| d3i6va_ |
| ID: | 1447475988 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 218 (215) | ||
| Sequences: | 20545 (14415.1) | ||
| Seq/Len: | 95.558 | ||
| Nf(neff/√len): | 983.1 |
HHblits Results: (2015_06)
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: 95.558).
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 |
| 110_T | 141_A | 4.154 | 1.00 |
| 5_G | 60_Y | 3.766 | 1.00 |
| 1_T | 42_E | 3.227 | 1.00 |
| 36_R | 196_S | 2.636 | 1.00 |
| 126_F | 135_A | 2.567 | 1.00 |
| 69_I | 74_D | 2.462 | 1.00 |
| 54_N | 60_Y | 2.406 | 1.00 |
| 81_Q | 195_T | 2.256 | 1.00 |
| 3_R | 42_E | 2.183 | 1.00 |
| 132_T | 144_V | 2.132 | 1.00 |
| 56_V | 76_V | 2.124 | 1.00 |
| 17_N | 23_D | 2.060 | 1.00 |
| 32_E | 35_K | 2.059 | 1.00 |
| 1_T | 40_T | 2.040 | 1.00 |
| 3_R | 44_V | 2.035 | 1.00 |
| 32_E | 202_T | 2.031 | 1.00 |
| 128_T | 131_E | 2.030 | 1.00 |
| 80_T | 191_D | 2.025 | 1.00 |
| 34_C | 41_C | 2.023 | 1.00 |
| 146_A | 151_L | 2.015 | 1.00 |
| 77_I | 178_G | 2.012 | 1.00 |
| 69_I | 176_G | 2.012 | 1.00 |
| 54_N | 59_N | 1.987 | 1.00 |
| 28_E | 209_K | 1.985 | 1.00 |
| 179_L | 187_R | 1.928 | 1.00 |
| 187_R | 191_D | 1.916 | 1.00 |
| 78_D | 187_R | 1.913 | 1.00 |
| 71_D | 74_D | 1.909 | 1.00 |
| 81_Q | 191_D | 1.889 | 1.00 |
| 204_N | 208_K | 1.873 | 1.00 |
| 202_T | 205_T | 1.870 | 1.00 |
| 91_Y | 151_L | 1.824 | 1.00 |
| 179_L | 190_F | 1.793 | 1.00 |
| 28_E | 210_W | 1.786 | 1.00 |
| 4_M | 30_G | 1.752 | 1.00 |
| 93_A | 139_G | 1.736 | 1.00 |
| 135_A | 140_E | 1.725 | 1.00 |
| 195_T | 199_E | 1.697 | 1.00 |
| 118_E | 125_E | 1.653 | 1.00 |
| 4_M | 62_T | 1.621 | 1.00 |
| 51_I | 63_I | 1.619 | 1.00 |
| 32_E | 197_M | 1.600 | 1.00 |
| 62_T | 179_L | 1.575 | 1.00 |
| 33_L | 193_A | 1.569 | 1.00 |
| 15_F | 23_D | 1.568 | 1.00 |
| 108_T | 124_V | 1.564 | 1.00 |
| 36_R | 193_A | 1.559 | 1.00 |
| 46_N | 54_N | 1.532 | 1.00 |
| 184_G | 188_G | 1.527 | 1.00 |
| 53_P | 57_S | 1.512 | 1.00 |
| 193_A | 197_M | 1.511 | 1.00 |
| 85_P | 174_G | 1.493 | 1.00 |
| 89_S | 148_R | 1.480 | 1.00 |
| 90_S | 143_A | 1.470 | 1.00 |
| 188_G | 192_A | 1.464 | 1.00 |
| 113_A | 127_A | 1.462 | 1.00 |
| 180_R | 183_D | 1.454 | 1.00 |
| 26_E | 83_Y | 1.452 | 1.00 |
| 87_T | 148_R | 1.452 | 1.00 |
| 93_A | 96_D | 1.414 | 1.00 |
| 78_D | 184_G | 1.400 | 0.99 |
