| channelrhodopsin2 20-280 |
| ID: | 1470447357 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 261 (223) | ||
| Sequences: | 811 (547.5) | ||
| Seq/Len: | 3.637 | ||
| Nf(neff/√len): | 36.7 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 3.637).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 69_K | 102_L | 3.097 | 1.00 |
| 40_V | 71_V | 2.702 | 1.00 |
| 94_W | 98_G | 2.602 | 1.00 |
| 99_E | 233_K | 2.523 | 1.00 |
| 104_C | 132_D | 2.495 | 1.00 |
| 99_E | 103_T | 2.325 | 1.00 |
| 198_S | 231_L | 2.273 | 1.00 |
| 38_L | 230_L | 2.157 | 1.00 |
| 43_L | 68_T | 2.154 | 1.00 |
| 46_Y | 237_G | 1.941 | 1.00 |
| 33_W | 78_F | 1.924 | 1.00 |
| 76_H | 153_F | 1.904 | 1.00 |
| 134_G | 160_Y | 1.891 | 1.00 |
| 138_W | 157_G | 1.859 | 1.00 |
| 64_C | 237_G | 1.705 | 0.99 |
| 103_T | 233_K | 1.684 | 0.99 |
| 39_S | 70_V | 1.624 | 0.98 |
| 104_C | 233_K | 1.613 | 0.98 |
| 35_A | 226_T | 1.598 | 0.98 |
| 142_A | 206_F | 1.573 | 0.98 |
| 201_M | 205_L | 1.570 | 0.98 |
| 97_Y | 100_W | 1.547 | 0.98 |
| 101_L | 133_V | 1.541 | 0.98 |
| 68_T | 237_G | 1.535 | 0.98 |
| 131_S | 163_N | 1.530 | 0.97 |
| 31_L | 35_A | 1.507 | 0.97 |
| 155_L | 159_M | 1.504 | 0.97 |
| 206_F | 212_G | 1.501 | 0.97 |
| 138_W | 232_S | 1.496 | 0.97 |
| 32_Q | 222_T | 1.484 | 0.97 |
| 103_T | 106_V | 1.475 | 0.97 |
| 154_F | 158_C | 1.466 | 0.96 |
| 70_V | 103_T | 1.444 | 0.96 |
| 135_T | 139_G | 1.438 | 0.96 |
| 42_I | 46_Y | 1.436 | 0.96 |
| 42_I | 234_N | 1.424 | 0.96 |
| 109_I | 129_L | 1.419 | 0.96 |
| 223_I | 227_I | 1.417 | 0.95 |
| 45_Y | 49_A | 1.407 | 0.95 |
| 137_V | 141_T | 1.406 | 0.95 |
| 211_E | 221_S | 1.389 | 0.95 |
| 64_C | 110_H | 1.388 | 0.95 |
| 99_E | 104_C | 1.366 | 0.94 |
| 132_D | 135_T | 1.361 | 0.94 |
| 138_W | 156_L | 1.337 | 0.93 |
| 205_L | 224_G | 1.326 | 0.93 |
| 104_C | 135_T | 1.324 | 0.93 |
| 47_A | 65_V | 1.317 | 0.93 |
| 37_A | 72_I | 1.303 | 0.92 |
| 42_I | 238_L | 1.303 | 0.92 |
| 63_C | 106_V | 1.302 | 0.92 |
| 36_F | 71_V | 1.272 | 0.91 |
| 75_F | 145_S | 1.261 | 0.90 |
| 151_V | 207_L | 1.256 | 0.90 |
| 244_R | 247_I | 1.240 | 0.89 |
| 139_G | 233_K | 1.235 | 0.89 |
| 127_R | 167_H | 1.235 | 0.89 |
| 199_W | 233_K | 1.221 | 0.88 |
| 145_S | 149_I | 1.215 | 0.88 |
| 149_I | 213_F | 1.212 | 0.88 |
| 70_V | 233_K | 1.204 | 0.87 |
