| Tm13 |
| ID: | 1506715902 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 253 (235) | ||
| Sequences: | 7681 (4914.7) | ||
| Seq/Len: | 32.685 | ||
| Nf(neff/√len): | 320.6 |
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: 32.685).
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 |
| 136_E | 154_P | 3.977 | 1.00 |
| 157_K | 215_D | 3.674 | 1.00 |
| 95_K | 118_V | 3.229 | 1.00 |
| 126_K | 134_E | 3.147 | 1.00 |
| 10_N | 13_H | 3.127 | 1.00 |
| 73_Y | 84_I | 3.056 | 1.00 |
| 40_E | 69_R | 2.669 | 1.00 |
| 140_A | 150_V | 2.644 | 1.00 |
| 126_K | 136_E | 2.632 | 1.00 |
| 210_S | 231_K | 2.565 | 1.00 |
| 44_L | 74_T | 2.519 | 1.00 |
| 70_H | 97_Y | 2.387 | 1.00 |
| 128_K | 134_E | 2.386 | 1.00 |
| 153_D | 156_A | 2.267 | 1.00 |
| 60_A | 90_I | 2.159 | 1.00 |
| 33_Y | 160_F | 2.112 | 1.00 |
| 207_D | 234_L | 2.086 | 1.00 |
| 70_H | 95_K | 1.950 | 1.00 |
| 100_S | 121_S | 1.949 | 1.00 |
| 133_N | 156_A | 1.903 | 1.00 |
| 44_L | 160_F | 1.895 | 1.00 |
| 135_L | 151_L | 1.889 | 1.00 |
| 158_I | 216_M | 1.860 | 1.00 |
| 158_I | 218_A | 1.828 | 1.00 |
| 152_Y | 157_K | 1.825 | 1.00 |
| 72_F | 151_L | 1.797 | 1.00 |
| 97_Y | 118_V | 1.789 | 1.00 |
| 74_T | 151_L | 1.760 | 1.00 |
| 134_E | 155_V | 1.737 | 1.00 |
| 36_L | 41_G | 1.691 | 1.00 |
| 10_N | 16_M | 1.684 | 1.00 |
| 231_K | 235_E | 1.677 | 1.00 |
| 123_K | 208_M | 1.629 | 1.00 |
| 16_M | 36_L | 1.608 | 1.00 |
| 137_I | 151_L | 1.591 | 1.00 |
| 58_N | 61_E | 1.590 | 1.00 |
| 71_I | 84_I | 1.569 | 1.00 |
| 34_L | 41_G | 1.562 | 1.00 |
| 210_S | 234_L | 1.562 | 1.00 |
| 42_I | 129_L | 1.550 | 1.00 |
| 157_K | 213_K | 1.535 | 1.00 |
| 120_I | 149_F | 1.521 | 1.00 |
| 71_I | 94_A | 1.521 | 1.00 |
| 15_F | 153_D | 1.498 | 1.00 |
| 36_L | 66_S | 1.494 | 1.00 |
| 235_E | 239_N | 1.494 | 1.00 |
| 34_L | 59_V | 1.484 | 1.00 |
| 98_I | 102_W | 1.479 | 1.00 |
| 99_S | 139_P | 1.474 | 1.00 |
| 148_N | 162_G | 1.460 | 1.00 |
| 118_V | 125_T | 1.455 | 1.00 |
| 207_D | 238_R | 1.454 | 1.00 |
| 46_P | 71_I | 1.435 | 1.00 |
| 134_E | 154_P | 1.431 | 1.00 |
| 38_G | 132_G | 1.422 | 1.00 |
| 101_L | 104_R | 1.409 | 1.00 |
| 42_I | 72_F | 1.401 | 0.99 |
| 53_P | 57_S | 1.398 | 0.99 |
| 14_K | 133_N | 1.392 | 0.99 |
| 80_V | 163_D | 1.378 | 0.99 |
| 42_I | 70_H | 1.373 | 0.99 |
| 91_C | 94_A | 1.368 | 0.99 |
| 15_F | 35_I | 1.366 | 0.99 |
| 33_Y | 218_A | 1.365 | 0.99 |
| 14_K | 156_A | 1.364 | 0.99 |
| 42_I | 135_L | 1.362 | 0.99 |
| 133_N | 153_D | 1.349 | 0.99 |
| 52_F | 86_L | 1.349 | 0.99 |
| 44_L | 151_L | 1.321 | 0.99 |
| 37_D | 132_G | 1.319 | 0.99 |