| 27_R | 31_D | 1.398 | 0.99 |
| 109_A | 143_A | 1.389 | 0.99 |
| 126_F | 132_T | 1.367 | 0.99 |
| 32_E | 36_R | 1.366 | 0.99 |
| 134_A | 138_N | 1.364 | 0.99 |
| 135_A | 141_A | 1.361 | 0.99 |
| 92_V | 143_A | 1.359 | 0.99 |
| 148_R | 152_V | 1.359 | 0.99 |
| 64_I | 177_M | 1.352 | 0.99 |
| 37_A | 193_A | 1.348 | 0.99 |
| 110_T | 132_T | 1.328 | 0.99 |
| 189_K | 193_A | 1.328 | 0.99 |
| 189_K | 192_A | 1.324 | 0.99 |
| 17_N | 21_E | 1.318 | 0.99 |
| 193_A | 196_S | 1.314 | 0.99 |
| 36_R | 200_D | 1.312 | 0.99 |
| 67_M | 178_G | 1.311 | 0.99 |
| 108_T | 142_D | 1.308 | 0.99 |
| 52_I | 77_I | 1.295 | 0.99 |
| 107_Q | 142_D | 1.295 | 0.99 |
| 16_I | 45_K | 1.285 | 0.99 |
| 198_K | 203_L | 1.275 | 0.99 |
| 78_D | 182_S | 1.270 | 0.99 |
| 31_D | 43_W | 1.266 | 0.99 |
| 53_P | 56_V | 1.266 | 0.99 |
| 136_V | 144_V | 1.243 | 0.98 |
| 47_D | 50_S | 1.215 | 0.98 |
| 79_F | 178_G | 1.211 | 0.98 |
| 108_T | 122_T | 1.204 | 0.98 |
| 29_L | 203_L | 1.191 | 0.98 |
| 134_A | 137_R | 1.178 | 0.98 |
| 88_A | 117_A | 1.157 | 0.97 |
| 25_F | 206_M | 1.141 | 0.97 |
| 124_V | 135_A | 1.137 | 0.97 |
| 113_A | 125_E | 1.128 | 0.97 |
| 137_R | 161_E | 1.121 | 0.97 |
| 25_F | 207_I | 1.119 | 0.96 |
| 127_A | 131_E | 1.115 | 0.96 |
| 196_S | 200_D | 1.114 | 0.96 |
| 110_T | 126_F | 1.108 | 0.96 |
| 70_T | 73_R | 1.099 | 0.96 |
| 58_G | 180_R | 1.090 | 0.96 |
| 23_D | 28_E | 1.084 | 0.96 |
| 31_D | 35_K | 1.074 | 0.95 |
| 136_V | 162_L | 1.066 | 0.95 |
| 95_S | 163_M | 1.066 | 0.95 |
| 30_G | 64_I | 1.064 | 0.95 |
| 63_I | 67_M | 1.059 | 0.95 |
| 80_T | 190_F | 1.031 | 0.94 |
| 50_S | 54_N | 1.023 | 0.93 |
| 191_D | 195_T | 1.021 | 0.93 |
| 192_A | 196_S | 1.015 | 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 | |
| 3i6vA | 1 | 0.9725 | 100 | 0.097 | Contact Map |
| 4ohnA | 1 | 0.9954 | 100 | 0.105 | Contact Map |
| 4powA | 2 | 0.9908 | 100 | 0.11 | Contact Map |
| 3hv1A | 2 | 0.9954 | 100 | 0.112 | Contact Map |
| 3k4uA | 6 | 0.9954 | 100 | 0.115 | Contact Map |
| 4kqpA | 1 | 0.9771 | 100 | 0.124 | Contact Map |
| 4g4pA | 1 | 0.9633 | 100 | 0.124 | Contact Map |
| 2vhaA | 2 | 0.9954 | 100 | 0.125 | Contact Map |
| 2ieeA | 2 | 0.9954 | 100 | 0.127 | Contact Map |
| 1pb7A | 1 | 0.9358 | 100 | 0.129 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)