| Rgx |
| ID: | 1383636204 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 226 (224) | ||
| Sequences: | 29283 (22020.2) | ||
| Seq/Len: | 130.728 | ||
| Nf(neff/√len): | 1471.3 |
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: 130.728).
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_A | 30_V | 3.586 | 1.00 |
| 14_A | 32_T | 2.838 | 1.00 |
| 35_P | 57_G | 2.597 | 1.00 |
| 18_A | 30_V | 2.594 | 1.00 |
| 7_V | 37_A | 2.530 | 1.00 |
| 33_D | 57_G | 2.480 | 1.00 |
| 192_K | 195_D | 2.452 | 1.00 |
| 29_T | 46_A | 2.380 | 1.00 |
| 157_K | 160_D | 2.356 | 1.00 |
| 58_M | 66_Q | 2.350 | 1.00 |
| 175_R | 195_D | 2.347 | 1.00 |
| 18_A | 22_R | 2.234 | 1.00 |
| 158_E | 204_K | 2.215 | 1.00 |
| 84_E | 104_S | 2.191 | 1.00 |
| 87_K | 107_E | 2.165 | 1.00 |
| 34_G | 58_M | 2.118 | 1.00 |
| 33_D | 36_A | 2.090 | 1.00 |
| 20_L | 105_A | 2.028 | 1.00 |
| 38_L | 66_Q | 1.964 | 1.00 |
| 3_S | 27_E | 1.944 | 1.00 |
| 59_S | 62_D | 1.903 | 1.00 |
| 135_P | 148_N | 1.886 | 1.00 |
| 32_T | 36_A | 1.835 | 1.00 |
| 31_V | 40_E | 1.815 | 1.00 |
| 77_M | 90_G | 1.777 | 1.00 |
| 163_E | 167_R | 1.775 | 1.00 |
| 3_S | 29_T | 1.774 | 1.00 |
| 216_V | 224_K | 1.772 | 1.00 |
| 197_H | 200_R | 1.763 | 1.00 |
| 132_E | 137_R | 1.738 | 1.00 |
| 48_I | 112_I | 1.734 | 1.00 |
| 21_L | 112_I | 1.719 | 1.00 |
| 64_C | 75_V | 1.680 | 1.00 |
| 76_I | 115_V | 1.673 | 1.00 |
| 144_V | 151_T | 1.667 | 1.00 |
| 54_M | 81_R | 1.641 | 1.00 |
| 96_D | 118_R | 1.639 | 1.00 |
| 5_L | 31_V | 1.621 | 1.00 |
| 51_L | 63_V | 1.619 | 1.00 |
| 138_M | 166_M | 1.588 | 1.00 |
| 53_L | 77_M | 1.585 | 1.00 |
| 168_N | 171_R | 1.541 | 1.00 |
| 137_R | 146_S | 1.533 | 1.00 |
| 97_D | 111_R | 1.529 | 1.00 |
| 92_E | 113_R | 1.526 | 1.00 |
| 64_C | 77_M | 1.520 | 1.00 |
| 51_L | 64_C | 1.514 | 1.00 |
| 81_R | 86_D | 1.497 | 1.00 |
| 164_Y | 178_L | 1.480 | 1.00 |
| 7_V | 55_L | 1.477 | 1.00 |
| 49_V | 73_V | 1.463 | 1.00 |
| 8_E | 14_A | 1.461 | 1.00 |
| 168_N | 172_V | 1.455 | 1.00 |
| 66_Q | 69_A | 1.452 | 1.00 |
| 164_Y | 181_R | 1.452 | 1.00 |
| 68_R | 96_D | 1.443 | 1.00 |
| 77_M | 95_A | 1.441 | 1.00 |
| 174_T | 177_Q | 1.435 | 1.00 |
| 34_G | 63_V | 1.409 | 1.00 |
| 29_T | 40_E | 1.396 | 0.99 |
| 198_V | 202_R | 1.392 | 0.99 |
| 38_L | 63_V | 1.372 | 0.99 |
| 58_M | 62_D | 1.368 | 0.99 |
| 24_E | 109_I | 1.354 | 0.99 |
| 61_T | 93_L | 1.316 | 0.99 |
| 35_P | 58_M | 1.300 | 0.99 |
| 40_E | 44_A | 1.280 | 0.99 |
| 169_S | 173_L | 1.277 | 0.99 |
