| ccka hhb -4 - 4 75- 75 -75 320-540 |
| ID: | 1433169217 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (212) | ||
| Sequences: | 53421 (43523.7) | ||
| Seq/Len: | 251.986 | ||
| Nf(neff/√len): | 2989.2 |
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: 251.986).
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 |
| 64_L | 100_A | 2.932 | 1.00 |
| 160_D | 164_G | 2.842 | 1.00 |
| 159_S | 216_A | 2.820 | 1.00 |
| 206_H | 218_R | 2.809 | 1.00 |
| 195_Y | 199_K | 2.618 | 1.00 |
| 157_E | 216_A | 2.417 | 1.00 |
| 100_A | 201_S | 2.380 | 1.00 |
| 157_E | 218_R | 2.269 | 1.00 |
| 153_T | 220_F | 2.236 | 1.00 |
| 166_P | 169_V | 2.197 | 1.00 |
| 16_L | 36_I | 2.155 | 1.00 |
| 155_F | 218_R | 2.106 | 1.00 |
| 170_M | 209_S | 2.084 | 1.00 |
| 63_V | 99_R | 2.058 | 1.00 |
| 132_R | 157_E | 2.045 | 1.00 |
| 13_Q | 41_V | 1.998 | 1.00 |
| 120_V | 161_D | 1.997 | 1.00 |
| 88_I | 130_R | 1.983 | 1.00 |
| 13_Q | 40_G | 1.981 | 1.00 |
| 210_R | 213_E | 1.962 | 1.00 |
| 120_V | 124_K | 1.899 | 1.00 |
| 198_V | 203_G | 1.887 | 1.00 |
| 155_F | 220_F | 1.873 | 1.00 |
| 207_V | 217_F | 1.872 | 1.00 |
| 170_M | 207_V | 1.848 | 1.00 |
| 108_A | 198_V | 1.842 | 1.00 |
| 90_D | 132_R | 1.813 | 1.00 |
| 172_K | 178_F | 1.799 | 1.00 |
| 194_V | 205_I | 1.793 | 1.00 |
| 130_R | 159_S | 1.785 | 1.00 |
| 88_I | 128_V | 1.767 | 1.00 |
| 128_V | 161_D | 1.766 | 1.00 |
| 167_P | 170_M | 1.766 | 1.00 |
| 72_E | 106_E | 1.761 | 1.00 |
| 208_H | 218_R | 1.752 | 1.00 |
| 174_F | 205_I | 1.747 | 1.00 |
| 165_I | 173_I | 1.740 | 1.00 |
| 208_H | 216_A | 1.731 | 1.00 |
| 132_R | 159_S | 1.728 | 1.00 |
| 44_A | 48_R | 1.673 | 1.00 |
| 169_V | 172_K | 1.658 | 1.00 |
| 65_D | 68_E | 1.657 | 1.00 |
| 63_V | 97_Q | 1.654 | 1.00 |
| 108_A | 194_V | 1.643 | 1.00 |
| 134_A | 155_F | 1.606 | 1.00 |
| 62_E | 102_K | 1.593 | 1.00 |
| 20_L | 37_R | 1.590 | 1.00 |
| 172_K | 175_D | 1.569 | 1.00 |
| 114_V | 118_D | 1.547 | 1.00 |
| 165_I | 169_V | 1.536 | 1.00 |
| 169_V | 178_F | 1.535 | 1.00 |
| 134_A | 157_E | 1.515 | 1.00 |
| 12_I | 40_G | 1.504 | 1.00 |
| 77_L | 110_M | 1.503 | 1.00 |
| 204_W | 220_F | 1.501 | 1.00 |
| 13_Q | 44_A | 1.493 | 1.00 |
| 86_K | 128_V | 1.482 | 1.00 |
| 209_S | 215_A | 1.460 | 1.00 |
