKFTNFSLVRKEIEDETDRI
_11991512              FLPRGSGIVTRRPLVLQLHKTEN----GTEDNAEFLHLTNKKFTNFSLVRKEIEDETDRI
AF323965_11991654      HFWRENGTHRIHYHHMQNFQKYGPIYREKLGNKDSVYILDPEDAAQLFLSEGPYPERYLV
hp9                    ------------------------------------------------------------
AF036708_2766514       ------------------------------------------------------------


AY011100_11992579      ------------------------------------------------------------
AY011043_11992470      ------------------------------------------------------------
_11991512              TGKNKQISSIPIHLSIFSPNEGQPETIVEDIESMVRSYVEKPNCLILAISPANQDIATSD
_11991512              TGKNKQISSIPIHLSIFSPNEGQPETIVEDIESMVRSYVEKPNCLILAISPANQDIATSD
_11991512              TGKNKQISSIPIHLSIFSPNEGQPETIVEDIESMVRSYVEKPNCLILAISPANQDIATSD
AF323965_11991654      PPWVAYHQYYKRPIGVLFKSSEAWKKDRLVLNQEVMAPEAIKNFVPLLEGVVQDFINVLH
hp9                    ------------------------------------------------------------
AF036708_2766514       ------------------------------------------------------------


AY011100_11992579      EMEKEGKISKIGP-------------------------ENPYNTPVFAIKKKNSTRWRKL
AY011043_11992470      ELEKEGKISKIGP-------------------------ENPYNTPVFAIKKKDSTKWRKL
_11991512              AMKLAKEVDPIGDRTFGVLTKLDLMDKGTNALDVINGRSYKLKYPWVGIVNRSQADINKN
_11991512              AMKLAKEVDPIGDRTFGVLTKLDLMDKGTNALDVINGRSYKLKYPWVGIVNRSQADINKN
_11991512              AMKLAKEVDPIGDRTFGVLTKLDLMDKGTNALDVINGRSYKLKYPWVGIVNRSQADINKN
AF323965_11991654      RRIKQQKSGNFSG-------------------------DISDDLFRFAFESITSVVFGER
hp9                    --------------------------------------MNKPQTIYEKLGGENAMKAAVP
AF036708_2766514       --------------------------------------MQRIKKGDKVVIIAGKHKQKTG
                                                                 .     .           

AY011100_11992579      VDFRELNK--RTQDFWEVQLGIPHPAG---------------------------------
AY011043_11992470      VDFRELDK--RTQDFWEVQLGIPHPAG---------------------------------
_11991512              VDMMVARR--KEREYFETSPDYGHLATRMGSEYLAKLLSKLLESVIRSRIPSILSLINNN
_11991512              VDMMVARR--KEREYFETSPDYGHLATRMGSEYLAKLLSKLLESVIRSRIPSILSLINNN
_11991512              VDMMVARR--KEREYFETSPDYGHLATRMGSEYLAKLLSKLLESVIRSRIPSILSLINNN
AF323965_11991654      LGMLEEIVDPESQRFIDAIYQMFHTSVPMLN---------------------LPPELFRF
hp9                    LFYKKVLADERVKHFFKN-TDMDHQT----------------------------------
AF036708_2766514       IVLQVFVK--EQRAIVEGINMVKR------------------------------------
                       :         . :   .      :                                    

AY011100_11992579      -------LKKKKSVTVLDEGDAYFSVP-----LDKDFRKYT-------------------
AY011043_11992470      -------LKKKNSVTVLDVGDAYFSVP-----LDKDFRKYT-------------------
_11991512              IEELERELDQLGRPIAIDAGAQLYTILGMCRAFEKIFKEHLDGGRPGGARIYGIFDYNLP
_11991512              IEELERELDQLGRPIAIDAGAQLYTILGMCRAFEKIFKEHLDGGRPGGARIYGIFDYNLP
_11991512              IEELERELDQLGRPIAIDAGAQLYTILGMCRAFEKIFKEHLDGGRPGGARIYGIFDYNLP
AF323965_11991654      FRTKTWKEHAAAWDMIFKKADDYTQTFYWDLRQKQEFSKYPG------------------
hp9                    -------KQQTDFLTMLLGGPNHYKG-------KNMTEAHKG------------------
AF036708_2766514       --------HTKENAQNQKGG---------------IIEKEAP------------------
                               .          .                                        

