Wed Jul  5 12:42:27 PDT 2000

	T0106 Secreted frizzled protein 3, mouse
	
	wu-blast has only weak hits (1ery, 1zaq)
	double-blast has moderate hits 1pi2 and 1cgjI.

	There are 128 sequences in T2K alignment, and first in
	Swissprot is FRIZ_DROME.

	2ry structure prediction is 2 long helices (possibly first is
	split into 2).  Tiny single beta-strand prediction near end.

	Target model predictions are
	ID	E-value	FSSP	SCOP
	1eaiD	33	1eaiC	7.22.1.1.2
	1eaiC	33	1eaiC	7.22.1.1.2

	Template model predictions are
	1qatB	0.28	1djxB	1.41.1.7.1,2.6.1.1.1,3.1.17.1.1

	This is a CYS-rich protein, so we should look for information
	about known disulphide bridges.

	Note: 1eaiC is a CSY-rich protein, but none of the alignments
	have more than 2 of the 5 disulphide bridges fully conserved,
	making it a very unconvincing template.

Tue Jul 11 11:54:37 PDT 2000

	CAFASP servers have no consensus
	fold	num	num	num
		server	found	first
	7.3	6	10	1
	7.22	6	10	2
	1.53	6	8	1
	1.110	5	6	2

	SAM-T99 liked 1qatB (E-value 0.27)

	The 7.3 hits were
	1c2aA	1c2aA	7.3.13
	1ayj	1ayj	7.3.7
	1dec	1dec	7.3.15
	1acw	?	7.3.7
	1urk	5hpgA	7.3.11
	1boe	1boeA	7.3.9
	4htcI	4htcI	7.3.15
	1c4eA	1c4eA	7.3.4
	1klo 	1klo	7.3.11

Best-scoring alignments so far:
1qatB/1qatB-T0106-vit		T0106 1.4e-05
1qatB/1qatB-T0106-local		T0106 1.4e-04
1eaiC/1eaiC-T0106-vit		T0106 2.3e-03
1eaiC/T0106-1eaiC-vit		1eaiC 2.7e-03
1eaiC/1eaiC-T0106-global	T0106 3.1e-03
1eaiC/T0106-1eaiC-local		1eaiC 4.4e-03
1eaiC/1eaiC-T0106-local		T0106 1.3e-02
1eaiC/T0106-1eaiC-global	1eaiC 3.7e-02
1klo/1klo-T0106-global		T0106 9.7e-02
1ayj/1ayj-T0106-vit		T0106 1.2e-01
1klo/1klo-T0106-vit		T0106 1.7e-01
1by2/T0106-1by2-vit		1by2  1.8e-01
1klo/1klo-T0106-local		T0106 1.9e-01
1dqgA/T0106-1dqgA-vit		1dqgA 2.9e-01
1boeA/1boeA-T0106-vit		T0106 3.0e-01
1boeA/T0106-1boeA-vit		1boeA 4.3e-01
1dqgA/1dqgA-T0106-vit		T0106 4.9e-01
1ayj/1ayj-T0106-local		T0106 5.0e-01
1c2aA/T0106-1c2aA-vit		1c2aA 5.2e-01
1ayj/T0106-1ayj-vit		1ayj  5.6e-01
1eaiC/1eaiC-T0106-fssp-global	T0106 6.0e-01
1boeA/1boeA-T0106-local		T0106 7.1e-01
1by2/1by2-T0106-fssp-global	T0106 7.3e-01

1qatB/1qatB-T0106-vit	does not conserve disulphide bridges.
1qatB/1qatB-T0106-local does not conserve disulphide bridges.
1klo/1klo-T0106-global	has lots of disulphides, but only one bridge is conserved.
1klo/1klo-T0106-vit	has lots of disulphides, but only one bridge is conserved.
1klo/1klo-T0106-local	has lots of disulphides, but only one bridge is conserved.
1ayj/1ayj-T0106-vit	does not conserve disulphide bridges.
1by2/T0106-1by2-vit	is too small to be useful (one nice turn).
1dqgA/T0106-1dqgA-vit	is too small to be useful.
1boeA/1boeA-T0106-vit	is very small and doesn't conserve disulphides.
1boeA/T0106-1boeA-vit	is very small and doesn't conserve disulphides.
...
1c2aA/T0106-1c2aA-vit	only conserves one disulphide bridge.

None of the alignments I've looked at look at all feasible.
I suspect this is a NEW FOLD.

6/24/00 Rachel
proteins with 5 disulfide bridges:
  long-chain neurotoxins
     1ntn
     1lsi
     1txb
  lipase protein cofactor
    1pcn
    1pco


6/24/00 Christian

1txb is probably not a good template because it is too short to align
any more than about half of T0106. Thus only three cysteine bridges
are conserved.

1lpbA/1lpbA-T0106-global.pw conserves 5 of the cysteines but none of
the disulfide bridges. Looks bad.

1aksA aligns only conserve 3 cysteines, and none of the bridges.

1icfA aligns only conserve 3 cysteines, and one of the bridges.

1p05A aligns only conserve 4 cysteines, and one of the bridges.


24 July 2000 Kevin Karplus

Will try undertaker with 1 disulphide bridge given.
I'll try pairing the first CYS with each of the others, to get 9 starting
points.

CYS are
3 11 48 57 64 76 80 87 104 115

(SSBond commands use residue numbering starting at 0, so the bonds to
try are
ssbond 2 10
ssbond 2 47
ssbond 2 56
ssbond 2 63
ssbond 2 75
ssbond 2 79
ssbond 2 86
ssbond 2 103
ssbond 2 114