| RR |
| ID: | 1384481639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 235 (224) | ||
| Sequences: | 27955 (20913.8) | ||
| Seq/Len: | 124.799 | ||
| Nf(neff/√len): | 1397.4 |
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: 124.799).
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 |
| 14_S | 30_T | 3.467 | 1.00 |
| 14_S | 32_F | 2.758 | 1.00 |
| 35_R | 57_E | 2.535 | 1.00 |
| 7_V | 37_A | 2.487 | 1.00 |
| 33_D | 57_E | 2.467 | 1.00 |
| 18_K | 30_T | 2.430 | 1.00 |
| 29_I | 46_P | 2.366 | 1.00 |
| 198_R | 201_D | 2.313 | 1.00 |
| 163_R | 166_E | 2.309 | 1.00 |
| 164_E | 210_K | 2.305 | 1.00 |
| 181_R | 201_D | 2.291 | 1.00 |
| 58_L | 66_E | 2.283 | 1.00 |
| 84_E | 104_S | 2.280 | 1.00 |
| 18_K | 22_A | 2.242 | 1.00 |
| 33_D | 36_E | 2.116 | 1.00 |
| 34_G | 58_L | 2.096 | 1.00 |
| 87_K | 107_E | 2.062 | 1.00 |
| 141_D | 154_R | 1.971 | 1.00 |
| 59_D | 62_E | 1.971 | 1.00 |
| 20_N | 105_N | 1.949 | 1.00 |
| 3_K | 27_D | 1.940 | 1.00 |
| 38_L | 66_E | 1.893 | 1.00 |
| 222_L | 232_K | 1.848 | 1.00 |
| 169_H | 173_T | 1.811 | 1.00 |
| 150_V | 157_E | 1.796 | 1.00 |
| 31_A | 40_K | 1.789 | 1.00 |
| 222_L | 230_Y | 1.788 | 1.00 |
| 32_F | 36_E | 1.781 | 1.00 |
| 138_I | 143_Q | 1.774 | 1.00 |
| 144_I | 172_A | 1.762 | 1.00 |
| 48_L | 112_V | 1.750 | 1.00 |
| 76_I | 115_H | 1.742 | 1.00 |
| 203_T | 206_R | 1.732 | 1.00 |
| 3_K | 29_I | 1.731 | 1.00 |
| 77_M | 90_G | 1.727 | 1.00 |
| 64_A | 75_I | 1.696 | 1.00 |
| 53_L | 77_M | 1.675 | 1.00 |
| 51_L | 63_V | 1.669 | 1.00 |
| 92_E | 113_K | 1.636 | 1.00 |
| 21_L | 112_V | 1.629 | 1.00 |
| 96_D | 118_R | 1.620 | 1.00 |
| 174_H | 177_Q | 1.611 | 1.00 |
| 51_L | 64_A | 1.589 | 1.00 |
| 54_M | 81_K | 1.585 | 1.00 |
| 143_Q | 152_K | 1.575 | 1.00 |
| 170_H | 184_L | 1.568 | 1.00 |
| 64_A | 77_M | 1.560 | 1.00 |
| 66_E | 69_K | 1.547 | 1.00 |
| 49_I | 73_V | 1.496 | 1.00 |
| 7_V | 55_L | 1.483 | 1.00 |
| 5_L | 31_A | 1.483 | 1.00 |
| 81_K | 86_D | 1.473 | 1.00 |
| 77_M | 95_A | 1.445 | 1.00 |
| 8_D | 14_S | 1.443 | 1.00 |
| 42_E | 70_N | 1.440 | 1.00 |
| 170_H | 187_T | 1.423 | 1.00 |
| 97_D | 111_R | 1.420 | 1.00 |
| 29_I | 40_K | 1.413 | 1.00 |
| 68_R | 96_D | 1.411 | 1.00 |
| 38_L | 63_V | 1.401 | 0.99 |
| 24_E | 109_L | 1.378 | 0.99 |
| 204_V | 208_R | 1.377 | 0.99 |
| 180_T | 183_H | 1.376 | 0.99 |
| 58_L | 62_E | 1.372 | 0.99 |
| 34_G | 63_V | 1.361 | 0.99 |
| 61_L | 93_I | 1.347 | 0.99 |
| 39_S | 43_E | 1.296 | 0.99 |