AY011100_11992579      ----------TFTILSIN---NETPGIRYQYNVLPRGWK----GSPAIFQ----------
AY011043_11992470      ----------AFTIPSIN---NETPGIRYQYNVLPQGWK----GSPSIFQ----------
_11991512              TAIKKLPFDRHLSLQSVKRIVSESDGYQPHLIAPELGYRRLIEGSLNHFRGPAEASVNAI
_11991512              TAIKKLPFDRHLSLQSVKRIVSESDGYQPHLIAPELGYRRLIEGSLNHFRGPAEASVNAI
_11991512              TAIKKLPFDRHLSLQSVKRIVSESDGYQPHLIAPELGYRRLIEGSLNHFRGPAEASVNAI
AF323965_11991654      -VLYSLLGGNKLPFKNIQANITEMLAGGVDTTSMTLQWSLYEMAHNLKVQEMLRAEVLAA
hp9                    -----------MNLQNLH------------------------------------------
AF036708_2766514       -----------IHLSNLA------------------------------------------
                                  : : .:                                           

AY011100_11992579      ---------------------------------CSMTKILEP------------------
AY011043_11992470      ---------------------------------SSMTKILEP------------------
_11991512              HLILKELVRKAIAETEELKRFPSLQIELVAAANSSLDKFREESMKSVLRLVDMESSYLTV
_11991512              HLILKELVRKAIAETEELKRFPSLQIELVAAANSSLDKFREESMKSVLRLVDMESSYLTV
_11991512              HLILKELVRKAIAETEELKRFPSLQIELVAAANSSLDKFREESMKSVLRLVDMESSYLTV
AF323965_11991654      RRQAQGDMVKMVQLVPLLKASIKETLRLHPISVTVQRYLVDDLVLRNYRIPAKMLVQVAN
hp9                    -----------------------------------FDAIIEN------------------
AF036708_2766514       ----------------------------------LLDHKAKD------------------
                                                               .                   

AY011100_11992579      -----------------------------LRKQNPDIVIYQYMDDLY-VGSDLEIGQHRT
AY011043_11992470      -----------------------------FRKQNPDIVIYQYMDDLY-VGSDLEIGQHRT
_11991512              DFFRKLHVESQNMSLSSPTSAIDQYGDGHFRKIASNVAAYIKMVAET-LVNTIPKAVVHC
_11991512              DFFRKLHVESQNMSLSSPTSAIDQYGDGHFRKIASNVAAYIKMVAET-LVNTIPKAVVHC
_11991512              DFFRKLHVESQNMSLSSPTSAIDQYGDGHFRKIASNVAAYIKMVAET-LVNTIPKAVVHC
AF323965_11991654      YAMGRE---------PSFFPNPNKFDPTRWLEKSKNTTHFRYLSFGWGVRQCLGRRIAEL
hp9                    ------------------------------------------------LAATLKELGVTD
AF036708_2766514       -------------------------------------------------VRPVKVKYGTD
                                                                           :       

AY011100_11992579      KIEELRQHLLRWGFYTPDEKH---------------------------------------
AY011043_11992470      KIEELRQHLLRWGFYTPDKKH---------------------------------------
_11991512              QVRQAKLSLLNYFYAQISQSQGKRLGQLLDENPALMERRMQCAKRLELYKKARDEIDAAV
_11991512              QVRQAKLSLLNYFYAQISQSQGKRLGQLLDENPALMERRMQCAKRLELYKKARDEIDAAV
_11991512              QVRQAKLSLLNYFYAQISQSQGKRLGQLLDENPALMERRMQCAKRLELYKKARDEIDAAV
AF323965_11991654      EMTIFLINVLENFRIELQSLHDVGTKFNLILMPEKPILFNLQPLKKDLGTTTNR------
hp9                    AVINEAAKVIEHTRKDMLGK----------------------------------------
AF036708_2766514       PKTNKKVRLSRKTNNLVGGQ----------------------------------------
                               : .                                                 

