Table III. Results from Analyses that Identify Conserved and Semi-Conserved Positions.
| Linker positions (LacI numbers) | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | ||
| ca | c | c | c | c | h | h | h | h | h | h | h | h | h/cb | c | c | c | c | ||
| Y | P | A | L | ||||||||||||||||
| Consurf | Scores 8-9 are denoted as functionally and/or structurally important | ||||||||||||||||||
| Automatic MSAc | 8 | 6 | 9 | 6 | 9 | 9 | 6 | 5 | 9 | 8 | 7 | 8 | 6 | 5 | 6 | 4 | 8 | 4 | |
| All Seq | 8 | 7 | 9 | 7 | 9 | 9 | 7 | 7 | 9 | 8 | 7 | 8 | 8 | 6 | 6 | 5 | 8 | 5 | |
| YPAL+YPALlike | 8 | 7 | 9 | 7 | 9 | 9 | 7 | 7 | 9 | 9 | 8 | 9 | 8 | 7 | 6 | 5 | 8 | 6 | |
| YPALonly | 8 | 7 | 9 | 7 | 9 | 9 | 8 | 7 | 9 | 9 | 8 | 9 | 8 | 7 | 6 | 5 | 8 | 6 | |
| Evol. Trace | top 25% of conservation scores | ||||||||||||||||||
| Report_Makerd | R | R | R | R | R | R | R | R | |||||||||||
| All Seq | X | X | X | X | X | X | X | X | |||||||||||
| YPAL+YPALlike | X | X | X | X | X | X | X | ||||||||||||
| YPALonly | X | X | X | X | X | X | X | X | X | ||||||||||
| TEA-O | top 25% of conservation scores | ||||||||||||||||||
| 2002 seq set13,e | O | O | O | O | O | O | O | O | |||||||||||
| All Seq | X | X | X | X | X | X | X | ||||||||||||
| YPAL+YPALlike | X | X | X | X | X | X | X | ||||||||||||
| YPALonly | X | X | X | X | X | X | X | X | |||||||||||
Secondary structure: “c” coil’ “h”, helix.
The end of the helix differs in LacI and PurR49 and presumably differs in other homologs.
Predictions were generated by the online version of Consurf19, 20 that automatically selects sequences and generates an unoptimized alignment. Parameters of the analyses were to allow a range of 10 to 99% sequence identities, perform 5 iterations PSI-BLAST, with up 350 sequences allowed; however, only 197 sequences were identified. The alignment algorithm was MUSCLE.
Predictions were generated by the online “Report_Maker implementation of Evolutionary Trace Analysis52. “R” is used to differentiate these predictions from those generated by our optimized sequence selection and alignment (denoted “X”).
Predictions generated from the 2002 LacI/GalR dataset are denoted with “O” to differentiate them from predictions generated with the current, optimized sequence set (denoted “X”).