From: psa@darwin.bu.edu (Protein Structure Analysis server)
To: wb@darwin.bu.edu
Subject: Request 425 result (1 of 3): [Seq 42]
Date: Tue, 5 Jan 1999 18:05:46 -0500

The analysis of your protein sequence has been completed.

The tertiary class and profile probabilities we computed for your
sequence are appended below.  The profile probabilities "profile1" and
"profile2" shown below identify residues that match the two diagnostic
profiles, to which the regular expression on the WD-repeat protein
webpage at http://bmerc-www.bu.edu/wdrepeat/ is an approximation.  A
page of additional graphical output, in PostScript format, is being
sent to you in an additional e-mail message.  This plot shows the
tertiary-class probability distributions, indicating the degree to
which the psa-request server believes that the sequence you submitted
could be a WD-repeat and how many repeats it believes the sequence
has.  The final message contains a core format file with backbone
coordinates for the sequence as a beta propeller.  For more
information, please see the WD repeat example on the
http://bmerc-www.bu.edu/psa/wd-example.htm page.

If your mail reader is MIME-compliant, it may be able to preview or
print this plot for you.  Otherwise, you will need to use an editor to
remove the e-mail header from the PostScript message manually, in
order to send the result to a PostScript previewer or printer.  Two
widely used previewers are `ghostview' (which runs on Unix and MS-DOS
systems), and `GSview' (for OS/2 and Windows variants).  Both use
`ghostscript', which also runs on the Macintosh, and both are freely
available.  See http://www.cs.wisc.edu/~ghost/ or
http://www.fsf.org/software/ghostscript/ghostscript.html for more
information.

-------------------------- Original sequence ---------------------------
; This is the actual sequence used.
Sequence 42
MKVITCEIAW HNKEPVYSLD FQHGTAGRIH RLASAGVDTN VRIWKVEKGP
DGKAIVEFLS NLARHTKAVN VVRFSPTGEI LASGGDDAVI LLWKVNDNKE
PEQIAFQDED EAQLNKENWT VVKTLRGHLE DVYDICWATD GNLMASASVD
NTAIIWDVSK GQKISIFNEH KSYVQGVTWD PLGQYVATLS CDRVLRVYSI
QKKRVAFNVS KMLSGIGAEG EARSYRMFHD DSMKSFFRRL SFTPDGSLLL
TPAGCVESGE NVMNTTYVFS RKNLKRPIAH LPCPGKATLA VRCCPVYFEL
RPVVETGVEL MSLPYRLVFA VASEDSVLLY DTQQSFPFGY VSNIHYHTLS
DISWSSDGAF LAISSTDGYC SFVTFEKDEL GIPLKEKPVL NMRTPDTAKK
TKSQTHRGSS PGPRPVEGTP ASRTQDPSSP GTTPPQARQA PAPTVIRDPP
SITPAVKSPL PGPSEEKTLQ PSSQNTKAHP SRRVTLNTLQ AWSKTTPRRI
NLTPLKTDTP PSSVPTSVIS TPSTEEIQSE TPGDAQGSPP ELKRPRLDEN
KGGTESLDP1

--------------------- Predicted WD-repeat structure --------------------

Sequence42      [  1]  MKVITCEIAW
                               ------            ------       ------  
Sequence42.1    [ 11]  HNKEPV  YSLDFQ  HGTAGRIH  RLASAG  VDT  NVRIWK  VEKGPDGKAI
                [ 56]  VEFLSNLA
Sequence42.2    [ 64]  RHTKAV  NVVRFS  PTGE      ILASGG  DDA  VILLWK  VNDNKEPEQI
                [105]  AFQDEDEAQLNKENWTVVKTLR
Sequence42.3    [127]  GHLEDV  YDICWA  TDGN      LMASAS  VDN  TAIIWD  VSKGQKISIF
                [168]  N
Sequence42.4    [169]  EHKSYV  QGVTWD  PLGQ      YVATLS  CDR  VLRVYS  IQKKRVAFNV
                [210]  SKMLSGIGAEGEARSYRMFHDDSMKSFFRRLSFTPDGSLLLTPAGCVESG
                [260]  ENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVE
                [310]  LMSLPYRLVFAVASEDSVLLYDTQQSFPFGYVSNIHYHTLSDISWSSDGA
                [360]  FLAISSTDGYCSFVTFEKDELGIPLKEKPVLNMRTPDTAKKTKSQTHRGS
                [410]  SPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTVIRDPPSITPAVKSP
                [460]  LPGPSEEKTLQPSSQNTKAHPSRRVTLNTLQAWSKTTPRRINLTPLKTDT
                [510]  PPSSVPTSVISTPSTEEIQSETPGDAQGSPPELKRPRLDENKGGTESLDP
                               ------            ------       ------  

Residues in columns marked with "------" are predicted to fold into
beta-strands.

