| T0849 |
| ID: | 1404964482 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 240 (199) | ||
| Sequences: | 10143 (7029.7) | ||
| Seq/Len: | 50.970 | ||
| Nf(neff/√len): | 498.3 |
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: 50.970).
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 |
| 25_D | 199_R | 4.181 | 1.00 |
| 73_S | 94_E | 3.632 | 1.00 |
| 191_A | 195_R | 3.393 | 1.00 |
| 6_I | 33_L | 3.223 | 1.00 |
| 77_R | 90_I | 2.960 | 1.00 |
| 23_L | 30_F | 2.861 | 1.00 |
| 9_Y | 16_A | 2.833 | 1.00 |
| 6_I | 31_R | 2.828 | 1.00 |
| 24_A | 30_F | 2.751 | 1.00 |
| 24_A | 204_Q | 2.577 | 1.00 |
| 135_V | 188_H | 2.513 | 1.00 |
| 139_T | 188_H | 2.310 | 1.00 |
| 63_V | 88_G | 2.223 | 1.00 |
| 140_R | 148_A | 2.208 | 1.00 |
| 149_G | 195_R | 2.201 | 1.00 |
| 132_G | 186_L | 2.193 | 1.00 |
| 44_K | 53_G | 2.135 | 1.00 |
| 25_D | 201_A | 2.104 | 1.00 |
| 86_D | 89_E | 2.041 | 1.00 |
| 21_H | 202_L | 1.933 | 1.00 |
| 26_A | 76_A | 1.906 | 1.00 |
| 149_G | 154_E | 1.876 | 1.00 |
| 190_C | 194_R | 1.775 | 1.00 |
| 8_R | 59_R | 1.746 | 1.00 |
| 59_R | 64_E | 1.744 | 1.00 |
| 96_V | 137_R | 1.740 | 1.00 |
| 6_I | 59_R | 1.685 | 1.00 |
| 22_A | 72_A | 1.676 | 1.00 |
| 43_H | 57_T | 1.643 | 1.00 |
| 46_S | 57_T | 1.616 | 1.00 |
| 77_R | 94_E | 1.608 | 1.00 |
| 5_I | 58_L | 1.608 | 1.00 |
| 9_Y | 32_D | 1.600 | 1.00 |
| 164_A | 196_M | 1.594 | 1.00 |
| 59_R | 62_G | 1.592 | 1.00 |
| 8_R | 35_I | 1.583 | 1.00 |
| 22_A | 82_Y | 1.564 | 1.00 |
| 152_G | 157_V | 1.548 | 1.00 |
| 60_W | 74_F | 1.543 | 1.00 |
| 135_V | 187_P | 1.537 | 1.00 |
| 156_P | 161_Y | 1.520 | 1.00 |
| 128_P | 185_R | 1.518 | 1.00 |
| 194_R | 198_Q | 1.502 | 1.00 |
| 198_Q | 203_A | 1.465 | 1.00 |
| 203_A | 207_S | 1.460 | 1.00 |
| 41_S | 45_D | 1.454 | 1.00 |
| 19_L | 72_A | 1.422 | 1.00 |
| 43_H | 46_S | 1.420 | 1.00 |
| 132_G | 136_A | 1.405 | 0.99 |
| 156_P | 199_R | 1.400 | 0.99 |
| 188_H | 191_A | 1.399 | 0.99 |
| 150_W | 196_M | 1.392 | 0.99 |
| 84_G | 93_L | 1.387 | 0.99 |
| 28_L | 79_L | 1.381 | 0.99 |
| 92_R | 95_A | 1.377 | 0.99 |
| 46_S | 59_R | 1.369 | 0.99 |
| 60_W | 63_V | 1.367 | 0.99 |
| 5_I | 28_L | 1.354 | 0.99 |
| 25_D | 156_P | 1.337 | 0.99 |
| 42_Q | 45_D | 1.317 | 0.99 |
| 122_D | 125_A | 1.305 | 0.99 |
| 135_V | 139_T | 1.286 | 0.99 |
| 167_I | 192_L | 1.274 | 0.99 |
| 137_R | 148_A | 1.264 | 0.99 |
| 151_F | 163_A | 1.263 | 0.99 |
| 7_L | 23_L | 1.263 | 0.99 |
| 83_E | 94_E | 1.242 | 0.98 |
| 22_A | 26_A | 1.226 | 0.98 |
| 65_V | 91_A | 1.202 | 0.98 |
| 83_E | 93_L | 1.192 | 0.98 |
| 25_D | 161_Y | 1.179 | 0.98 |
| 184_T | 190_C | 1.156 | 0.97 |
| 153_G | 160_D | 1.143 | 0.97 |
| 18_A | 68_T | 1.140 | 0.97 |
| 98_S | 102_T | 1.134 | 0.97 |
| 164_A | 197_A | 1.131 | 0.97 |
| 75_L | 79_L | 1.125 | 0.97 |
| 18_A | 162_F | 1.118 | 0.96 |
| 82_Y | 161_Y | 1.116 | 0.96 |
| 73_S | 98_S | 1.094 | 0.96 |
| 66_A | 95_A | 1.087 | 0.96 |
| 182_L | 185_R | 1.086 | 0.96 |
| 9_Y | 20_R | 1.082 | 0.96 |
| 132_G | 185_R | 1.075 | 0.95 |
| 7_L | 58_L | 1.074 | 0.95 |
| 72_A | 158_M | 1.072 | 0.95 |
| 151_F | 159_A | 1.068 | 0.95 |
| 125_A | 129_L | 1.064 | 0.95 |
| 54_S | 67_E | 1.056 | 0.95 |
| 20_R | 24_A | 1.055 | 0.95 |
| 93_L | 159_A | 1.052 | 0.95 |
| 201_A | 204_Q | 1.048 | 0.94 |
| 87_N | 91_A | 1.046 | 0.94 |
| 136_A | 140_R | 1.040 | 0.94 |
| 16_A | 55_L | 1.039 | 0.94 |
| 124_A | 128_P | 1.039 | 0.94 |
| 92_R | 137_R | 1.037 | 0.94 |
| 194_R | 197_A | 1.036 | 0.94 |
| 60_W | 79_L | 1.034 | 0.94 |
| 88_G | 92_R | 1.027 | 0.94 |
| 60_W | 78_S | 1.027 | 0.94 |
| 150_W | 195_R | 1.023 | 0.93 |
| 156_P | 196_M | 1.005 | 0.93 |
| 97_V | 158_M | 1.005 | 0.93 |
| 200_P | 204_Q | 1.001 | 0.92 |
| 5_I | 79_L | 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
- 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 | |
| 1tw9A | 8 | 0.825 | 100 | 0.322 | Contact Map |
| 2on7A | 4 | 0.825 | 100 | 0.322 | Contact Map |
| 2on5A | 8 | 0.825 | 100 | 0.323 | Contact Map |
| 1m0uA | 2 | 0.825 | 100 | 0.328 | Contact Map |
| 3vurA | 1 | 0.8208 | 100 | 0.33 | Contact Map |
| 2ws2A | 2 | 0.8167 | 100 | 0.332 | Contact Map |
| 1yq1A | 2 | 0.7958 | 100 | 0.338 | Contact Map |
| 1zl9A | 2 | 0.8292 | 100 | 0.338 | Contact Map |
| 2a2rA | 2 | 0.8667 | 100 | 0.341 | Contact Map |
| 2gsqA | 1 | 0.825 | 100 | 0.342 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)