| 175_T | 179_M | 1.292 | 0.99 |
| 53_L | 61_L | 1.270 | 0.99 |
| 62_E | 65_K | 1.262 | 0.99 |
| 35_R | 58_L | 1.253 | 0.99 |
| 145_L | 148_A | 1.239 | 0.98 |
| 149_F | 166_E | 1.238 | 0.98 |
| 40_K | 43_E | 1.237 | 0.98 |
| 40_K | 44_E | 1.236 | 0.98 |
| 48_L | 116_L | 1.230 | 0.98 |
| 224_R | 230_Y | 1.214 | 0.98 |
| 29_I | 44_E | 1.201 | 0.98 |
| 41_Y | 67_V | 1.199 | 0.98 |
| 26_Y | 113_K | 1.177 | 0.98 |
| 35_R | 39_S | 1.173 | 0.98 |
| 115_H | 118_R | 1.163 | 0.97 |
| 65_K | 89_I | 1.159 | 0.97 |
| 149_F | 227_V | 1.159 | 0.97 |
| 83_S | 86_D | 1.157 | 0.97 |
| 170_H | 179_M | 1.142 | 0.97 |
| 199_T | 203_T | 1.141 | 0.97 |
| 38_L | 58_L | 1.136 | 0.97 |
| 202_V | 205_R | 1.133 | 0.97 |
| 31_A | 37_A | 1.132 | 0.97 |
| 161_T | 210_K | 1.130 | 0.97 |
| 144_I | 165_F | 1.128 | 0.97 |
| 188_V | 193_Y | 1.127 | 0.97 |
| 146_P | 169_H | 1.113 | 0.96 |
| 11_K | 32_F | 1.111 | 0.96 |
| 36_E | 39_S | 1.105 | 0.96 |
| 4_I | 26_Y | 1.101 | 0.96 |
| 152_K | 157_E | 1.100 | 0.96 |
| 177_Q | 183_H | 1.087 | 0.96 |
| 17_I | 78_L | 1.082 | 0.96 |
| 182_E | 197_V | 1.081 | 0.95 |
| 54_M | 80_A | 1.064 | 0.95 |
| 85_F | 89_I | 1.057 | 0.95 |
| 9_D | 52_D | 1.056 | 0.95 |
| 163_R | 189_W | 1.055 | 0.95 |
| 7_V | 49_I | 1.054 | 0.95 |
| 25_G | 113_K | 1.049 | 0.94 |
| 84_E | 88_V | 1.048 | 0.94 |
| 197_V | 201_D | 1.041 | 0.94 |
| 214_T | 217_R | 1.039 | 0.94 |
| 36_E | 40_K | 1.039 | 0.94 |
| 5_L | 37_A | 1.037 | 0.94 |
| 127_A | 132_S | 1.035 | 0.94 |
| 37_A | 41_Y | 1.032 | 0.94 |
| 114_A | 119_T | 1.026 | 0.94 |
| 6_I | 28_T | 1.025 | 0.93 |
| 136_E | 143_Q | 1.023 | 0.93 |
| 55_L | 63_V | 1.022 | 0.93 |
| 8_D | 55_L | 1.021 | 0.93 |
| 24_E | 113_K | 1.009 | 0.93 |
| 198_R | 202_V | 1.008 | 0.93 |
| 139_I | 231_M | 1.008 | 0.93 |
| 147_D | 177_Q | 1.006 | 0.93 |
| 5_L | 46_P | 1.005 | 0.93 |
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 | |
| 2oqrA | 1 | 0.9617 | 100 | 0.155 | Contact Map |
| 1ys7A | 2 | 0.9574 | 100 | 0.162 | Contact Map |
| 2gwrA | 1 | 0.9447 | 100 | 0.162 | Contact Map |
| 3r0jA | 2 | 0.9319 | 100 | 0.171 | Contact Map |
| 4b09A | 12 | 0.8979 | 100 | 0.186 | Contact Map |
| 1kgsA | 1 | 0.9277 | 100 | 0.187 | Contact Map |
| 1p2fA | 1 | 0.9149 | 100 | 0.207 | Contact Map |
| 2hqrA | 2 | 0.9191 | 100 | 0.217 | Contact Map |
| 3q9sA | 1 | 0.8936 | 100 | 0.223 | Contact Map |
| 3kloA | 4 | 0.8894 | 100 | 0.301 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)