| clustal_alignment |
| ID: | 1382092153 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 312 (309) | ||
| Sequences: | 13977 (11518) | ||
| Seq/Len: | 45.233 | ||
| Nf(neff/√len): | 655.2 |
HHblits Results: (2013_03)
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: 45.233).
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 |
| 224_D | 238_L | 3.836 | 1.00 |
| 25_F | 41_V | 3.340 | 1.00 |
| 209_H | 225_D | 3.176 | 1.00 |
| 228_S | 249_V | 3.034 | 1.00 |
| 73_D | 93_T | 3.033 | 1.00 |
| 243_E | 255_L | 2.811 | 1.00 |
| 143_G | 177_I | 2.709 | 1.00 |
| 230_A | 249_V | 2.669 | 1.00 |
| 139_H | 142_R | 2.629 | 1.00 |
| 227_L | 231_R | 2.625 | 1.00 |
| 251_F | 254_L | 2.574 | 1.00 |
| 166_T | 170_E | 2.474 | 1.00 |
| 113_Y | 134_V | 2.455 | 1.00 |
| 198_R | 222_L | 2.346 | 1.00 |
| 22_N | 45_D | 2.242 | 1.00 |
| 202_A | 232_A | 2.229 | 1.00 |
| 209_H | 227_L | 2.225 | 1.00 |
| 71_T | 95_V | 2.202 | 1.00 |
| 176_H | 185_R | 2.192 | 1.00 |
| 288_T | 302_E | 2.184 | 1.00 |
| 72_A | 92_E | 2.169 | 1.00 |
| 138_D | 142_R | 2.154 | 1.00 |
| 198_R | 224_D | 2.107 | 1.00 |
| 258_A | 261_H | 2.070 | 1.00 |
| 132_S | 183_V | 2.069 | 1.00 |
| 31_G | 34_G | 2.027 | 1.00 |
| 256_R | 266_D | 2.007 | 1.00 |
| 29_F | 39_G | 1.973 | 1.00 |
| 213_A | 225_D | 1.947 | 1.00 |
| 128_G | 187_I | 1.940 | 1.00 |
| 219_M | 300_V | 1.931 | 1.00 |
| 165_E | 175_N | 1.929 | 1.00 |
| 268_P | 286_Y | 1.880 | 1.00 |
| 226_V | 235_A | 1.856 | 1.00 |
| 213_A | 217_D | 1.851 | 1.00 |
| 256_R | 286_Y | 1.842 | 1.00 |
| 128_G | 185_R | 1.825 | 1.00 |
| 142_R | 145_Q | 1.784 | 1.00 |
| 228_S | 231_R | 1.764 | 1.00 |
| 170_E | 174_E | 1.736 | 1.00 |
| 203_M | 209_H | 1.729 | 1.00 |
| 230_A | 234_E | 1.728 | 1.00 |
| 74_G | 77_T | 1.727 | 1.00 |
| 140_V | 143_G | 1.712 | 1.00 |
| 233_G | 255_L | 1.707 | 1.00 |
| 243_E | 256_R | 1.700 | 1.00 |
| 224_D | 235_A | 1.680 | 1.00 |
| 29_F | 42_A | 1.678 | 1.00 |
| 101_P | 169_G | 1.672 | 1.00 |
| 260_E | 287_S | 1.650 | 1.00 |
| 130_H | 183_V | 1.648 | 1.00 |
| 133_K | 137_E | 1.638 | 1.00 |
| 36_D | 210_D | 1.633 | 1.00 |
| 250_A | 258_A | 1.633 | 1.00 |
| 279_G | 283_D | 1.622 | 1.00 |
| 30_A | 218_R | 1.614 | 1.00 |
| 254_L | 258_A | 1.612 | 1.00 |
| 177_I | 184_L | 1.602 | 1.00 |
| 240_D | 303_V | 1.595 | 1.00 |
| 267_L | 302_E | 1.538 | 1.00 |
| 199_L | 221_S | 1.536 | 1.00 |
| 201_L | 212_V | 1.527 | 1.00 |
| 138_D | 146_L | 1.510 | 1.00 |
| 246_W | 272_Y | 1.495 | 1.00 |
| 101_P | 168_G | 1.494 | 1.00 |
| 241_L | 264_I | 1.462 | 1.00 |
| 143_G | 179_L | 1.456 | 1.00 |
| 42_A | 46_Q | 1.433 | 1.00 |
| 28_L | 38_D | 1.422 | 1.00 |
| 145_Q | 151_L | 1.422 | 1.00 |
| 126_L | 187_I | 1.419 | 1.00 |
| 26_E | 42_A | 1.419 | 1.00 |
| 201_L | 223_I | 1.416 | 1.00 |
| 250_A | 254_L | 1.405 | 0.99 |
| 178_S | 183_V | 1.402 | 0.99 |
| 182_G | 186_D | 1.400 | 0.99 |
| 19_R | 208_H | 1.396 | 0.99 |
| 101_P | 165_E | 1.392 | 0.99 |
| 148_E | 151_L | 1.388 | 0.99 |
| 97_A | 100_D | 1.379 | 0.99 |
| 147_I | 175_N | 1.376 | 0.99 |
| 130_H | 185_R | 1.368 | 0.99 |
| 28_L | 34_G | 1.355 | 0.99 |
| 229_L | 255_L | 1.355 | 0.99 |
| 1_N | 5_A | 1.343 | 0.99 |
| 288_T | 305_E | 1.343 | 0.99 |
| 288_T | 306_A | 1.341 | 0.99 |
| 295_L | 298_S | 1.338 | 0.99 |
| 81_R | 99_A | 1.332 | 0.99 |
