| T0852 1-260 |
| ID: | 1405102180 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 260 (234) | ||
| Sequences: | 4729 (3402.8) | ||
| Seq/Len: | 20.209 | ||
| Nf(neff/√len): | 222.4 |
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: 20.209).
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 |
| 149_M | 160_I | 4.482 | 1.00 |
| 162_S | 165_P | 2.888 | 1.00 |
| 124_Q | 129_I | 2.705 | 1.00 |
| 53_L | 85_V | 2.622 | 1.00 |
| 202_Y | 206_I | 2.546 | 1.00 |
| 209_E | 213_R | 2.536 | 1.00 |
| 39_I | 85_V | 2.523 | 1.00 |
| 83_I | 129_I | 2.482 | 1.00 |
| 124_Q | 133_K | 2.466 | 1.00 |
| 206_I | 227_D | 2.459 | 1.00 |
| 27_S | 34_K | 2.452 | 1.00 |
| 51_Y | 83_I | 2.438 | 1.00 |
| 211_A | 215_A | 2.380 | 1.00 |
| 54_I | 136_I | 2.257 | 1.00 |
| 113_E | 117_A | 2.181 | 1.00 |
| 54_I | 82_C | 2.165 | 1.00 |
| 45_Y | 51_Y | 2.128 | 1.00 |
| 25_T | 34_K | 2.114 | 1.00 |
| 41_K | 83_I | 2.112 | 1.00 |
| 145_A | 160_I | 2.088 | 1.00 |
| 45_Y | 128_P | 2.080 | 1.00 |
| 122_Y | 126_K | 2.065 | 1.00 |
| 209_E | 223_Y | 1.990 | 1.00 |
| 112_F | 152_E | 1.937 | 1.00 |
| 44_K | 81_K | 1.881 | 1.00 |
| 195_D | 229_K | 1.843 | 1.00 |
| 28_S | 118_E | 1.834 | 1.00 |
| 160_I | 189_Y | 1.786 | 1.00 |
| 55_V | 124_Q | 1.770 | 1.00 |
| 210_R | 214_S | 1.749 | 1.00 |
| 134_G | 159_M | 1.749 | 1.00 |
| 27_S | 32_N | 1.731 | 1.00 |
| 161_V | 244_A | 1.730 | 1.00 |
| 24_E | 37_I | 1.695 | 1.00 |
| 123_I | 129_I | 1.660 | 1.00 |
| 56_V | 136_I | 1.632 | 1.00 |
| 226_V | 243_Q | 1.627 | 1.00 |
| 112_F | 148_Y | 1.597 | 1.00 |
| 120_V | 157_F | 1.571 | 1.00 |
| 26_F | 114_F | 1.546 | 1.00 |
| 114_F | 119_L | 1.532 | 1.00 |
| 190_Y | 226_V | 1.520 | 1.00 |
| 146_N | 162_S | 1.514 | 1.00 |
| 167_A | 208_F | 1.512 | 1.00 |
| 135_V | 148_Y | 1.476 | 1.00 |
| 55_V | 120_V | 1.457 | 1.00 |
| 23_S | 36_K | 1.456 | 1.00 |
| 53_L | 129_I | 1.452 | 1.00 |
| 55_V | 85_V | 1.448 | 1.00 |
| 56_V | 86_G | 1.431 | 1.00 |
| 146_N | 189_Y | 1.430 | 1.00 |
| 130_A | 133_K | 1.417 | 1.00 |
| 191_M | 209_E | 1.408 | 1.00 |
| 39_I | 83_I | 1.373 | 0.99 |
| 163_L | 244_A | 1.356 | 0.99 |
| 165_P | 205_A | 1.350 | 0.99 |
| 195_D | 230_G | 1.333 | 0.99 |
| 85_V | 123_I | 1.319 | 0.99 |
| 162_S | 191_M | 1.309 | 0.99 |
| 57_L | 144_L | 1.309 | 0.99 |
| 55_V | 123_I | 1.308 | 0.99 |
