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]

We show simple explanation of this output.

[ALINGMENT]
- Ncomp_aa : Number of compared (aligned) amino acids
- Ncomp_sse : Number of compared (aligned ) SSEs
[SIMILARITY]
- Seq : sequence identity (%), defined as number of identical amino acid pairs divided by Ncomp_aa.
- Sec : secondary structure identitiy(%), defined as number of identical secondary structure residue pairs divided by Ncomp_aa. 8 states secondary structure of DSSP are used.
- CRMS : Root mean square deviation (angstrom) of Calpha atom positions of aligned residues, after optimal superimposition.
- DRMS : Root mean square deviation (angstrom) of distances between Cbeta atom positions of aligned residues.
[SCORE]
- ScSSE: SSE score(S_sse).
- ScDIS: Distance score(S_dis).
- Rdis : Normalized S_dis score (%) using the maximum and minimum value of the score. This is for understanding the similarity more intuitively than the raw value of S_dis. The score R_dis between protein A and B i s defined as follow :
  Rdis(A,B) = 100 * (Sdis(A,B) - Smin)/(Smax - Smin);
  where Sdis(A,B) is a raw distance score between protein A and B, Smax and Smin is the maximum and minimum value of the score correspondingly. We set Smin = 0, Smax is defined as the averaged value among the self scores:
  Smax = (Sdis(A,A) + Sdis(B,B))/2
[RELIABLITY]
This values shows a probability that a structure pair with a normalized score Rdis is classified as the same Superfamily/Fold relationship of SCOP database. They are estimated by all-vs-all comparison of protein domains in SCOP 1.59 database.
[BEGIN SSE ALIGNMENT] ... [END SSE ALIGNMENT]
Alignment of SSE (Secondary Structure Element). 'H' is a SSE of alpha helix,
[BEGIN ALIGNMENT]...[END ALIGNMENT]
A residue-based pairwise alignment. The lines with "SecA" and "SecB" are secondary structures of proteinA and proteinB, respectively. These secondary structures are determined by the DSSP program. The DSSP codes for secondary structures are as follows:
```
 H = alpha helix, 
 B = residue in isolated beta-bridge
 E = extended strand, participates in beta ladder
 G = 3-helix (3/10 helix)
 I = 5 helix (pi helix)
 T = hydrogen bonded turn
 S = bend
```

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Help Page "Pairwise 3D Alignment"

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"Pairwise 3D Alignment"