| 2016-11-9_irk_prg |
| ID: | 1478711583 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 303 (268) | ||
| Sequences: | 62521 (36698.9) | ||
| Seq/Len: | 233.287 | ||
| Nf(neff/√len): | 2241.7 |
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: 233.287).
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 |
| 255_Q | 260_M | 3.684 | 1.00 |
| 23_E | 37_R | 3.372 | 1.00 |
| 124_A | 207_L | 3.127 | 1.00 |
| 150_M | 160_G | 3.026 | 1.00 |
| 14_R | 23_E | 2.790 | 1.00 |
| 15_E | 20_M | 2.725 | 1.00 |
| 132_A | 136_A | 2.599 | 1.00 |
| 252_M | 270_L | 2.497 | 1.00 |
| 91_A | 153_H | 2.473 | 1.00 |
| 132_A | 265_L | 2.428 | 1.00 |
| 15_E | 18_Q | 2.388 | 1.00 |
| 200_M | 253_C | 2.290 | 1.00 |
| 66_T | 72_R | 2.233 | 1.00 |
| 126_E | 157_V | 2.208 | 1.00 |
| 152_A | 156_T | 2.154 | 1.00 |
| 128_A | 203_F | 2.152 | 1.00 |
| 149_C | 157_V | 2.148 | 1.00 |
| 253_C | 267_I | 2.111 | 1.00 |
| 252_M | 262_P | 2.080 | 1.00 |
| 88_E | 158_K | 2.063 | 1.00 |
| 127_I | 149_C | 2.062 | 1.00 |
| 126_E | 156_T | 2.027 | 1.00 |
| 96_K | 147_R | 2.014 | 1.00 |
| 204_G | 253_C | 1.967 | 1.00 |
| 257_N | 260_M | 1.917 | 1.00 |
| 185_A | 198_S | 1.828 | 1.00 |
| 131_M | 203_F | 1.828 | 1.00 |
| 24_G | 40_V | 1.801 | 1.00 |
| 23_E | 89_L | 1.788 | 1.00 |
| 24_G | 38_V | 1.769 | 1.00 |
| 152_A | 158_K | 1.766 | 1.00 |
| 25_N | 37_R | 1.739 | 1.00 |
| 144_L | 206_V | 1.727 | 1.00 |
| 124_A | 210_I | 1.725 | 1.00 |
| 131_M | 264_F | 1.714 | 1.00 |
| 67_C | 133_Y | 1.710 | 1.00 |
| 94_D | 97_S | 1.682 | 1.00 |
| 131_M | 144_L | 1.680 | 1.00 |
| 15_E | 22_Y | 1.670 | 1.00 |
| 11_T | 25_N | 1.642 | 1.00 |
| 125_A | 129_D | 1.617 | 1.00 |
| 125_A | 272_K | 1.616 | 1.00 |
| 130_G | 159_I | 1.614 | 1.00 |
| 200_M | 264_F | 1.612 | 1.00 |
| 74_L | 88_E | 1.612 | 1.00 |
| 13_L | 25_N | 1.609 | 1.00 |
| 122_Q | 126_E | 1.554 | 1.00 |
| 129_D | 268_V | 1.541 | 1.00 |
| 11_T | 27_R | 1.530 | 1.00 |
| 72_R | 88_E | 1.509 | 1.00 |
| 40_V | 86_V | 1.503 | 1.00 |
| 96_K | 100_R | 1.501 | 1.00 |
| 136_A | 265_L | 1.483 | 1.00 |
| 128_A | 267_I | 1.482 | 1.00 |
| 132_A | 268_V | 1.479 | 1.00 |
| 90_M | 152_A | 1.476 | 1.00 |
| 211_T | 246_V | 1.473 | 1.00 |
| 250_M | 254_W | 1.458 | 1.00 |
| 117_L | 120_M | 1.456 | 1.00 |
| 116_T | 119_E | 1.429 | 1.00 |
| 183_W | 209_E | 1.427 | 1.00 |
| 263_T | 266_E | 1.415 | 1.00 |
| 36_T | 74_L | 1.396 | 0.99 |
| 124_A | 203_F | 1.388 | 0.99 |
| 247_T | 251_R | 1.383 | 0.99 |
| 138_K | 196_T | 1.382 | 0.99 |
| 69_H | 129_D | 1.357 | 0.99 |
| 149_C | 206_V | 1.347 | 0.99 |
| 197_S | 263_T | 1.347 | 0.99 |
| 264_F | 267_I | 1.343 | 0.99 |
| 139_F | 165_T | 1.343 | 0.99 |
| 146_A | 183_W | 1.340 | 0.99 |
| 9_K | 26_A | 1.339 | 0.99 |
| 205_V | 254_W | 1.336 | 0.99 |
| 129_D | 272_K | 1.321 | 0.99 |
| 93_G | 101_S | 1.317 | 0.99 |
| 38_V | 86_V | 1.302 | 0.99 |
| 120_M | 211_T | 1.282 | 0.99 |
| 26_A | 29_I | 1.273 | 0.99 |
