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# 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 occurance of >', #' and *' characters should occur outside of these contexts.

The As and Bs just above the `*' symble 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 atoms

#G corrected Pij value ( )

Note that the program POSTSTAMP adds two new fields:

#B 1 if all pairiwse the user defined minimum, 0 otherwise

#R the total number of pairwise comparisons having the cutoff out of

Next: Output from SCANS Up: Input and Output format Previous: Sequence format
Geoff Barton
1999-04-16