| 4DUR_A 430-791 30-362 |
| ID: | 1412290664 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 333 (331) | ||
| Sequences: | 993 (510.9) | ||
| Seq/Len: | 3.000 | ||
| Nf(neff/√len): | 28.1 |
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: 3.000).
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 |
| 142_T | 147_L | 3.508 | 1.00 |
| 134_L | 198_A | 3.505 | 1.00 |
| 222_C | 289_C | 3.318 | 1.00 |
| 133_T | 207_A | 3.175 | 1.00 |
| 173_Q | 204_V | 2.808 | 1.00 |
| 139_W | 191_L | 2.365 | 1.00 |
| 141_L | 297_L | 2.186 | 1.00 |
| 120_S | 128_H | 2.168 | 1.00 |
| 187_K | 322_F | 2.037 | 1.00 |
| 178_S | 193_K | 2.026 | 1.00 |
| 80_V | 83_C | 1.977 | 1.00 |
| 118_Q | 225_T | 1.962 | 1.00 |
| 184_P | 329_V | 1.947 | 1.00 |
| 134_L | 160_L | 1.943 | 1.00 |
| 75_Y | 78_C | 1.864 | 0.99 |
| 132_G | 140_V | 1.858 | 0.99 |
| 224_I | 301_T | 1.803 | 0.99 |
| 207_A | 297_L | 1.793 | 0.99 |
| 242_A | 276_T | 1.787 | 0.99 |
| 110_A | 115_W | 1.748 | 0.99 |
| 25_C | 54_C | 1.718 | 0.98 |
| 277_D | 314_G | 1.715 | 0.98 |
| 207_A | 288_V | 1.709 | 0.98 |
| 114_S | 241_E | 1.704 | 0.98 |
| 175_I | 198_A | 1.665 | 0.98 |
| 49_L | 53_Y | 1.648 | 0.98 |
| 134_L | 140_V | 1.632 | 0.98 |
| 43_T | 49_L | 1.632 | 0.98 |
| 159_I | 174_E | 1.629 | 0.98 |
| 75_Y | 79_D | 1.628 | 0.98 |
| 49_L | 60_D | 1.624 | 0.98 |
| 75_Y | 80_V | 1.612 | 0.97 |
| 105_V | 308_A | 1.610 | 0.97 |
| 186_R | 263_Q | 1.588 | 0.97 |
| 60_D | 69_T | 1.511 | 0.96 |
| 277_D | 316_Y | 1.480 | 0.95 |
| 160_L | 198_A | 1.453 | 0.95 |
| 306_G | 309_R | 1.412 | 0.93 |
| 74_L | 80_V | 1.408 | 0.93 |
| 78_C | 83_C | 1.405 | 0.93 |
| 57_P | 60_D | 1.400 | 0.93 |
| 49_L | 69_T | 1.382 | 0.92 |
| 77_Y | 80_V | 1.377 | 0.92 |
| 60_D | 75_Y | 1.370 | 0.92 |
| 186_R | 265_T | 1.362 | 0.92 |
| 22_G | 28_W | 1.359 | 0.92 |
| 304_G | 314_G | 1.354 | 0.91 |
| 65_W | 78_C | 1.354 | 0.91 |
| 133_T | 300_V | 1.351 | 0.91 |
| 278_S | 301_T | 1.349 | 0.91 |
| 57_P | 65_W | 1.341 | 0.91 |
| 49_L | 57_P | 1.339 | 0.91 |
| 26_Q | 34_H | 1.336 | 0.91 |
| 43_T | 60_D | 1.335 | 0.91 |
| 263_Q | 266_E | 1.329 | 0.90 |
| 145_H | 283_S | 1.325 | 0.90 |
| 19_T | 22_G | 1.314 | 0.90 |
| 67_Y | 75_Y | 1.307 | 0.89 |
| 277_D | 283_S | 1.307 | 0.89 |
| 192_L | 224_I | 1.295 | 0.89 |
| 55_R | 58_D | 1.290 | 0.89 |
| 53_Y | 60_D | 1.288 | 0.88 |
| 90_C | 93_P | 1.283 | 0.88 |
| 49_L | 58_D | 1.274 | 0.88 |
| 305_L | 312_K | 1.274 | 0.88 |
| 300_V | 317_V | 1.272 | 0.88 |
| 56_N | 78_C | 1.254 | 0.87 |
| 103_R | 314_G | 1.251 | 0.86 |
| 188_D | 302_S | 1.245 | 0.86 |
| 158_V | 192_L | 1.242 | 0.86 |
| 103_R | 106_G | 1.239 | 0.86 |
| 160_L | 204_V | 1.238 | 0.86 |
| 67_Y | 71_P | 1.230 | 0.85 |
| 53_Y | 58_D | 1.229 | 0.85 |
| 104_V | 107_G | 1.220 | 0.85 |
| 283_S | 302_S | 1.219 | 0.84 |
| 266_E | 314_G | 1.215 | 0.84 |
| 57_P | 66_C | 1.211 | 0.84 |
| 58_D | 78_C | 1.211 | 0.84 |
| 57_P | 78_C | 1.200 | 0.83 |
| 145_H | 281_G | 1.197 | 0.83 |
| 230_T | 240_K | 1.196 | 0.83 |
| 45_P | 49_L | 1.194 | 0.83 |
| 43_T | 48_G | 1.193 | 0.83 |
| 183_E | 187_K | 1.191 | 0.83 |
| 130_C | 146_C | 1.190 | 0.82 |
| 304_G | 316_Y | 1.187 | 0.82 |
