Multiple alignment format

STAMP alignment output consists first of a list of domain descriptions and relevant transformations. After this an alignment may or may not be output.

Multiple alignments are displayed as follows (see STAMPDIR/examples/globin_stamp_trans.6):

    /data/newpdb/pdb/pdb1lh1.ent 1lh1 { ALL 
    1.00000    0.00000    0.00000         0.00000 
    0.00000    1.00000    0.00000         0.00000 
    0.00000    0.00000    1.00000         0.00000  }
    /data/newpdb/pdb/pdb2hhb.ent 2hhba { CHAIN A 
    0.71639    0.34414    0.60691        19.45435 
    <Etc.>
    -0.31092   -0.94263    0.12159        68.85890  }


    Alignment Score  Sc = 7.665619
    Alignment length Lp = 156
    RMS deviation after fitting on 116 atoms =  2.434597
    Secondary structures are from DSSP

    >1lh1    (cluster A) sequence
    >2hhba   (cluster B) sequence
    >2hhbb   (cluster B) sequence
    >4mbn    (cluster B) sequence
    >1ecd    (cluster B) sequence
    >2lhb    (cluster B) sequence
    >space 
    >1lh1_dssp  (cluster A) secondary structure from DSSP
    >2hhba_dssp  (cluster B) secondary structure from DSSP
    >2hhbb_dssp  (cluster B) secondary structure from DSSP
    >4mbn_dssp   (cluster B) secondary structure from DSSP
    >1ecd_dssp   (cluster B) secondary structure from DSSP
    >2lhb_dssp   (cluster B) secondary structure from DSSP
    #T -- '1' = used in the final fit
    #P -- averaged Pij
    #A -- distance between averaged CA atoms in angtroms
    #G -- $P_{ij}{\prime}$ value
    ABBBBB ABBBBB use  Pij      Distance $P_{ij}{\prime}$
    * iteration 1
    P
    I
    V
    D
    T
    G
    S
    V
    G V  A - -  - 
    AVHV P ---- - 
    LLLLLL ------ 1  0.50337  1.90006   6.98400 
    TSTSSS ------ 1  0.49631  2.00483   6.88900 
    EPPEAA HHHHHH 1  0.55533  1.89926   7.68300 
    SAEGDA HHHHHH 1  0.60834  1.80863   8.39600 
    QDEEQE HHHHHH 1  0.70134  1.64212   9.64700 
    AKKWIK HHHHHH 1  0.75434  1.52204  10.36000 
    ATSQST HHHHHH 1  0.75137  1.51092  10.32000 
    LNALTK HHHHHH 1  0.80831  1.36142  11.08600 
    VVVVVI HHHHHH 1  0.85737  1.21626  11.74600 
    KKTLQR HHHHHH 1  0.83537  1.27448  11.45000 

    <Etc.>

    ITNKGI HHHHHH 1  0.85737  1.04393  11.74600 
    VVADML HHHHHH 1  0.84332  1.11847  11.55700 
    ILLIIL HHHHHH 1  0.81232  1.20349  11.14000 
    KTAAFR HTHHHH 1  0.80035  1.22529  10.97900 
    KSHASS HTTHHT 1  0.73137  1.29476  10.05100 
    EKKKKA HTTHHT 1  0.60031  1.66495   8.28800 
    M  Y   H  H   
    D  K   H  H   
    D  E   H  H   
    A  L   H  H   
    *

The `$>$' and `#' characters tell the routines that read alignments what is to be contained in each field. A `$>$' character denotes a character string which is to be displayed vertically, and a `#' character denotes a string of numbers to be displayed separated by spaces. Thus in the above example we have 13 character strings vertically (6 amino acid sequences, 1 string of spaces and 6 DSSP assignments) and 6 numeric fields (corresponding to various details from STAMP) specified. The actual alignment will be contained within `*' characters as shown. Accordingly, no occurrence of `$>$', `#' and `*' characters should occur outside of these contexts.

The As and Bs just above the `*' symbol refer to the members of the two cluster (branches) which are brought together during this alignment.

Briefly, the numeric fields are:

#T 1 or 0, 1 shows those residues used to determine the fit of the two sets of structures.

#P averaged Rossmann and Argos Pij value

#A distance between averaged ${\rm C}_{\alpha}$ atoms

#G corrected Pij value ( $P_{ij}{\prime}$)

Note that the program POSTSTAMP adds two new fields:

#B $1$ if all pairiwse $P_{ij} \geq$ the user defined minimum, $0$ otherwise

#R the total number of pairwise comparisons having $P_{ij} \geq$ the cutoff out of $N \times (N-1)/2$