----------------------- Similar WD repeat proteins ---------------------

Identification of the WD repeat 'domain' implicitly divides the
protein into three fragments:  the WD repeat region itself, and the
subsequences before and after it.  Regions that were at least 40
residues in length were used independently to search a BLASTP database
of corresponding regions in known WD repeat proteins.  The conserved
portions of the WD repeat region itself were shadowed with X's in
order to search for sequences with similar loops, disregarding the
conserved repeat region.  For more information, please see the WD
repeat example on the http://bmerc-www.bu.edu/psa/wd-example.htm page.

The BLASTP search results are as follows:

   * The amino subsequence is too small for BLASTP searching (less
than 40 residues).

   * The loop subsequence (length 189) has no BLASTP matches.

   * The carboxy subsequence (length 349) matches CAFA_HUMAN (length
360) with a score of 1825 (P=1.7e-191).

This may help to characterize the protein.

------------------------------ Transcript ------------------------------
Analyzing Sequence 42. This is 5-Jan-99 (18:0:25).
 
Using the Type-3 DSM library mdatawd.
 
The sequence contains 559 residues.
 
FILTERING RESULTS:
3 Most Probable Super Classes:
1st Superclass wd repeat  has probability 1
2nd Superclass generic    has probability 2.414e-34
 
3 Most Probable Macro Classes:
1st Macroclass wd4        has probability 1
2nd Macroclass wd7        has probability 4.2808e-08
3rd Macroclass wd5        has probability 1.0328e-08