| 162_A | 172_V | 1.186 | 0.82 |
| 43_T | 53_Y | 1.182 | 0.82 |
| 178_S | 195_S | 1.174 | 0.81 |
| 58_D | 65_W | 1.172 | 0.81 |
| 107_G | 285_G | 1.169 | 0.81 |
| 188_D | 304_G | 1.167 | 0.81 |
| 245_P | 270_G | 1.161 | 0.80 |
| 236_A | 240_K | 1.160 | 0.80 |
| 163_H | 227_W | 1.159 | 0.80 |
| 63_G | 68_T | 1.155 | 0.80 |
| 224_I | 242_A | 1.148 | 0.79 |
| 228_G | 282_D | 1.143 | 0.79 |
| 73_K | 78_C | 1.136 | 0.78 |
| 303_W | 314_G | 1.136 | 0.78 |
| 115_W | 225_T | 1.134 | 0.78 |
| 188_D | 283_S | 1.129 | 0.78 |
| 73_K | 80_V | 1.126 | 0.77 |
| 58_D | 75_Y | 1.125 | 0.77 |
| 143_A | 188_D | 1.123 | 0.77 |
| 22_G | 25_C | 1.123 | 0.77 |
| 54_C | 67_Y | 1.122 | 0.77 |
| 43_T | 69_T | 1.118 | 0.77 |
| 248_E | 251_V | 1.108 | 0.76 |
| 281_G | 316_Y | 1.107 | 0.76 |
| 57_P | 64_P | 1.105 | 0.76 |
| 23_T | 29_A | 1.098 | 0.75 |
| 49_L | 55_R | 1.095 | 0.75 |
| 74_L | 77_Y | 1.094 | 0.74 |
| 107_G | 145_H | 1.092 | 0.74 |
| 274_G | 310_P | 1.091 | 0.74 |
| 247_I | 258_L | 1.090 | 0.74 |
| 106_G | 274_G | 1.089 | 0.74 |
| 59_G | 66_C | 1.083 | 0.73 |
| 55_R | 65_W | 1.080 | 0.73 |
| 29_A | 32_E | 1.080 | 0.73 |
| 222_C | 313_P | 1.079 | 0.73 |
| 60_D | 77_Y | 1.078 | 0.73 |
| 25_C | 28_W | 1.077 | 0.73 |
| 73_K | 76_D | 1.074 | 0.73 |
| 53_Y | 66_C | 1.071 | 0.72 |
| 19_T | 28_W | 1.069 | 0.72 |
| 138_E | 193_K | 1.068 | 0.72 |
| 227_W | 240_K | 1.067 | 0.72 |
| 222_C | 287_L | 1.062 | 0.71 |
| 119_V | 160_L | 1.056 | 0.71 |
| 66_C | 78_C | 1.056 | 0.71 |
| 266_E | 303_W | 1.055 | 0.71 |
| 49_L | 75_Y | 1.054 | 0.71 |
| 56_N | 75_Y | 1.053 | 0.70 |
| 53_Y | 69_T | 1.051 | 0.70 |
| 56_N | 67_Y | 1.050 | 0.70 |
| 286_P | 314_G | 1.049 | 0.70 |
| 72_R | 75_Y | 1.046 | 0.70 |
| 145_H | 188_D | 1.042 | 0.69 |
| 32_E | 38_I | 1.032 | 0.68 |
| 113_H | 116_P | 1.031 | 0.68 |
| 65_W | 80_V | 1.031 | 0.68 |
| 115_W | 241_E | 1.027 | 0.68 |
| 52_N | 55_R | 1.024 | 0.67 |
| 45_P | 57_P | 1.023 | 0.67 |
| 61_V | 83_C | 1.023 | 0.67 |
| 107_G | 282_D | 1.022 | 0.67 |
| 26_Q | 33_P | 1.022 | 0.67 |
| 199_V | 330_M | 1.022 | 0.67 |
| 122_R | 165_E | 1.019 | 0.67 |
| 109_V | 240_K | 1.018 | 0.67 |
| 65_W | 76_D | 1.018 | 0.67 |
| 122_R | 133_T | 1.016 | 0.66 |
| 164_Q | 301_T | 1.016 | 0.66 |
| 43_T | 52_N | 1.015 | 0.66 |
| 55_R | 83_C | 1.014 | 0.66 |
| 145_H | 314_G | 1.013 | 0.66 |
| 201_T | 263_Q | 1.007 | 0.65 |
| 247_I | 313_P | 1.007 | 0.65 |
| 69_T | 75_Y | 1.004 | 0.65 |
| 48_G | 66_C | 1.004 | 0.65 |
| 198_A | 204_V | 1.003 | 0.65 |
| 48_G | 53_Y | 1.001 | 0.65 |
| 73_K | 77_Y | 1.001 | 0.65 |
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 | |
| 4durA | 2 | 0.991 | 100 | 0.209 | Contact Map |
| 3nxpA | 1 | 0.979 | 100 | 0.22 | Contact Map |
| 4nzqA | 1 | 0.991 | 100 | 0.233 | Contact Map |
| 2f83A | 1 | 0.9039 | 100 | 0.372 | Contact Map |
| 4kkdA | 2 | 0.979 | 100 | 0.373 | Contact Map |
| 4igdA | 1 | 0.964 | 100 | 0.374 | Contact Map |
| 4bxwA | 2 | 0.7297 | 100 | 0.375 | Contact Map |
| 1ddjA | 4 | 0.7417 | 100 | 0.384 | Contact Map |
| 2xrcA | 4 | 0.8318 | 100 | 0.386 | Contact Map |
| 4f4oC | 4 | 0.8348 | 100 | 0.387 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)