| 146_N | 165_P | 1.295 | 0.99 |
| 135_V | 160_I | 1.291 | 0.99 |
| 136_I | 163_L | 1.275 | 0.99 |
| 25_T | 36_K | 1.264 | 0.99 |
| 147_Y | 151_A | 1.252 | 0.99 |
| 195_D | 227_D | 1.250 | 0.99 |
| 164_N | 197_E | 1.250 | 0.99 |
| 159_M | 188_F | 1.239 | 0.98 |
| 116_S | 152_E | 1.231 | 0.98 |
| 152_E | 155_P | 1.222 | 0.98 |
| 28_S | 31_L | 1.216 | 0.98 |
| 37_I | 119_L | 1.215 | 0.98 |
| 228_F | 240_G | 1.213 | 0.98 |
| 139_E | 233_V | 1.211 | 0.98 |
| 49_Q | 81_K | 1.206 | 0.98 |
| 213_R | 223_Y | 1.196 | 0.98 |
| 211_A | 214_S | 1.178 | 0.98 |
| 22_I | 41_K | 1.177 | 0.98 |
| 146_N | 167_A | 1.164 | 0.97 |
| 40_Y | 71_R | 1.148 | 0.97 |
| 112_F | 151_A | 1.147 | 0.97 |
| 57_L | 111_F | 1.143 | 0.97 |
| 53_L | 83_I | 1.141 | 0.97 |
| 55_V | 133_K | 1.137 | 0.97 |
| 116_S | 156_T | 1.112 | 0.96 |
| 46_T | 49_Q | 1.106 | 0.96 |
| 231_S | 237_K | 1.104 | 0.96 |
| 63_M | 86_G | 1.091 | 0.96 |
| 192_A | 240_G | 1.086 | 0.96 |
| 191_M | 208_F | 1.085 | 0.96 |
| 120_V | 133_K | 1.081 | 0.95 |
| 24_E | 122_Y | 1.081 | 0.95 |
| 209_E | 225_F | 1.078 | 0.95 |
| 241_I | 245_L | 1.071 | 0.95 |
| 202_Y | 227_D | 1.064 | 0.95 |
| 212_M | 223_Y | 1.063 | 0.95 |
| 177_H | 180_A | 1.057 | 0.95 |
| 242_A | 246_D | 1.054 | 0.95 |
| 203_D | 207_Q | 1.043 | 0.94 |
| 114_F | 118_E | 1.037 | 0.94 |
| 143_F | 147_Y | 1.033 | 0.94 |
| 138_S | 164_N | 1.028 | 0.94 |
| 117_A | 121_P | 1.027 | 0.94 |
| 26_F | 37_I | 1.025 | 0.93 |
| 207_Q | 210_R | 1.022 | 0.93 |
| 42_P | 83_I | 1.017 | 0.93 |
| 196_V | 230_G | 1.013 | 0.93 |
| 57_L | 87_V | 1.009 | 0.93 |
| 206_I | 225_F | 1.004 | 0.93 |
| 133_K | 158_N | 1.003 | 0.93 |
| 41_K | 51_Y | 1.001 | 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 | |
| 3gffA | 2 | 0.9038 | 100 | 0.453 | Contact Map |
| 3c8dA | 4 | 0.9154 | 100 | 0.531 | Contact Map |
| 2gzsA | 1 | 0.8808 | 100 | 0.531 | Contact Map |
| 4folA | 4 | 0.9 | 100 | 0.541 | Contact Map |
| 1jjfA | 1 | 0.8731 | 100 | 0.544 | Contact Map |
| 2qm0A | 2 | 0.9269 | 99.9 | 0.55 | Contact Map |
| 3ls2A | 4 | 0.9077 | 99.9 | 0.556 | Contact Map |
| 4h18A | 4 | 0.8615 | 99.9 | 0.573 | Contact Map |
| 4b6gA | 2 | 0.9192 | 99.9 | 0.578 | Contact Map |
| 3i6yA | 2 | 0.9231 | 99.9 | 0.583 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)