AY011100_11992579      ---
AY011043_11992470      ---
_11991512              WVR
_11991512              WVR
_11991512              WVR
AF323965_11991654      ---
hp9                    ---
AF036708_2766514       ---

Clustal W dendogram

Unrooted Tree (generated by Phylip's Drawtree)

Download a PostScript version of the output

Phylip-format dendogram

(
(
(
(
_11991512:0.00000,
_11991512:0.00000)
:0.00000,
_11991512:0.00000)
:0.43155,
AF036708_2766514:0.45835)
:0.01855,
(
AF323965_11991654:0.43256,
(
AY011100_11992579:0.05113,
AY011043_11992470:0.02030)
:0.38612)
:0.03854,
hp9:0.38550);

Clustal W options and diagnostic messages

Alignment type: Protein                 Alignment order: aligned                

                    Pairwise alignment parameters

Method: accurate                        
Matrix: Gonnet                          
Gap open pentalty: 10.00                Gap extension pentalty: 0.10            

                    Multiple alignment parameters

Matrix: Gonnet                          Negative matrix?: no                    
Gap open pentalty: 10.00                Gap extension pentalty: 0.20            
% identity for delay: 30                Residue-specific gap penalties: on      
Penalize end gaps: on                   Hydrophylic gap penalties: on           
Gap separation distance: 0              Hydrophylic residues: GPSNDQEKR         




 CLUSTAL W (1.81) Multiple Sequence Alignments



Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: _11991512              595 aa
Sequence 2: _11991512              595 aa
Sequence 3: _11991512              595 aa
Sequence 4: AF323965_11991654      520 aa
Sequence 5: AY011100_11992579      182 aa
Sequence 6: AF036708_2766514       109 aa
Sequence 7: AY011043_11992470      182 aa
Sequence 8: hp9                    121 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  100
Sequences (1:3) Aligned. Score:  100
Sequences (1:4) Aligned. Score:  5
Sequences (1:5) Aligned. Score:  6
Sequences (1:6) Aligned. Score:  11
Sequences (1:7) Aligned. Score:  12
Sequences (1:8) Aligned. Score:  17
Sequences (2:3) Aligned. Score:  100
Sequences (2:4) Aligned. Score:  5
Sequences (2:5) Aligned. Score:  6
Sequences (2:6) Aligned. Score:  11
Sequences (2:7) Aligned. Score:  12
Sequences (2:8) Aligned. Score:  17
Sequences (3:4) Aligned. Score:  5
Sequences (3:5) Aligned. Score:  6
Sequences (3:6) Aligned. Score:  11
Sequences (3:7) Aligned. Score:  12
Sequences (3:8) Aligned. Score:  17
Sequences (4:5) Aligned. Score:  14
Sequences (4:6) Aligned. Score:  5
Sequences (4:7) Aligned. Score:  14
Sequences (4:8) Aligned. Score:  16
Sequences (5:6) Aligned. Score:  7
Sequences (5:7) Aligned. Score:  92
Sequences (5:8) Aligned. Score:  13
Sequences (6:7) Aligned. Score:  8
Sequences (6:8) Aligned. Score:  12
Sequences (7:8) Aligned. Score:  13
Guide tree        file created:   [../tmp-dir/22449.CLUSTALW.dnd]
Start of Multiple Alignment
There are 7 groups
Aligning...
Group 1: Sequences:   2      Score:3873
Group 2:                     Delayed
Group 3:                     Delayed
Group 4: Sequences:   2      Score:12814
Group 5: Sequences:   3      Score:12814
Group 6:                     Delayed
Group 7: Sequences:   5      Score:1404
Sequence:4     Score:1897
Sequence:8     Score:795
Sequence:6     Score:690
Alignment Score 10200
CLUSTAL-Alignment file created  [../tmp-dir/22449.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.