| 207_L | 213_F | 1.187 | 0.86 |
| 116_G | 175_S | 1.182 | 0.86 |
| 67_L | 106_V | 1.182 | 0.86 |
| 70_V | 110_H | 1.167 | 0.85 |
| 35_A | 72_I | 1.125 | 0.82 |
| 70_V | 135_T | 1.125 | 0.82 |
| 217_S | 220_G | 1.124 | 0.82 |
| 100_W | 203_P | 1.123 | 0.82 |
| 138_W | 153_F | 1.102 | 0.80 |
| 64_C | 164_T | 1.100 | 0.80 |
| 39_S | 99_E | 1.093 | 0.79 |
| 97_Y | 236_W | 1.091 | 0.79 |
| 86_L | 146_T | 1.083 | 0.79 |
| 110_H | 195_F | 1.081 | 0.78 |
| 70_V | 99_E | 1.080 | 0.78 |
| 195_F | 236_W | 1.076 | 0.78 |
| 136_I | 139_G | 1.074 | 0.78 |
| 161_G | 165_F | 1.065 | 0.77 |
| 108_L | 117_L | 1.061 | 0.77 |
| 168_A | 196_F | 1.060 | 0.77 |
| 135_T | 164_T | 1.058 | 0.76 |
| 97_Y | 105_P | 1.054 | 0.76 |
| 91_R | 209_G | 1.053 | 0.76 |
| 129_L | 159_M | 1.052 | 0.76 |
| 46_Y | 68_T | 1.050 | 0.76 |
| 70_V | 77_E | 1.050 | 0.76 |
| 43_L | 71_V | 1.049 | 0.75 |
| 201_M | 224_G | 1.046 | 0.75 |
| 36_F | 40_V | 1.046 | 0.75 |
| 73_E | 143_A | 1.045 | 0.75 |
| 100_W | 105_P | 1.044 | 0.75 |
| 101_L | 223_I | 1.043 | 0.75 |
| 104_C | 139_G | 1.040 | 0.75 |
| 67_L | 70_V | 1.036 | 0.74 |
| 32_Q | 162_A | 1.034 | 0.74 |
| 163_N | 167_H | 1.032 | 0.74 |
| 140_A | 144_M | 1.026 | 0.73 |
| 206_F | 228_I | 1.022 | 0.73 |
| 103_T | 132_D | 1.020 | 0.73 |
| 206_F | 221_S | 1.018 | 0.72 |
| 152_I | 220_G | 1.016 | 0.72 |
| 67_L | 107_I | 1.016 | 0.72 |
| 169_A | 196_F | 1.012 | 0.72 |
| 82_G | 211_E | 1.012 | 0.72 |
| 39_S | 139_G | 1.010 | 0.71 |
| 98_G | 141_T | 1.009 | 0.71 |
| 35_A | 133_V | 1.007 | 0.71 |
| 38_L | 234_N | 1.005 | 0.71 |
| 104_C | 199_W | 1.001 | 0.70 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- See coupling matrix (for protein design or mutagenesis)
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3ug9A | 1 | 0.9617 | 100 | 0.231 | Contact Map |
| 1xioA | 1 | 0.8199 | 100 | 0.341 | Contact Map |
| 4fbzA | 1 | 0.8851 | 100 | 0.341 | Contact Map |
| 3am6A | 4 | 0.8506 | 100 | 0.342 | Contact Map |
| 3qapA | 1 | 0.8352 | 100 | 0.344 | Contact Map |
| 3wt9A | 1 | 0.8812 | 100 | 0.347 | Contact Map |
| 3wqjA | 1 | 0.8697 | 100 | 0.352 | Contact Map |
| 4qi1A | 3 | 0 | 100 | 0.353 | Contact Map |
| 1m0kA | 1 | 0.8276 | 100 | 0.354 | Contact Map |
| 4l35A | 1 | 0.8889 | 100 | 0.354 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)