| adk |
| ID: | 1494970788 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 217 (214) | ||
| Sequences: | 4140 (2483.5) | ||
| Seq/Len: | 19.346 | ||
| Nf(neff/√len): | 169.8 |
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: 19.346).
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 |
| 117_K | 176_M | 3.649 | 1.00 |
| 50_K | 54_D | 2.978 | 1.00 |
| 71_R | 76_D | 2.820 | 1.00 |
| 122_E | 140_V | 2.817 | 1.00 |
| 52_Y | 60_P | 2.731 | 1.00 |
| 97_E | 189_K | 2.713 | 1.00 |
| 35_F | 64_T | 2.668 | 1.00 |
| 199_Q | 207_D | 2.646 | 1.00 |
| 23_D | 209_K | 2.574 | 1.00 |
| 69_K | 102_E | 2.476 | 1.00 |
| 48_E | 51_S | 2.469 | 1.00 |
| 161_A | 164_N | 2.435 | 1.00 |
| 128_R | 139_L | 2.427 | 1.00 |
| 199_Q | 203_D | 2.362 | 1.00 |
| 38_A | 70_E | 2.326 | 1.00 |
| 173_E | 177_K | 2.309 | 1.00 |
| 114_E | 194_N | 2.300 | 1.00 |
| 112_N | 194_N | 2.298 | 1.00 |
| 19_R | 205_Y | 2.279 | 1.00 |
| 37_A | 41_E | 2.272 | 1.00 |
| 65_I | 86_F | 2.226 | 1.00 |
| 126_G | 138_H | 2.193 | 1.00 |
| 130_C | 133_C | 2.172 | 1.00 |
| 187_S | 194_N | 2.165 | 1.00 |
| 113_I | 197_G | 2.148 | 1.00 |
| 131_S | 158_Y | 2.067 | 1.00 |
| 131_S | 155_G | 1.988 | 1.00 |
| 44_P | 48_E | 1.876 | 1.00 |
| 42_E | 47_L | 1.807 | 1.00 |
| 65_I | 95_A | 1.772 | 1.00 |
| 24_Y | 209_K | 1.767 | 1.00 |
| 165_E | 169_S | 1.675 | 1.00 |
| 109_Y | 193_A | 1.674 | 1.00 |
| 170_K | 173_E | 1.674 | 1.00 |
| 150_C | 153_D | 1.652 | 1.00 |
| 149_I | 156_E | 1.647 | 1.00 |
| 44_P | 47_L | 1.634 | 1.00 |
| 193_A | 211_L | 1.623 | 1.00 |
| 97_E | 185_F | 1.622 | 1.00 |
| 23_D | 205_Y | 1.618 | 1.00 |
| 48_E | 66_G | 1.599 | 1.00 |
| 124_L | 168_V | 1.589 | 1.00 |
| 39_M | 53_I | 1.546 | 1.00 |
| 75_D | 78_E | 1.546 | 1.00 |
| 180_Q | 184_D | 1.507 | 1.00 |
| 71_R | 74_K | 1.501 | 1.00 |
| 130_C | 153_D | 1.469 | 1.00 |
| 116_D | 198_Q | 1.445 | 1.00 |
| 119_V | 198_Q | 1.440 | 1.00 |
| 51_S | 55_K | 1.433 | 1.00 |
| 174_V | 178_Q | 1.410 | 1.00 |
| 119_V | 122_E | 1.409 | 1.00 |
| 16_Q | 208_V | 1.405 | 0.99 |
| 131_S | 156_E | 1.403 | 0.99 |
| 133_C | 153_D | 1.399 | 0.99 |
| 132_V | 153_D | 1.397 | 0.99 |
| 200_D | 203_D | 1.391 | 0.99 |
| 146_T | 149_I | 1.386 | 0.99 |
| 11_A | 115_V | 1.372 | 0.99 |
| 126_G | 139_L | 1.361 | 0.99 |
| 19_R | 202_Q | 1.349 | 0.99 |