Profile probabilities 

seq	profile1	profile2
M	0	0
K	0	0
V	0	0
I	0	0
T	0	0
C	0	0
E	0	0
I	0	0
A	0	0
W	0	0
H	1	0
N	1	0
K	1	0
E	1	0
P	1	0
V	1	0
Y	1	0
S	1	0
L	1	0
D	1	0
F	1	0
Q	1	0
H	0	0
G	0	0
T	0	0
A	0	0
G	0	0
R	0	0
I	0	0
H	0	0
R	0	1
L	0	1
A	0	1
S	0	1
A	0	1
G	0	1
V	0	1
D	0	1
T	0	1
N	0	1
V	0	1
R	0	1
I	0	1
W	0	1
K	0	1
V	0	0
E	0	0
K	0	0
G	0	0
P	0	0
D	0	0
G	0	0
K	0	0
A	0	0
I	0	0
V	0	0
E	0	0
F	0	0
L	0	0
S	0	0
N	0	0
L	0	0
A	0	0
R	1	0
H	1	0
T	1	0
K	1	0
A	1	0
V	1	0
N	1	0
V	1	0
V	1	0
R	1	0
F	1	0
S	1	0
P	0	0
T	0	0
G	0	0
E	0	0
I	0	1
L	0	1
A	0	1
S	0	1
G	0	1
G	0	1
D	0	1
D	0	1
A	0	1
V	0	1
I	0	1
L	0	1
L	0	1
W	0	1
K	0	1
V	0	0
N	0	0
D	0	0
N	0	0
K	0	0
E	0	0
P	0	0
E	0	0
Q	0	0
I	0	0
A	0	0
F	0	0
Q	0	0
D	0	0
E	0	0
D	0	0
E	0	0
A	0	0
Q	0	0
L	0	0
N	0	0
K	0	0
E	0	0
N	0	0
W	0	0
T	0	0
V	0	0
V	0	0
K	0	0
T	0	0
L	0	0
R	0	0
G	1	0
H	1	0
L	1	0
E	1	0
D	1	0
V	1	0
Y	1	0
D	1	0
I	1	0
C	1	0
W	1	0
A	1	0
T	0	0
D	0	0
G	0	0
N	0	0
L	0	1
M	0	1
A	0	1
S	0	1
A	0	1
S	0	1
V	0	1
D	0	1
N	0	1
T	0	1
A	0	1
I	0	1
I	0	1
W	0	1
D	0	1
V	0	0
S	0	0
K	0	0
G	0	0
Q	0	0
K	0	0
I	0	0
S	0	0
I	0	0
F	0	0
N	0	0
E	1	0
H	1	0
K	1	0
S	1	0
Y	1	0
V	1	0
Q	1	0
G	1	0
V	1	0
T	1	0
W	1	0
D	1	0
P	0	0
L	0	0
G	0	0
Q	0	0
Y	0	1
V	0	1
A	0	1
T	0	1
L	0	1
S	0	1
C	0	1
D	0	1
R	0	1
V	0	1
L	0	1
R	0	1
V	0	1
Y	0	1
S	0	1
I	0	0
Q	0	0
K	0	0
K	0	0
R	0	0
V	0	0
A	0	0
F	0	0
N	0	0
V	0	0
S	0	0
K	0	0
M	0	0
L	0	0
S	0	0
G	0	0
I	0	0
G	0	0
A	0	0
E	0	0
G	0	0
E	0	0
A	0	0
R	0	0
S	0	0
Y	0	0
R	0	0
M	0	0
F	0	0
H	0	0
D	0	0
D	0	0
S	0	0
M	0	0
K	0	0
S	0	0
F	0	0
F	0	0
R	0	0
R	0	0
L	0	0
S	0	0
F	0	0
T	0	0
P	0	0
D	0	0
G	0	0
S	0	0
L	0	0
L	0	0
L	0	0
T	0	0
P	0	0
A	0	0
G	0	0
C	0	0
V	0	0
E	0	0
S	0	0.93197
G	0	0.94991
E	0	0.97816
N	0	0.95538
V	0	0.95738
M	0	0.95893
N	0	0.95997
T	0	0.9614
T	0	0.96319
Y	0	0.89681
V	0	0
F	0	0
S	0	0
R	0	0
K	0	0
N	0	0
L	0	0
K	0	0
R	0	0
P	0	0
I	0	0
A	0	0
H	0	0
L	0	0
P	0	0
C	0	0
P	0	0
G	0	0
K	0	0
A	0	0
T	0	0
L	0	0
A	0	0
V	0	0
R	0	0
C	0	0
C	0	0
P	0	0
V	0	0
Y	0	0
F	0	0
E	0	0.90498
L	0	0
R	0	0
P	0	0
V	0	0
V	0	0
E	0	0
T	0	0
G	0	0
V	0	0
E	0	0
L	0	0
M	0	0
S	0	0
L	0	0
P	0	0
Y	0	0
R	0	0
L	0	0
V	0	0
F	0	0
A	0	0
V	0	0
A	0	0
S	0	0
E	0	0
D	0	0
S	0	0.83773
V	0	0.88452
L	0	0.92581
L	0	0.95591
Y	0	0.97733
D	0	0.99999
T	0	0
Q	0	0
Q	0	0
S	0	0
F	0	0
P	0	0
F	0	0
G	0	0
Y	0	0
V	0	0
S	0	0
N	0	0
I	0	0
H	0	0
Y	0	0
H	0	0
T	0	0
L	0	0
S	0	0
D	0	0
I	0	0
S	0	0
W	0	0
S	0	0
S	0	0
D	0	0
G	0	0
A	0	0
F	0	0
L	0	0
A	0	0
I	0	0
S	0	1
S	0	1
T	0	1
D	0	1
G	0	1
Y	0	1
C	0	1
S	0	1
F	0	1
V	0	1
T	0	1
F	0	0
E	0	0
K	0	0
D	0	0
E	0	0
L	0	0
G	0	0
I	0	0
P	0	0
L	0	0
K	0	0
E	0	0
K	0	0
P	0	0
V	0	0
L	0	0
N	0	0
M	0	0
R	0	0
T	0	0
P	0	0
D	0	0
T	0	0
A	0	0
K	0	0
K	0	0
T	0	0
K	0	0
S	0	0
Q	0	0
T	0	0
H	0	0
R	0	0
G	0	0
S	0	0
S	0	0
P	0	0
G	0	0
P	0	0
R	0	0
P	0	0
V	0	0
E	0	0
G	0	0
T	0	0
P	0	0
A	0	0
S	0	0
R	0	0
T	0	0
Q	0	0
D	0	0
P	0	0
S	0	0
S	0	0
P	0	0
G	0	0
T	0	0
T	0	0
P	0	0
P	0	0
Q	0	0
A	0	0
R	0	0
Q	0	0
A	0	0
P	0	0
A	0	0
P	0	0
T	0	0
V	0	0
I	0	0
R	0	0
D	0	0
P	0	0
P	0	0
S	0	0
I	0	0
T	0	0
P	0	0
A	0	0
V	0	0
K	0	0
S	0	0
P	0	0
L	0	0
P	0	0
G	0	0
P	0	0
S	0	0
E	0	0
E	0	0
K	0	0
T	0	0
L	0	0
Q	0	0
P	0	0
S	0	0
S	0	0
Q	0	0
N	0	0
T	0	0.80234
K	0	0.81075
A	0	0.81907
H	0	0.82692
P	0	0.83562
S	0	0
R	0	0
R	0	0
V	0	0
T	0	0
L	0	0
N	0	0
T	0	0
L	0	0
Q	0	0
A	0	0
W	0	0
S	0	0
K	0	0
T	0	0
T	0	0
P	0	0
R	0	0
R	0	0
I	0	0
N	0	0
L	0	0
T	0	0
P	0	0
L	0	0
K	0	0
T	0	0
D	0	0
T	0	0
P	0	0
P	0	0
S	0	0
S	0	0
V	0	0
P	0	0
T	0	0
S	0	0
V	0	0
I	0	0
S	0	0
T	0	0
P	0.85239	0
S	0.85033	0
T	0.85091	0
E	0.83977	0
E	0	0
I	0	0
Q	0	0
S	0	0
E	0	0
T	0	0
P	0	0
G	0	0
D	0	0
A	0	0.99989
Q	0	0.99989
G	0	0.9999
S	0	0.9999
P	0	0.99991
P	0	0.99992
E	0	0.99993
L	0	0.99994
K	0	0.99994
R	0	0.99995
P	0	0.99995
R	0	0.99996
L	0	0.99996
D	0	0.99996
E	0	0.99996
N	0	0
K	0	0
G	0	0
G	0	0
T	0	0
E	0	0
S	0	0
L	0	0
D	0	0
P	0	0
O	0	0
 
End of Log file for Sequence 42.