| NR2_TM |
| ID: | 1402710447 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 303 (288) | ||
| Sequences: | 1220 (910.8) | ||
| Seq/Len: | 4.236 | ||
| Nf(neff/√len): | 53.7 |
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: 4.236).
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 |
| 189_C | 244_C | 5.208 | 1.00 |
| 156_S | 159_D | 2.377 | 1.00 |
| 271_A | 282_E | 2.332 | 1.00 |
| 6_P | 89_Y | 2.331 | 1.00 |
| 155_R | 159_D | 2.167 | 1.00 |
| 13_V | 17_V | 2.106 | 1.00 |
| 216_K | 220_D | 2.087 | 1.00 |
| 156_S | 160_A | 1.918 | 1.00 |
| 160_A | 163_S | 1.910 | 1.00 |
| 91_A | 94_A | 1.882 | 1.00 |
| 174_Y | 179_L | 1.874 | 1.00 |
| 162_L | 167_G | 1.836 | 1.00 |
| 83_V | 87_A | 1.814 | 1.00 |
| 158_Q | 162_L | 1.778 | 1.00 |
| 268_L | 271_A | 1.749 | 0.99 |
| 106_V | 111_D | 1.713 | 0.99 |
| 220_D | 223_I | 1.685 | 0.99 |
| 174_Y | 178_V | 1.682 | 0.99 |
| 154_Q | 160_A | 1.674 | 0.99 |
| 287_K | 290_A | 1.656 | 0.99 |
| 79_A | 95_A | 1.614 | 0.99 |
| 159_D | 163_S | 1.602 | 0.99 |
| 210_Q | 213_S | 1.577 | 0.99 |
| 165_K | 190_K | 1.558 | 0.98 |
| 55_L | 60_S | 1.547 | 0.98 |
| 92_N | 95_A | 1.512 | 0.98 |
| 175_D | 178_V | 1.507 | 0.98 |
| 160_A | 164_L | 1.494 | 0.98 |
| 112_K | 171_A | 1.490 | 0.98 |
| 288_S | 291_E | 1.483 | 0.98 |
| 133_S | 138_I | 1.477 | 0.98 |
| 95_A | 98_I | 1.461 | 0.97 |
| 209_I | 213_S | 1.452 | 0.97 |
| 87_A | 90_T | 1.448 | 0.97 |
| 128_T | 149_M | 1.445 | 0.97 |
| 179_L | 183_A | 1.421 | 0.97 |
| 209_I | 219_V | 1.416 | 0.97 |
| 57_F | 60_S | 1.405 | 0.96 |
| 275_S | 282_E | 1.401 | 0.96 |
| 89_Y | 97_M | 1.396 | 0.96 |
| 258_I | 265_F | 1.384 | 0.96 |
| 50_W | 79_A | 1.370 | 0.96 |
| 54_G | 59_N | 1.355 | 0.95 |
| 268_L | 282_E | 1.352 | 0.95 |
| 280_I | 286_Y | 1.351 | 0.95 |
| 91_A | 95_A | 1.351 | 0.95 |
| 279_F | 282_E | 1.339 | 0.95 |
| 54_G | 58_N | 1.339 | 0.95 |
| 262_A | 266_Y | 1.337 | 0.95 |
| 236_E | 240_L | 1.334 | 0.95 |
| 106_V | 112_K | 1.323 | 0.95 |
| 98_I | 102_Y | 1.316 | 0.94 |
| 157_V | 160_A | 1.312 | 0.94 |
| 89_Y | 127_G | 1.311 | 0.94 |
| 86_L | 98_I | 1.310 | 0.94 |
| 8_S | 11_V | 1.308 | 0.94 |
| 287_K | 291_E | 1.293 | 0.94 |
| 27_V | 59_N | 1.290 | 0.94 |
| 87_A | 95_A | 1.288 | 0.93 |
| 6_P | 12_W | 1.264 | 0.93 |
| 57_F | 93_L | 1.262 | 0.93 |
| 6_P | 97_M | 1.261 | 0.92 |
| 278_T | 282_E | 1.253 | 0.92 |
| 124_F | 138_I | 1.244 | 0.92 |
| 110_S | 114_F | 1.240 | 0.92 |
| 135_E | 139_R | 1.235 | 0.91 |
| 161_L | 180_N | 1.231 | 0.91 |
| 232_M | 236_E | 1.228 | 0.91 |
| 271_A | 275_S | 1.208 | 0.90 |
| 126_F | 148_Y | 1.207 | 0.90 |
| 126_F | 137_N | 1.204 | 0.90 |
| 87_A | 92_N | 1.192 | 0.89 |
