21 May 2000 Kevin Karplus
	target t92  HI0319 
	YECO_HAEIN
	
	No good hits with blast or double-blast.
	No PDB chain in T2K alignment of 131 sequences.

	Good hits with target model 
			E	FSSP
	1xva[AB]	9.5e-16	1xvaA	glycine n-methyltransferase
	1bhj[AB]	9.5e-16 1xvaA
	1d2c[AB]	9.5e-16 1xvaA
	1d2h[ACD]	1.1e-15	1xvaA
	1d2g[AB]	1.1e-15	1xvaA
	1aq[ij][AB]	3.2e-08	2admA	adenine-n6-DNA-methyltransferase taqi
	2adm[AB]	3.2e-08	2admA
	
	1xvaA/T0092-1xvaA-local seems to be a good alignment.
	May want to move the insertion off the end of the helix into
	the nearby loop region.  Conservation on beta sheet is very
	well clustered.
	
	1xvaA/T0092-1xvaA-global also seems to be a good alignment,
	though different in several ways from the local one.
	
	1xvaA/1xvaA-T0092-fssp-global also looks pretty good.
	
	I suspect our main job on this target will be choosing an alignment.
	
	For the template models, 1xvaA again comes out on top:
		1xvaA	1.7e-6	1xvaA
		1bhjA	3.6e-16	1xvaA
		1admA	2.1e-06 2admA
		2admA	2.7e-06	2admA
		1fbnA	4.0e-05	1fbnA	mj fibrillarin homologue  
		1bc5A	8.7e-05	1af7	chemotaxis receptor methyltransferase (cher, chemotaxi
		1af7	9.5e-04	1af7

	The two FSSP reps are all similar to 1xvaA
  NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
  14: 1xvaA  1af7   12.8  5.0  160   275   19      0      0    17 S    chemotaxis receptor methyltransferase cher biological_u
  15: 1xvaA  1fbnA  12.7  3.0  153   230    9      0      0    16 S    mj fibrillarin homologue 
  16: 1xvaA  2admA  10.4  3.5  152   386   19      0      0    14 S    adenine-n6-DNA-methyltransferase taqi 

	Since 1xvaA scores best with the target model, it is probably
	the best to use as the template, though we could look at how
	2admA and 1af7 do as well.
Tue Jun  6 13:35:30 PDT 2000
Redid 2ry prediction with new neural net.

Mon Jun 26 09:52:06 PDT 2000
Remade 2ry predictions


Thurs 20 July 2000 Kevin Karplus

Rachel Karchin found a web site 
	http://www.hwi.buffalo.edu/ACA/ACA00/abstracts/text/W0146.html
with what appears to be information about both t92 and t93.

Both are described as a "core methyltransferase fold of a central
beta-sheet surrounded by alpha-helices on both faces."

This makes 1xvaA sound like a good model.

Fri 21 July 2000 Rachel Karchin

measure_shift analysis of the three best-looking alignments.
   T0092-1xvaA-global
   1xvaA-T0092-fssp-global
   T0092-1xvaA-local

The two global alignments look best.

On the basis of our secondary structure prediction, the fssp alignment
looks better than the global.

fssp alignment was edited -- gaps closed to erase unconvincing parts of
the alignment.