Tue Jun 13 12:43:16 PDT 2000 Kevin Karplus T0101 Pectate lyase PelL, Erwinia chrysanthemi blast finds only very weak hits: 1hn[rs] 1dbogA, 1dbgA, 1qbe[ABC] double-blast finds nothing The T2k alignment has 4 or 5 distinct sequences (13 total). Swissprot sequences are PELL_ERWCH (the target) and PELX_ERWCH. The target model finds some strong hits: chain E-value FSSP SCOP 1dboA 9.3e-07 1dbgA 2.75.1 1dbgA 9.3e-07 1dbgA 2.75.1 1rmg 7.0e-02 1rmg 2.75.1 1iiv[ABC] 0.12 theoretical models 1a8q 0.77 1brt 3.64.1 So do the template models: 1dbgA 6.6e-102 1dbgA 2.75.1 1rmg 2.9e-02 1rmg 2.75.1 1fepA 1.8 1fepA 6.4.3 1bhe 2.9 1bhe 2.75.1 1cnsA 7.3 1cnsA 4.2.1 2baa 7.8 1cnsA 4.2.1 1evhA 8.2 1evhA 2.52.1 The 2.75.1 hits (particularly 1dbgA) look like the ones to go with, unless they only cover one domain. Fri Jun 16 12:05:52 PDT 2000 Kevin Karplus I looked at the CAFASP hits today. It seems that the SAM-T99 server failed (probably due to overload) for the T101 prediction. I've asked Spencer to run the scripts manually and send the results to Leszek. The rest of the servers had pretty strong consensus: 30 2.75.1 13 2.9.1 10 2.64.1 5 2.1.1 Since our best hits are in 2.75.1, those look like the ones to go with--let's try each of the FSSP representatives in this superfamily. The alignment 1dbgA/T0101-1dbgA-global.pw has good striping of conservation patterns across the beta sheets, but is missing one interior beta sheet in (or near) the binding pocket. 1dbgA/1dbgA-T0101-fssp-global.pw does not look as good to me. The 1dbgA/T0101-1dbgA-local.pw. alignment seems to be a subset of the global one. The alignment 1qa1A/T0101-1qa1A-global.pw looks pretty good for the N-terminus, but moves a separate domain for the C-terminus. The deletion seems unlikely---the 1dbgA alignment looks much better. 1qa1A/T0101-1qa1A-local.pw picks out a good chunk of beta helix in the middle. 1tyv/T0101-1tyv-global.pw has the same problems as 1qa1A/T0101-1qa1A-global.pw, but the 1tyv/T0101-1tyv-local.pw alignment also picks out a good section of the beta helix with no skipped strands and a good conservation pattern. 1dabA/T0101-1dabA-global.pw has the same problems, though the C-terminus is just the other end of the beta helix, not unraveled. The 1dabA/1dabA-T0101-fssp-global.pw alignment seems unconvincing to me. A couple of skipped turns of the helix, not a clear striping of the conservation. 1czfA/1czfA-T0101-fssp-global.pw is the best scoring of the fssp-based alignments, and it looks pretty good. THere are unaligned portions, but only one missing strand. 1bhe/T0101-1bhe-global.pw looks pretty good, with good striping of the conserved residues across the sheets. parts of 1rmg/T0101-1rmg-local.pw look pretty good, with good striping, but there is a missing turn of the helix near the C-terminus. 1rmg/1rmg-T0101-fssp-global.pw is very unconvincing--lots of missing pieces of the beta helix. 1air/T0101-1air-global.pw looks good in the loops that stick out over the binding site, but skips a turn of the helix. 1air/1air-T0101-fssp-global.pw gets a very good pattern of conservation, leaving the loops mostly unaligned---half a turn of the helix is also missing, which may be hard to fix. The alignment 1air/T0101-1air-local.pw also looks quite good. It loosk so far like the "good" alignments are 1dbgA/T0101-1dbgA-global.pw 1qa1A/T0101-1qa1A-local.pw 1tyv/T0101-1tyv-local.pw 1czfA/1czfA-T0101-fssp-global.pw 1air/T0101-1air-local.pw I wonder if we can combine any of these predictions? Mon Jun 26 09:52:01 PDT 2000 Remade 2ry predictions Wed Jul 5 12:12:05 PDT 2000 SAM-T99 submission on CAFASP site ok, has 1dbgA as top hit in both directions. Tues Aug 15, 2000 Christian This is my rank order preferences for a template: 1air/T0101-1air-local.pw mainly because it aligns to most of the structure, whereas the others (aside from 1cvfA) align to the middle of a much larger structure. 1tyv/T0101-1tyv-local.pw still looks good though 1czfA/1czfA-T0101-fssp-global.pw (with possible hand editing, otherwise no) 1dbgA/T0101-1dbgA-global.pw 1qa1A/T0101-1qa1A-local.pw Sat Aug 26 00:14:09 PDT 2000 Remade 2track predictions Sat Aug 26 14:14:09 PDT 2000 Kevin Karplus Remade 2track predictions and 2track joint alignments The 2track.dist clearly prefers 1dbgA: 1dbgA 506 -70.70 -30.13 3.2e-10 2.75.1.6.1 1qjvA 342 -53.27 -17.29 1.4e-04 1idk 359 -55.46 -15.85 1.0e-03 2.75.1.2.1 1rmg 422 -69.75 -15.45 1.0e-03 2.75.1.4.1 1cjdA 394 -43.93 -15.23 1.0e-03 2.12.2.1.1 1qcxA 359 -55.97 -15.01 1.0e-03 2.75.1.2.2 1tgoA 773 -35.63 -13.48 7.7e-03 3.50.3.6.4,5.8.1.1.5 2pec 353 -49.25 -12.93 2.1e-02 2.75.1.1.1 1air 353 -49.25 -12.93 2.1e-02 2.75.1.1.1 1cf1A 404 -47.70 -10.37 1.6e-01 2.1.1.5.19 1c8uA 285 -35.92 -10.11 1.6e-01 Perhaps we should look at the 2track joint alignments for 1dbgA again. Fri Sep 1 13:04:57 PDT 2000 Kevin Karplus The top scoring alignment is 1dbgA/T0101-1dbgA-2track-local I did a little hand-editing to create 1dbgA/T0101-1dbgA-karplus1.a2m, which looks pretty good to me. The 1dbgA/T0101-1dbgA-2track-global alignment is essentially the same for the first part, but skips some turns of the beta helix. The best alignment based on a template HMM is 1czfA/1czfA-T0101-fssp-global, which gets good striping down the beta sheets, though it is a much gappier alignment. I say let's go with 1dbgA/T0101-1dbgA-karplus1.a2m, and not fuss any more over this one. I did a bit more editing: 1dbgA/T0101-1dbgA-karplus2.a2m Tue Sep 5 10:35:22 PDT 2000 remaking 2track Mon Nov 27 13:26:15 PST 2000 1dbgA is correct superfamily (but 30 hits in CAFASP, so not too hard).