| 39_A | 43_R | 1.271 | 0.99 |
| 173_L | 181_R | 1.263 | 0.99 |
| 62_D | 65_K | 1.250 | 0.99 |
| 139_D | 142_R | 1.249 | 0.99 |
| 53_L | 61_T | 1.241 | 0.98 |
| 216_V | 226_E | 1.238 | 0.98 |
| 40_E | 43_R | 1.233 | 0.98 |
| 218_V | 224_K | 1.220 | 0.98 |
| 26_F | 113_R | 1.207 | 0.98 |
| 83_S | 86_D | 1.201 | 0.98 |
| 35_P | 39_A | 1.195 | 0.98 |
| 164_Y | 173_L | 1.177 | 0.98 |
| 31_V | 37_A | 1.174 | 0.98 |
| 38_L | 58_M | 1.158 | 0.97 |
| 25_G | 113_R | 1.158 | 0.97 |
| 48_I | 116_L | 1.156 | 0.97 |
| 41_F | 67_L | 1.152 | 0.97 |
| 193_T | 197_H | 1.151 | 0.97 |
| 143_H | 221_L | 1.143 | 0.97 |
| 143_H | 160_D | 1.143 | 0.97 |
| 11_E | 32_T | 1.136 | 0.97 |
| 36_A | 39_A | 1.133 | 0.97 |
| 4_V | 26_F | 1.127 | 0.97 |
| 176_G | 191_T | 1.125 | 0.97 |
| 196_V | 199_K | 1.125 | 0.97 |
| 29_T | 44_A | 1.117 | 0.96 |
| 85_I | 89_V | 1.111 | 0.96 |
| 65_K | 89_V | 1.106 | 0.96 |
| 171_R | 177_Q | 1.105 | 0.96 |
| 7_V | 49_V | 1.098 | 0.96 |
| 140_V | 163_E | 1.097 | 0.96 |
| 115_V | 118_R | 1.082 | 0.96 |
| 138_M | 159_F | 1.080 | 0.95 |
| 155_P | 204_K | 1.076 | 0.95 |
| 17_L | 78_V | 1.074 | 0.95 |
| 37_A | 41_F | 1.072 | 0.95 |
| 6_I | 28_A | 1.070 | 0.95 |
| 54_M | 80_A | 1.067 | 0.95 |
| 130_V | 137_R | 1.066 | 0.95 |
| 114_A | 119_G | 1.063 | 0.95 |
| 9_D | 52_D | 1.057 | 0.95 |
| 61_T | 89_V | 1.053 | 0.95 |
| 146_S | 151_T | 1.053 | 0.95 |
| 5_L | 37_A | 1.051 | 0.94 |
| 84_E | 88_V | 1.048 | 0.94 |
| 157_K | 183_W | 1.043 | 0.94 |
| 176_G | 180_D | 1.033 | 0.94 |
| 55_L | 63_V | 1.023 | 0.93 |
| 192_K | 196_V | 1.019 | 0.93 |
| 36_A | 40_E | 1.018 | 0.93 |
| 141_E | 171_R | 1.018 | 0.93 |
| 42_D | 70_R | 1.017 | 0.93 |
| 133_S | 225_L | 1.016 | 0.93 |
| 191_T | 195_D | 1.013 | 0.93 |
| 208_D | 211_N | 1.012 | 0.93 |
| 87_K | 100_T | 1.006 | 0.93 |
| 5_L | 46_A | 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
- 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 | |
| 1ys7A | 2 | 0.9867 | 100 | 0.136 | Contact Map |
| 2gwrA | 1 | 0.9735 | 100 | 0.136 | Contact Map |
| 2oqrA | 1 | 1 | 100 | 0.139 | Contact Map |
| 3r0jA | 2 | 0.9602 | 100 | 0.147 | Contact Map |
| 1kgsA | 1 | 0.9558 | 100 | 0.16 | Contact Map |
| 4b09A | 12 | 0.9204 | 100 | 0.161 | Contact Map |
| 2hqrA | 2 | 0.9425 | 100 | 0.181 | Contact Map |
| 1p2fA | 1 | 0.9469 | 100 | 0.199 | Contact Map |
| 3q9sA | 1 | 0.9292 | 100 | 0.202 | Contact Map |
| 3kloA | 4 | 0.9248 | 100 | 0.278 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)