| 206_A | 210_D | 1.331 | 0.99 |
| 130_C | 150_C | 1.309 | 0.99 |
| 115_V | 197_G | 1.307 | 0.99 |
| 205_Y | 209_K | 1.303 | 0.99 |
| 164_N | 167_T | 1.281 | 0.99 |
| 91_A | 94_E | 1.264 | 0.99 |
| 38_A | 43_T | 1.249 | 0.99 |
| 10_G | 124_L | 1.239 | 0.98 |
| 121_M | 169_S | 1.225 | 0.98 |
| 38_A | 41_E | 1.221 | 0.98 |
| 203_D | 207_D | 1.217 | 0.98 |
| 27_P | 71_R | 1.208 | 0.98 |
| 125_T | 165_E | 1.199 | 0.98 |
| 133_C | 150_C | 1.181 | 0.98 |
| 184_D | 188_E | 1.179 | 0.98 |
| 129_I | 136_T | 1.176 | 0.98 |
| 176_M | 180_Q | 1.171 | 0.98 |
| 60_P | 63_V | 1.170 | 0.97 |
| 24_Y | 213_G | 1.168 | 0.97 |
| 117_K | 173_E | 1.164 | 0.97 |
| 128_R | 159_Q | 1.160 | 0.97 |
| 38_A | 67_I | 1.155 | 0.97 |
| 43_T | 46_G | 1.146 | 0.97 |
| 135_T | 152_K | 1.141 | 0.97 |
| 117_K | 169_S | 1.138 | 0.97 |
| 199_Q | 204_V | 1.133 | 0.97 |
| 63_V | 66_G | 1.130 | 0.97 |
| 111_I | 208_V | 1.127 | 0.97 |
| 121_M | 125_T | 1.125 | 0.97 |
| 2_N | 105_K | 1.124 | 0.97 |
| 170_K | 174_V | 1.120 | 0.96 |
| 196_N | 199_Q | 1.110 | 0.96 |
| 32_G | 36_R | 1.107 | 0.96 |
| 4_V | 107_I | 1.091 | 0.96 |
| 209_K | 213_G | 1.082 | 0.96 |
| 138_H | 141_F | 1.072 | 0.95 |
| 18_E | 22_E | 1.065 | 0.95 |
| 112_N | 183_L | 1.059 | 0.95 |
| 52_Y | 57_E | 1.056 | 0.95 |
| 69_K | 103_Y | 1.047 | 0.94 |
| 25_G | 79_R | 1.047 | 0.94 |
| 48_E | 62_E | 1.044 | 0.94 |
| 34_M | 38_A | 1.043 | 0.94 |
| 37_A | 71_R | 1.042 | 0.94 |
| 5_L | 20_I | 1.036 | 0.94 |
| 195_V | 204_V | 1.033 | 0.94 |
| 69_K | 73_G | 1.023 | 0.93 |
| 98_E | 102_E | 1.021 | 0.93 |
| 6_M | 183_L | 1.021 | 0.93 |
| 169_S | 173_E | 1.010 | 0.93 |
| 8_L | 175_N | 1.000 | 0.92 |
| 94_E | 97_E | 1.000 | 0.92 |
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 | |
| 4qbgB | 1 | 1 | 100 | 0.309 | Contact Map |
| 4jzkA | 2 | 0.9631 | 100 | 0.34 | Contact Map |
| 3be4A | 1 | 0.9677 | 100 | 0.345 | Contact Map |
| 3tlxA | 4 | 0.9862 | 100 | 0.347 | Contact Map |
| 3gmtA | 2 | 0.8894 | 100 | 0.347 | Contact Map |
| 2xb4A | 1 | 0.977 | 100 | 0.351 | Contact Map |
| 4pzlA | 4 | 0.9724 | 100 | 0.352 | Contact Map |
| 1ak2A | 1 | 1 | 100 | 0.355 | Contact Map |
| 1akyA | 1 | 0.9908 | 100 | 0.365 | Contact Map |
| 4nu0A | 2 | 0.9724 | 100 | 0.376 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)