[Circular Permutation (2)]


(1) Adenine-specific DNA Methyltransferase (1aqi) and PvuII DNA Methyltransferase (1boo)

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  "A large superfamily of S-adenosylmethionine-dependant methyltransferases is characterized by two highly conserved motifs that map to the C-termini of beta-strands a and d. It has been noticed that methyltransferase subfamilies differ in the sequence order of these motifs, suggesting a circular permutation." (Grishin, 2001)
1aqi (ResA21-222) 1boo (Res22-318)

1aqi <TPPEVVDFMVSLAEAPRGGRVLE   PACAHGPFLRAFREAHGTGYRFVGVEIDPK        ALDLPPWAE        GIL
code <00QAAAAAAAABG0000R00000   0
R0RR0QAAAAAAA800RRG000000RGQA        BG000QBG0        000
LCS    0QAAAAAAAA G0000R00000   0R    QAAAAAAA 00   000000RGQA        BG   QBG0        000
code   0QAAAAAAAA G0000R00000QB30R R  QAAAAAAAB00   000000RGQAAAAAAAAABG0  QBG0QAABO><3000
1boo   PAKLPEFFIR MLTEPDDLVVDIFGGS N  TTGLVAERESR   KWISFEMKPEYVAASAFRFLD  NNISEEKIT><AYTT

1aqi AD        F    LL WEPGE  AFDLILGNPP YGI VK   AVKDLYKK          AF ST          WKGK   YN LYGAFLEKAVRLLKPGGVL  VFV
code 
GR        Q    AB 00RRG  00R0000000 000 00   QAAAAAAA          BG QB          000R   00 QAAAAAAAAAABG00R000  000
LCS   R        Q    AB 00R G  00 0000000 000 00   QAAAAAAA          BG QB          000R   00 QAAAAAAAAA   00R000  000
code  R00000000QAAAAABG00R GGR00 0000000R000G00RR0QAAAAAAAAAAAAAAAAABG0QBG000000000000RGRG00RQAAAAAAAAA   00R000RR000
1boo  SNGSMYIGDSLELLESFPEE SISLV MTSPPFALQRKKEYGNLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDFGGAYMKGVPARSIYNFRVLIRMI   DEVGFFLAEDF


1aqi VPATWLVLED  F  ALLREFLAREG K  TSVYYLG        EVFPQKKVSAVV    I  RFQKSGKGL    S           LWDT>
code 00
RQAB00QA  B  QAAAAAAA1B0 0  00000R0        RRGQG1RG0000    0  000RG0000    0           0000>
LCS  00    00Q   B  Q      A B0 0  0000 R0        R     RG0000    0  000RG0000    0           0000
code 00    00QG0QBR0Q      A B0R0RR0000 R000000000R0    RG0000QAAB0RR000RG000031RG00QAAAAAAABR0000
1boo YW    FNPSKLPSPI      E WVNKRKIRVK DAVNTVWWFSKT    EWPKSDITKVLASIPPNLLQISNSESNGQYLANCKLMGIKAH



*RATIO :  lcs/trimmed_seq_a = 0.813 (=  152/  187), lcs/trimmed_seq_b = 0.596 (=  152/  255)
Structural alignment by ComSubstruct
DSSP <lLLLHHHHHHHHLLlLLLLLLEEEEELLLLLHHHHHHHHHHlllLEEEEEELLLLLLL.................  .LLLL.EEEEE
1aqi <vETPPEVVDFMVSLaEAPRGGRVLEPACAHGPFLRAFREAHgtgYRFVGVEIDPKALD.................  .LPPW.AEGIL
         |     |            |                           |  |
1boo  .RFPAKLPEFFIRM.LTEPDDLVVDIFGGSNTTGLVAERES...RKWISFEMKPEYVAasafrfldnniseekit><aYTTSnGSMYI
DSSP  .LLLLHHHHHHHHH.HLLLLLEEEELLLLLLHHHHHHHHLL...LEEEEEELLHHHHHhhhhhhllllllhhhhl><lEELLlEEEEE


DSSP LLHHHL.LLLL..LEEEEEELLLLLLLllHHHHhhhhllllLLLLL.HHHHHHHHHHHLEEEEEEEEEE
1aqi ADFLLW.EPGE..AFDLILGNPPYGIVkaVKDLykkafstwKGKYN.LYGAFLEKAVRLLKPGGVLVFV
      | |   |        |    ||       |             |      |       ||| |  |
1boo GDSLELlESFPeeSISLVMTSPPFALQ.rKKEY....gnleQHEYVdWFLSFAKVVNKKLKPDGSFVVD
DSSP LLHHHHhHHLLllLEEEEEELLLLLLL.lLLLL....lllhHHHHHhHHHHHHHHHHHHEEEEEEEEEE