| 197_G | 221_S | 1.332 | 0.99 |
| 24_A | 211_S | 1.330 | 0.99 |
| 245_C | 268_P | 1.325 | 0.99 |
| 206_S | 209_H | 1.317 | 0.99 |
| 302_E | 305_E | 1.300 | 0.99 |
| 23_P | 211_S | 1.282 | 0.99 |
| 215_S | 296_G | 1.276 | 0.99 |
| 102_M | 129_E | 1.270 | 0.99 |
| 245_C | 253_N | 1.263 | 0.99 |
| 118_T | 121_Y | 1.255 | 0.99 |
| 235_A | 238_L | 1.247 | 0.99 |
| 93_T | 98_T | 1.216 | 0.98 |
| 106_D | 120_G | 1.209 | 0.98 |
| 229_L | 250_A | 1.196 | 0.98 |
| 86_E | 106_D | 1.190 | 0.98 |
| 30_A | 296_G | 1.189 | 0.98 |
| 254_L | 257_N | 1.187 | 0.98 |
| 37_I | 214_Q | 1.186 | 0.98 |
| 33_V | 214_Q | 1.185 | 0.98 |
| 272_Y | 277_E | 1.181 | 0.98 |
| 49_E | 53_I | 1.179 | 0.98 |
| 200_E | 226_V | 1.178 | 0.98 |
| 277_E | 280_N | 1.177 | 0.98 |
| 198_R | 238_L | 1.174 | 0.98 |
| 199_L | 240_D | 1.173 | 0.98 |
| 26_E | 296_G | 1.172 | 0.98 |
| 270_G | 289_A | 1.162 | 0.97 |
| 86_E | 103_Y | 1.158 | 0.97 |
| 121_Y | 130_H | 1.158 | 0.97 |
| 198_R | 239_A | 1.156 | 0.97 |
| 117_E | 134_V | 1.144 | 0.97 |
| 241_L | 259_V | 1.135 | 0.97 |
| 121_Y | 132_S | 1.127 | 0.97 |
| 117_E | 121_Y | 1.114 | 0.96 |
| 29_F | 35_Q | 1.112 | 0.96 |
| 129_E | 186_D | 1.107 | 0.96 |
| 117_E | 132_S | 1.102 | 0.96 |
| 253_N | 281_V | 1.099 | 0.96 |
| 182_G | 185_R | 1.097 | 0.96 |
| 25_F | 42_A | 1.094 | 0.96 |
| 146_L | 177_I | 1.093 | 0.96 |
| 101_P | 186_D | 1.088 | 0.96 |
| 112_T | 152_S | 1.087 | 0.96 |
| 26_E | 295_L | 1.083 | 0.96 |
| 281_V | 285_G | 1.078 | 0.95 |
| 281_V | 286_Y | 1.074 | 0.95 |
| 263_T | 287_S | 1.069 | 0.95 |
| 165_E | 169_G | 1.068 | 0.95 |
| 302_E | 306_A | 1.067 | 0.95 |
| 226_V | 232_A | 1.065 | 0.95 |
| 169_G | 186_D | 1.063 | 0.95 |
| 20_D | 207_E | 1.062 | 0.95 |
| 21_A | 45_D | 1.061 | 0.95 |
| 203_M | 247_Q | 1.057 | 0.95 |
| 278_R | 282_L | 1.057 | 0.95 |
| 194_V | 221_S | 1.054 | 0.95 |
| 202_A | 247_Q | 1.052 | 0.95 |
| 179_L | 182_G | 1.049 | 0.94 |
| 243_E | 268_P | 1.047 | 0.94 |
| 245_C | 281_V | 1.046 | 0.94 |
| 178_S | 185_R | 1.042 | 0.94 |
| 20_D | 24_A | 1.041 | 0.94 |
| 233_G | 258_A | 1.040 | 0.94 |
| 245_C | 286_Y | 1.036 | 0.94 |
| 298_S | 302_E | 1.034 | 0.94 |
| 275_D | 279_G | 1.030 | 0.94 |
| 35_Q | 39_G | 1.030 | 0.94 |
| 212_V | 269_D | 1.024 | 0.93 |
| 233_G | 250_A | 1.020 | 0.93 |
| 281_V | 289_A | 1.014 | 0.93 |
| 138_D | 144_E | 1.014 | 0.93 |
| 118_T | 122_S | 1.010 | 0.93 |
| 269_D | 294_G | 1.009 | 0.93 |
| 86_E | 110_R | 1.009 | 0.93 |
| 70_E | 92_E | 1.007 | 0.93 |
| 197_G | 307_H | 1.006 | 0.93 |
| 230_A | 250_A | 1.005 | 0.93 |
| 160_F | 164_I | 1.003 | 0.93 |
| 20_D | 44_S | 1.001 | 0.92 |
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
- 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 | |
| 2c2aA | 1 | 0.6058 | 100 | 0.522 | Contact Map |
| 4i5sA | 2 | 0.6058 | 100 | 0.525 | Contact Map |
| 3a0rA | 1 | 0.5929 | 100 | 0.55 | Contact Map |
| 4ew8A | 2 | 0.6154 | 100 | 0.558 | Contact Map |
| 3jz3A | 2 | 0.4391 | 100 | 0.559 | Contact Map |
| 4gczA | 2 | 0.625 | 100 | 0.56 | Contact Map |
| 4mpcA | 1 | 0.6827 | 100 | 0.565 | Contact Map |
| 4e01A | 1 | 0.6122 | 100 | 0.567 | Contact Map |
| 2e0aA | 2 | 0.6667 | 100 | 0.569 | Contact Map |
| 1y8oA | 1 | 0.7179 | 100 | 0.571 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)