| 123_M | 157_V | 1.272 | 0.99 |
| 146_A | 206_V | 1.268 | 0.99 |
| 42_T | 84_L | 1.262 | 0.99 |
| 120_M | 210_I | 1.257 | 0.99 |
| 249_L | 270_L | 1.253 | 0.99 |
| 262_P | 267_I | 1.250 | 0.99 |
| 188_S | 198_S | 1.249 | 0.99 |
| 42_T | 82_P | 1.242 | 0.98 |
| 145_A | 180_P | 1.231 | 0.98 |
| 13_L | 23_E | 1.221 | 0.98 |
| 71_V | 90_M | 1.216 | 0.98 |
| 252_M | 255_Q | 1.212 | 0.98 |
| 249_L | 253_C | 1.212 | 0.98 |
| 90_M | 158_K | 1.209 | 0.98 |
| 207_L | 249_L | 1.208 | 0.98 |
| 117_L | 243_P | 1.206 | 0.98 |
| 249_L | 267_I | 1.206 | 0.98 |
| 40_V | 84_L | 1.205 | 0.98 |
| 37_R | 91_A | 1.198 | 0.98 |
| 96_K | 209_E | 1.190 | 0.98 |
| 194_F | 198_S | 1.177 | 0.98 |
| 128_A | 268_V | 1.177 | 0.98 |
| 143_D | 148_N | 1.175 | 0.98 |
| 142_R | 194_F | 1.166 | 0.97 |
| 122_Q | 156_T | 1.159 | 0.97 |
| 69_H | 130_G | 1.155 | 0.97 |
| 25_N | 35_E | 1.153 | 0.97 |
| 133_Y | 137_K | 1.153 | 0.97 |
| 127_I | 157_V | 1.142 | 0.97 |
| 21_V | 39_A | 1.135 | 0.97 |
| 203_F | 207_L | 1.134 | 0.97 |
| 119_E | 122_Q | 1.131 | 0.97 |
| 228_K | 232_D | 1.130 | 0.97 |
| 238_Q | 247_T | 1.127 | 0.97 |
| 129_D | 132_A | 1.125 | 0.97 |
| 141_H | 144_L | 1.116 | 0.96 |
| 248_D | 252_M | 1.113 | 0.96 |
| 90_M | 150_M | 1.113 | 0.96 |
| 22_Y | 42_T | 1.107 | 0.96 |
| 93_G | 97_S | 1.106 | 0.96 |
| 128_A | 264_F | 1.094 | 0.96 |
| 249_L | 262_P | 1.085 | 0.96 |
| 148_N | 161_D | 1.070 | 0.95 |
| 144_L | 159_I | 1.060 | 0.95 |
| 38_V | 74_L | 1.056 | 0.95 |
| 92_H | 155_F | 1.047 | 0.94 |
| 99_L | 209_E | 1.047 | 0.94 |
| 96_K | 146_A | 1.046 | 0.94 |
| 226_V | 229_F | 1.046 | 0.94 |
| 185_A | 188_S | 1.045 | 0.94 |
| 127_I | 144_L | 1.044 | 0.94 |
| 203_F | 253_C | 1.041 | 0.94 |
| 127_I | 130_G | 1.040 | 0.94 |
| 37_R | 89_L | 1.037 | 0.94 |
| 188_S | 194_F | 1.037 | 0.94 |
| 131_M | 135_N | 1.036 | 0.94 |
| 203_F | 264_F | 1.034 | 0.94 |
| 71_V | 87_M | 1.029 | 0.94 |
| 12_L | 22_Y | 1.027 | 0.94 |
| 146_A | 209_E | 1.027 | 0.94 |
| 151_V | 157_V | 1.025 | 0.93 |
| 13_L | 37_R | 1.022 | 0.93 |
| 71_V | 160_G | 1.020 | 0.93 |
| 252_M | 266_E | 1.019 | 0.93 |
| 70_V | 134_L | 1.019 | 0.93 |
| 114_P | 117_L | 1.012 | 0.93 |
| 200_M | 267_I | 1.012 | 0.93 |
| 197_S | 259_N | 1.008 | 0.93 |
| 64_G | 137_K | 1.008 | 0.93 |
| 21_V | 24_G | 1.006 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4rt7A | 1 | 0 | 100 | 0.197 | Contact Map |
| 4fl3A | 1 | 0.8482 | 100 | 0.202 | Contact Map |
| 5a46A | 2 | 0 | 100 | 0.203 | Contact Map |
| 4gt4A | 2 | 0.8911 | 100 | 0.214 | Contact Map |
| 4aojA | 3 | 0.8614 | 100 | 0.216 | Contact Map |
| 4aseA | 1 | 0.9175 | 100 | 0.217 | Contact Map |
| 4aszA | 1 | 0.9175 | 100 | 0.218 | Contact Map |
| 4xi2A | 1 | 0.8581 | 100 | 0.219 | Contact Map |
| 3cblA | 1 | 0.8713 | 100 | 0.22 | Contact Map |
| 1p4oA | 2 | 0.9736 | 100 | 0.222 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)