| T0780 |
| ID: | 1401928678 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (240) | ||
| Sequences: | 770 (681.2) | ||
| Seq/Len: | 3.208 | ||
| Nf(neff/√len): | 44.0 |
Jackhmmer Results: (2014_04_16)
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: 3.208).
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 |
| 132_G | 174_E | 3.531 | 1.00 |
| 93_V | 109_L | 3.192 | 1.00 |
| 206_D | 210_V | 3.176 | 1.00 |
| 184_A | 202_L | 2.680 | 1.00 |
| 140_V | 182_I | 2.611 | 1.00 |
| 100_A | 105_I | 2.576 | 1.00 |
| 158_E | 226_T | 2.560 | 1.00 |
| 74_G | 79_S | 2.448 | 1.00 |
| 184_A | 200_V | 2.405 | 1.00 |
| 204_A | 216_I | 2.401 | 1.00 |
| 4_N | 8_I | 2.341 | 1.00 |
| 203_Q | 211_V | 2.227 | 1.00 |
| 95_A | 109_L | 2.223 | 1.00 |
| 160_V | 226_T | 2.177 | 1.00 |
| 100_A | 131_I | 2.164 | 1.00 |
| 97_L | 107_V | 2.105 | 1.00 |
| 182_I | 204_A | 2.054 | 1.00 |
| 137_K | 140_V | 2.044 | 1.00 |
| 192_I | 196_Y | 2.029 | 1.00 |
| 145_E | 183_I | 2.014 | 1.00 |
| 138_D | 166_E | 1.929 | 1.00 |
| 167_V | 218_P | 1.920 | 1.00 |
| 50_I | 109_L | 1.737 | 0.99 |
| 51_D | 92_K | 1.676 | 0.98 |
| 232_P | 236_T | 1.611 | 0.98 |
| 114_L | 120_A | 1.607 | 0.98 |
| 202_L | 221_T | 1.602 | 0.98 |
| 133_K | 173_Q | 1.567 | 0.97 |
| 142_I | 202_L | 1.559 | 0.97 |
| 173_Q | 177_D | 1.526 | 0.97 |
| 162_V | 221_T | 1.517 | 0.96 |
| 140_V | 179_I | 1.514 | 0.96 |
| 195_N | 226_T | 1.504 | 0.96 |
| 164_D | 221_T | 1.489 | 0.96 |
| 50_I | 64_F | 1.474 | 0.96 |
| 183_I | 205_I | 1.465 | 0.95 |
| 152_D | 193_T | 1.461 | 0.95 |
| 94_T | 110_S | 1.454 | 0.95 |
| 7_Y | 11_S | 1.452 | 0.95 |
| 171_S | 176_L | 1.442 | 0.95 |
| 27_F | 39_E | 1.415 | 0.94 |
| 45_V | 72_L | 1.410 | 0.94 |
| 157_I | 226_T | 1.410 | 0.94 |
| 59_Y | 131_I | 1.410 | 0.94 |
| 5_S | 8_I | 1.409 | 0.94 |
| 195_N | 224_K | 1.404 | 0.94 |
| 178_R | 206_D | 1.401 | 0.94 |
| 142_I | 167_V | 1.378 | 0.93 |
| 45_V | 74_G | 1.376 | 0.93 |
| 135_A | 173_Q | 1.376 | 0.93 |
| 159_N | 226_T | 1.355 | 0.92 |
| 54_Y | 96_D | 1.355 | 0.92 |
| 70_V | 91_F | 1.348 | 0.92 |
| 8_I | 11_S | 1.329 | 0.91 |
| 235_S | 238_N | 1.328 | 0.91 |
| 197_S | 222_I | 1.323 | 0.91 |
| 176_L | 179_I | 1.310 | 0.91 |
| 188_T | 192_I | 1.295 | 0.90 |
| 136_Q | 170_T | 1.294 | 0.90 |
| 157_I | 160_V | 1.294 | 0.90 |
| 162_V | 223_M | 1.287 | 0.90 |
| 142_I | 164_D | 1.278 | 0.89 |
| 204_A | 212_L | 1.268 | 0.89 |
| 204_A | 218_P | 1.238 | 0.87 |
| 102_V | 173_Q | 1.236 | 0.87 |
| 95_A | 107_V | 1.233 | 0.87 |
| 155_V | 227_T | 1.230 | 0.87 |
| 106_E | 128_T | 1.228 | 0.86 |
| 73_T | 121_V | 1.216 | 0.86 |
| 50_I | 65_A | 1.206 | 0.85 |
| 106_E | 126_K | 1.204 | 0.85 |
| 15_A | 109_L | 1.199 | 0.85 |
| 48_V | 70_V | 1.196 | 0.84 |
| 186_L | 225_V | 1.193 | 0.84 |
| 55_N | 59_Y | 1.180 | 0.83 |
| 171_S | 214_A | 1.165 | 0.82 |
| 169_I | 176_L | 1.160 | 0.82 |
| 182_I | 202_L | 1.160 | 0.82 |
| 170_T | 179_I | 1.158 | 0.82 |
| 50_I | 68_V | 1.152 | 0.81 |
| 169_I | 180_D | 1.144 | 0.81 |
| 179_I | 216_I | 1.139 | 0.80 |
| 21_Y | 205_I | 1.126 | 0.79 |
| 68_V | 93_V | 1.123 | 0.79 |
| 6_L | 9_I | 1.119 | 0.79 |
| 68_V | 122_A | 1.100 | 0.77 |
| 101_G | 105_I | 1.098 | 0.77 |
| 144_P | 209_G | 1.092 | 0.76 |
| 204_A | 214_A | 1.091 | 0.76 |
| 59_Y | 102_V | 1.080 | 0.75 |
| 167_V | 182_I | 1.075 | 0.75 |
| 110_S | 227_T | 1.062 | 0.73 |
| 146_I | 157_I | 1.055 | 0.73 |
| 232_P | 242_S | 1.055 | 0.73 |
| 161_M | 226_T | 1.054 | 0.72 |
| 233_S | 236_T | 1.046 | 0.72 |
| 161_M | 165_K | 1.042 | 0.71 |
| 52_I | 95_A | 1.039 | 0.71 |
| 232_P | 235_S | 1.037 | 0.71 |
| 199_S | 222_I | 1.033 | 0.70 |
| 73_T | 119_T | 1.033 | 0.70 |
| 144_P | 186_L | 1.027 | 0.70 |
| 55_N | 134_K | 1.022 | 0.69 |
| 50_I | 127_I | 1.022 | 0.69 |
| 55_N | 58_K | 1.013 | 0.68 |
| 61_I | 103_G | 1.012 | 0.68 |
| 12_L | 16_C | 1.002 | 0.67 |
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 | |
| 2kq1A | 1 | 0.4517 | 99.8 | 0.683 | Contact Map |
| 2kpsA | 1 | 0.3784 | 99.6 | 0.726 | Contact Map |
| 3lywA | 1 | 0.3243 | 99.4 | 0.76 | Contact Map |
| 2kxyA | 1 | 0.3861 | 99.4 | 0.77 | Contact Map |
| 3pddA | 1 | 0.6718 | 16.9 | 0.953 | Contact Map |
| 3d33A | 2 | 0.2934 | 15 | 0.954 | Contact Map |
| 3vtaA | 2 | 0.4363 | 12.1 | 0.956 | Contact Map |
| 3j1rA | 21 | 0.0888 | 10 | 0.958 | Contact Map |
| 3sd2A | 1 | 0.305 | 9.5 | 0.958 | Contact Map |
| 2vo8A | 1 | 0.4981 | 8.5 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)