| 111_D | 232_M | 1.180 | 0.89 |
| 17_V | 20_L | 1.179 | 0.89 |
| 223_I | 259_D | 1.172 | 0.88 |
| 94_A | 98_I | 1.171 | 0.88 |
| 234_E | 238_L | 1.166 | 0.88 |
| 58_N | 94_A | 1.154 | 0.87 |
| 226_L | 231_E | 1.151 | 0.87 |
| 132_G | 137_N | 1.147 | 0.87 |
| 129_V | 132_G | 1.138 | 0.86 |
| 88_S | 98_I | 1.134 | 0.86 |
| 53_W | 76_S | 1.134 | 0.86 |
| 108_G | 211_K | 1.133 | 0.86 |
| 93_L | 98_I | 1.133 | 0.86 |
| 54_G | 57_F | 1.129 | 0.86 |
| 76_S | 79_A | 1.126 | 0.85 |
| 88_S | 260_N | 1.118 | 0.85 |
| 50_W | 81_F | 1.117 | 0.85 |
| 50_W | 82_A | 1.116 | 0.85 |
| 162_L | 166_S | 1.115 | 0.85 |
| 131_N | 135_E | 1.111 | 0.84 |
| 83_V | 192_V | 1.103 | 0.84 |
| 142_Y | 149_M | 1.096 | 0.83 |
| 90_T | 94_A | 1.095 | 0.83 |
| 230_G | 282_E | 1.094 | 0.83 |
| 78_W | 213_S | 1.092 | 0.83 |
| 49_I | 52_L | 1.091 | 0.83 |
| 265_F | 282_E | 1.085 | 0.82 |
| 231_E | 234_E | 1.080 | 0.82 |
| 139_R | 275_S | 1.078 | 0.82 |
| 231_E | 235_L | 1.077 | 0.82 |
| 9_A | 13_V | 1.077 | 0.82 |
| 161_L | 217_R | 1.071 | 0.81 |
| 91_A | 235_L | 1.069 | 0.81 |
| 87_A | 98_I | 1.065 | 0.81 |
| 149_M | 176_A | 1.065 | 0.81 |
| 74_M | 166_S | 1.062 | 0.81 |
| 55_L | 59_N | 1.057 | 0.80 |
| 161_L | 165_K | 1.057 | 0.80 |
| 161_L | 164_L | 1.056 | 0.80 |
| 89_Y | 93_L | 1.053 | 0.80 |
| 249_N | 277_I | 1.052 | 0.80 |
| 145_M | 148_Y | 1.051 | 0.80 |
| 209_I | 241_T | 1.051 | 0.80 |
| 180_N | 185_R | 1.047 | 0.79 |
| 233_E | 237_A | 1.043 | 0.79 |
| 16_F | 278_T | 1.043 | 0.79 |
| 68_G | 71_S | 1.042 | 0.79 |
| 261_M | 265_F | 1.039 | 0.79 |
| 126_F | 138_I | 1.037 | 0.78 |
| 90_T | 98_I | 1.033 | 0.78 |
| 243_I | 257_D | 1.031 | 0.78 |
| 80_F | 84_I | 1.030 | 0.78 |
| 100_R | 108_G | 1.023 | 0.77 |
| 225_Q | 229_D | 1.022 | 0.77 |
| 34_S | 37_G | 1.022 | 0.77 |
| 45_I | 248_K | 1.019 | 0.77 |
| 11_V | 264_V | 1.018 | 0.77 |
| 259_D | 274_L | 1.015 | 0.76 |
| 52_L | 97_M | 1.009 | 0.76 |
| 78_W | 265_F | 1.008 | 0.76 |
| 81_F | 205_Y | 1.008 | 0.76 |
| 108_G | 113_K | 1.005 | 0.75 |
| 4_L | 10_D | 1.001 | 0.75 |
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 | |
| 4pe5B | 2 | 0.7987 | 100 | 0.255 | Contact Map |
| 3kg2A | 4 | 0.8581 | 100 | 0.302 | Contact Map |
| 4pe5A | 2 | 0.8284 | 100 | 0.306 | Contact Map |
| 4jwxA | 1 | 0.637 | 99.5 | 0.77 | Contact Map |
| 1yaeA | 6 | 0.4884 | 99.5 | 0.771 | Contact Map |
| 2rc8A | 2 | 0.7426 | 99.4 | 0.777 | Contact Map |
| 1pb7A | 1 | 0.6238 | 99 | 0.816 | Contact Map |
| 3g3kA | 2 | 0.604 | 99 | 0.819 | Contact Map |
| 2v3uA | 1 | 0.604 | 98.8 | 0.829 | Contact Map |
| 4io2A | 2 | 0.604 | 98.7 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)