DSSP EELH.....hhLLHHHHHHHHHHHH..HLEE.EEEEEELllLLLL...............LLEEEEEEELLL..........lle
1aqi VPAT.....wlVLEDFALLREFLAR..EGKT.SVYYLGEvfPQKK...............VSAVVIRFQKSG..........kgl
                                        |                            |  | | 
1boo FGGAymkgvpaRSIYNFRVLIRMIDevGFFLaEDFYWFN.pSKLPspiewvnkrkirvkdAVNTVWWFSKTEwpksditkvlasi
DSSP ELLLeelleeeELLHHHHHHHHHHHllLLEEeEEEEEEL.lLLLLlllhhhhhlllllllLEEEEEEEELLLlllllhhhlllll


DSSP eeELLLL.......................>
1aqi slWDTQE.......................>
          |
1boo ppNLLQIsnsesngqylancklmgikahpa
DSSP llLEEELllllllhhhhhhhhhllllllll


*Z-score 12.2  AR 167  RMSD 3.4A  SI 14%
Structural alignment by DaliLite


(2) Phosphotyrosine Protein Phosphatase (1phr) and VH1 Dual-specificity Phosphatase (1vhr)

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 "1vhr is characterized by a unique topology, which can, however, be converted to 1phr by deletions/insertions and a circular permutation. The conversion results in a superposition of the active sites and produces sequence alignment with 20% identity." (Grishin, 2001)
1phr (Res4-157) 1vhr (ResA8-179)

1phr <KSVLFVCLG NICRSPIAEAVFRKLVTDQ NI  S        DNWVIDSGAVSDWNVGRSPDPRAVSCLRN                 H GINTAHKAR Q VTKE
code <00000000R 
RG01QAAAAAAAAAAAAAB RR  Q        ABG000000RGRQ80RG000QAAAAAAAA                 B R000R0000 0 00QA
LCS     000000R RG0     AAAAAAAAAAB RR  Q        AB 000000   Q        AAAAAAAA                 B R000 0000 0 0
code  BG000000R0RG00    AAAAAAAAAAB0RR00QAAAAAAAAAB 000000   Q        AAAAAAAAAAAAABP><JQAAAAAABGR000G0000R0R0
1vhr  NGRVLVHCREGYSR    SPTLVIAYLMMRQKMDVKSALSIVRQN REIGPN   D        GFLAQLCQLNDRLAK><SVQDLNDLLSDGSGCYSLPSQPC

1phr DFVTFD YI  LCMDESNL   RDLNRKSNQVKNCR     AK      I ELLGSYDPQK      QLIIEDP YYGNDAD  FETVYQQCVRCCRAFLEK>
code AAA
0GR 00  0000QAAA   AAAAAAAABG1R0R     G0      0 00QAAB0QBR      RRGR00R QBG0QAA  AAAAAAAAAAAAAAAAAA>
LCS     0 R 00  0000QAAA   AAAAA   B  R0R     G0      0 00QAAB0QBR      R   00R QBG QAA  AAAAAAAAAA
code    0 RR00RG0000QAAABBQAAAAA   B  R0R0000QG000GQBG0R00QAAB0QBR000000R   00R0QBGRQAABQAAAAAAAAAA
1vhr    N EVTPRIYVGNASVAQDIPKLQK   L  GITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIK   ANDTQEFNLSAYFERAADFIDQA



*RATIO :  lcs/trimmed_seq_a = 0.707 (=  106/  150), lcs/trimmed_seq_b = 0.631 (=  106/  168)
Structural alignment by ComSubstruct
DSSP <.LLEEEEEEELLLLLHHHHHHHHHHHHHHHlllhhheeeeeeelllllLLLLLLHHHHHHHHLLL.....  .............................lllllllllLLLL
1phr <.VTKSVLFVCLGNICRSPIAEAVFRKLVTDqnisdnwvidsgavsdwnVGRSPDPRAVSCLRNHG.....  .............................intahkarqVTKE
          ||  |     |||                                  |       |
1vhr  qKNGRVLVHCREGYSRSPTLVIAYLMMRQK.....mdvksalsivrqnREIGPNDGFLAQLCQLNdrlak><svqdlndllsdgsgcyslpsqpcnevtpriyvgnasvaQDIP
DSSP  lLLLLEEEELLLLLLHHHHHHHHHHHHHLL.....llhhhhhhhhhhhLLLLLLHHHHHHHHHHHhhhhl><lhhhhhhhhllllllllllllleeeeelleeeelhhhhLLHH


DSSP HHH..HLLEEEELLHH....HHHHHHHHHHlllLLLLEEEEhhhhllllllLLLLLllllHHHHhhHHHHHHHHHHHHHHHLL>
1phr DFV..TFDYILCMDES....NLRDLNRKSNqvkNCRAKIELlgsydpqkqlIIEDPyygnDADFetVYQQCVRCCRAFLEKVR>
               |   |                                       |                 |
1vhr KLQklGITHVLNAAEGrsfmHVNTNANFYK...DSGITYLG.........iKANDT....QEFN..LSAYFERAADFIDQALA
DSSP HHHhhLLLEEEELLLLllllLLLLLHHHHL...LLLLEEEE.........lLLLLL....LLLL..HHHHHHHHHHHHHHHHL


*Z-score 6.3  AR 108  RMSD 3.9A  SI 11%
Structural alignment by DaliLite



[The DSSP code]

[The 5-tile code]