| 75_H | 163_D | 1.318 | 0.99 |
| 137_I | 149_F | 1.317 | 0.99 |
| 152_Y | 214_I | 1.305 | 0.99 |
| 10_N | 14_K | 1.303 | 0.99 |
| 56_M | 90_I | 1.282 | 0.99 |
| 15_F | 158_I | 1.277 | 0.99 |
| 41_G | 69_R | 1.276 | 0.99 |
| 56_M | 60_A | 1.274 | 0.99 |
| 238_R | 242_C | 1.270 | 0.99 |
| 121_S | 125_T | 1.268 | 0.99 |
| 86_L | 89_S | 1.257 | 0.99 |
| 150_V | 164_I | 1.254 | 0.99 |
| 32_Q | 47_G | 1.251 | 0.99 |
| 57_S | 61_E | 1.243 | 0.98 |
| 128_K | 132_G | 1.242 | 0.98 |
| 100_S | 119_P | 1.240 | 0.98 |
| 34_L | 43_L | 1.235 | 0.98 |
| 12_Q | 156_A | 1.225 | 0.98 |
| 201_A | 204_K | 1.217 | 0.98 |
| 139_P | 149_F | 1.205 | 0.98 |
| 208_M | 211_K | 1.201 | 0.98 |
| 160_F | 218_A | 1.197 | 0.98 |
| 138_L | 208_M | 1.193 | 0.98 |
| 39_N | 130_L | 1.190 | 0.98 |
| 203_K | 238_R | 1.165 | 0.97 |
| 71_I | 96_I | 1.149 | 0.97 |
| 74_T | 162_G | 1.149 | 0.97 |
| 135_L | 153_D | 1.146 | 0.97 |
| 207_D | 211_K | 1.143 | 0.97 |
| 103_V | 107_P | 1.141 | 0.97 |
| 133_N | 155_V | 1.140 | 0.97 |
| 179_D | 226_R | 1.138 | 0.97 |
| 219_P | 222_G | 1.135 | 0.97 |
| 152_Y | 159_L | 1.131 | 0.97 |
| 99_S | 149_F | 1.127 | 0.97 |
| 79_D | 221_H | 1.122 | 0.97 |
| 52_F | 83_G | 1.121 | 0.97 |
| 203_K | 241_K | 1.121 | 0.97 |
| 136_E | 152_Y | 1.111 | 0.96 |
| 80_V | 221_H | 1.109 | 0.96 |
| 15_F | 160_F | 1.099 | 0.96 |
| 12_Q | 216_M | 1.099 | 0.96 |
| 98_I | 103_V | 1.091 | 0.96 |
| 35_I | 44_L | 1.079 | 0.95 |
| 16_M | 62_V | 1.077 | 0.95 |
| 41_G | 68_I | 1.068 | 0.95 |
| 43_L | 87_W | 1.059 | 0.95 |
| 144_H | 163_D | 1.050 | 0.94 |
| 103_V | 119_P | 1.046 | 0.94 |
| 216_M | 226_R | 1.039 | 0.94 |
| 12_Q | 215_D | 1.035 | 0.94 |
| 45_D | 75_H | 1.034 | 0.94 |
| 126_K | 154_P | 1.033 | 0.94 |
| 77_D | 80_V | 1.025 | 0.93 |
| 75_H | 80_V | 1.025 | 0.93 |
| 235_E | 238_R | 1.024 | 0.93 |
| 204_K | 207_D | 1.023 | 0.93 |
| 104_R | 107_P | 1.011 | 0.93 |
| 198_S | 201_A | 1.004 | 0.93 |
| 136_E | 212_K | 1.002 | 0.92 |
| 67_S | 93_N | 1.002 | 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 | |
| 2q9uA | 2 | 0.9763 | 100 | 0.323 | Contact Map |
| 2yheA | 6 | 0.9051 | 100 | 0.347 | Contact Map |
| 4nurA | 2 | 0.9091 | 100 | 0.353 | Contact Map |
| 2cfuA | 1 | 0.9012 | 100 | 0.354 | Contact Map |
| 1ycgA | 4 | 0.9526 | 100 | 0.355 | Contact Map |
| 2ohhA | 4 | 0.9605 | 100 | 0.355 | Contact Map |
| 4fekA | 2 | 0.9526 | 100 | 0.357 | Contact Map |
| 4pdxA | 2 | 0 | 100 | 0.357 | Contact Map |
| 2vw8A | 1 | 0.8972 | 100 | 0.358 | Contact Map |
| 4dikA | 2 | 0.9565 | 100 | 0.358 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)