Matras1.2 : Help Page for Pairwise 3D Alignment


Help Page
"Pairwise 3D Alignment"


To compare and align two structures is the most basic procedure for structural comparison. Other structural comparisons, such as multiple alignments and library searches, were developed based on the pairwise 3D alignment. In our web page, a user can assign structures either by inputting the PDB code or by uploading the PDB format files in the user's computer. An alignment, superimposed structures, and various kinds of structural similarities, such as raw score, RMSD, sequence identity are shown. The following is an example of Matras Pairwise 3D Alignment :
Pairwise 3D Alignment using Matras 1.2 : 4azuA and 7pcy-

[process_id]  4272
[ALIGN_RANK]  1
[PROTEIN A]   4azuA    Naa 128 Nsse 10 "AZURIN (PH 5.5)"
[PROTEIN B]   7pcy-    Naa  98 Nsse 10 "PLASTOCYANIN"
[ALIGNMENT]   Ncomp_aa 96 Ncomp_sse 8
[SIMILARITY]  Seq 26.0 %  Sec 70.8 % Exp 72.9 % CRMS 4.23 A  DRMS 3.36 A
[SCORE]       ScSSE 932.0 ScEnv 1682.3 ScDis 40716.2 Rdis 29.3 (%) Rsse 33.5 (%)
[RELIABILITY] Superfamily  69.6 %  Fold  95.4 %

[BEGIN SSE ALIGNMENT]
proA:1-23142-5678
    :E-EEHEH-EEEE
    :* ** *  ****
    :EEEE-E-HEEEE
proB:1234-5-16789
[END SSE ALIGNMENT]

[BEGIN ALIGNMENT]
     :  E1     -        E2       E3           H1      E4     H2   
SecA :TTEEEEEB -TTS BS SEEEE TT SEEEEEEE  SS  HHHH B  EEEETTTHHHHH
    2:ECSVDIQGN-DQMQFNTNAITVDKSCKQFTVNLSHPGNLPKNVMGHNWVLSTAADMQGVV:60
         *   *      *  * ***                       ** *    *   ** 
    0:AAIVKLGGDDGSLAFVpNNITVGAGE-SIEFINNAG-------FpHNIVFDEDAVPAGV-:50
SecB : EEEEES TT  SSEESSEEEE TT -EEEEEE SS-------S EEEEE TTSS TT -
     : E1           E2  E3      -E4       -------  E5            -

     :                     E5        E6              E7           
SecA :HHHHHH GGGTTS TT TT SEE   B TT EEEEEEEGGGS TT  EEEE  STTTTTT
   61:TDGMASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSAL:120
                      *   *             *     **     *   *    **  
     :----------------DADAISAEDYLN-SKGQTVVR---KLTTPGTYGVYCDP--HSGA:90
SecB :---------------- HHHH EEEEE -STT EEEE---E  S EEEEEE ST--TGGG
     :---------------- H1   E6    -    E7  ---     E8       --    

     :- E8     
SecA :-SEEEEEE 
     :-MKGTLTLK:128
       ** * *  
   91:GMKMTITVQ:99
SecB :T EEEEEE 
     :  E9     

[END ALIGNMENT]


3D VIEW:[3D(image)] [3D(Jmol)] [3D(Chime-plugin)] [superimposed PDB file]

ALIGNMENT: [Vertical] [ClustalW] [Horizontal]

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