| 108_A | 197_I | 1.447 | 1.00 |
| 4_D | 107_T | 1.447 | 1.00 |
| 100_A | 105_L | 1.439 | 1.00 |
| 198_V | 219_I | 1.408 | 1.00 |
| 90_D | 130_R | 1.384 | 0.99 |
| 127_G | 161_D | 1.335 | 0.99 |
| 165_I | 215_A | 1.332 | 0.99 |
| 17_D | 37_R | 1.313 | 0.99 |
| 206_H | 220_F | 1.311 | 0.99 |
| 37_R | 41_V | 1.302 | 0.99 |
| 101_D | 104_Q | 1.289 | 0.99 |
| 109_V | 156_I | 1.284 | 0.99 |
| 61_R | 99_R | 1.282 | 0.99 |
| 166_P | 211_P | 1.280 | 0.99 |
| 175_D | 178_F | 1.272 | 0.99 |
| 104_Q | 200_Q | 1.267 | 0.99 |
| 199_K | 204_W | 1.257 | 0.99 |
| 20_L | 34_N | 1.249 | 0.99 |
| 197_I | 201_S | 1.248 | 0.99 |
| 16_L | 37_R | 1.247 | 0.99 |
| 174_F | 207_V | 1.245 | 0.98 |
| 11_A | 15_R | 1.216 | 0.98 |
| 13_Q | 37_R | 1.203 | 0.98 |
| 26_G | 29_S | 1.187 | 0.98 |
| 6_N | 48_R | 1.185 | 0.98 |
| 104_Q | 107_T | 1.183 | 0.98 |
| 111_N | 194_V | 1.182 | 0.98 |
| 169_V | 180_T | 1.145 | 0.97 |
| 67_G | 71_S | 1.141 | 0.97 |
| 102_K | 106_E | 1.129 | 0.97 |
| 15_R | 32_G | 1.126 | 0.97 |
| 45_D | 103_S | 1.104 | 0.96 |
| 15_R | 35_E | 1.100 | 0.96 |
| 156_I | 219_I | 1.095 | 0.96 |
| 11_A | 39_T | 1.086 | 0.96 |
| 209_S | 213_E | 1.084 | 0.96 |
| 67_G | 133_T | 1.075 | 0.95 |
| 39_T | 42_R | 1.069 | 0.95 |
| 76_L | 106_E | 1.065 | 0.95 |
| 173_I | 207_V | 1.064 | 0.95 |
| 16_L | 40_G | 1.059 | 0.95 |
| 72_E | 102_K | 1.054 | 0.95 |
| 65_D | 97_Q | 1.048 | 0.94 |
| 150_D | 155_F | 1.048 | 0.94 |
| 153_T | 204_W | 1.039 | 0.94 |
| 120_V | 129_V | 1.027 | 0.94 |
| 73_F | 106_E | 1.023 | 0.93 |
| 130_R | 161_D | 1.022 | 0.93 |
| 120_V | 127_G | 1.022 | 0.93 |
| 196_G | 199_K | 1.012 | 0.93 |
| 71_S | 89_T | 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 | |
| 3a0rA | 1 | 0.8778 | 100 | -0.03 | Contact Map |
| 4i5sA | 2 | 0.8914 | 100 | 0.147 | Contact Map |
| 3jz3A | 2 | 0.6968 | 100 | 0.167 | Contact Map |
| 4gczA | 2 | 0.9276 | 100 | 0.167 | Contact Map |
| 4mpcA | 1 | 0.8643 | 100 | 0.174 | Contact Map |
| 4q20A | 2 | 0.905 | 100 | 0.176 | Contact Map |
| 3d36A | 2 | 0.9095 | 100 | 0.177 | Contact Map |
| 2e0aA | 2 | 0.9231 | 100 | 0.188 | Contact Map |
| 4e01A | 1 | 0.9005 | 100 | 0.189 | Contact Map |
| 1y8oA | 1 | 0.8914 | 100 | 0.21 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)