| T0776 |
| ID: | 1400003697 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 256 (214) | ||
| Sequences: | 1099 (912.4) | ||
| Seq/Len: | 5.136 | ||
| Nf(neff/√len): | 62.4 |
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: 5.136).
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 |
| 174_E | 211_F | 4.111 | 1.00 |
| 155_R | 206_E | 3.705 | 1.00 |
| 151_E | 202_K | 3.170 | 1.00 |
| 174_E | 213_P | 2.463 | 1.00 |
| 126_L | 161_T | 2.185 | 1.00 |
| 77_G | 99_N | 2.149 | 1.00 |
| 57_T | 101_G | 2.144 | 1.00 |
| 82_T | 249_W | 2.106 | 1.00 |
| 105_N | 113_R | 2.093 | 1.00 |
| 48_V | 96_K | 2.070 | 1.00 |
| 49_I | 127_S | 1.965 | 1.00 |
| 107_V | 153_D | 1.961 | 1.00 |
| 169_Q | 210_I | 1.894 | 1.00 |
| 173_C | 249_W | 1.875 | 1.00 |
| 82_T | 250_M | 1.867 | 1.00 |
| 56_I | 132_V | 1.856 | 1.00 |
| 160_Y | 164_K | 1.835 | 1.00 |
| 126_L | 168_T | 1.816 | 1.00 |
| 51_F | 57_T | 1.767 | 1.00 |
| 110_L | 130_I | 1.758 | 1.00 |
| 172_L | 204_S | 1.696 | 1.00 |
| 213_P | 216_S | 1.693 | 1.00 |
| 237_P | 245_M | 1.687 | 1.00 |
| 47_C | 124_D | 1.668 | 0.99 |
| 212_V | 252_A | 1.658 | 0.99 |
| 201_R | 211_F | 1.634 | 0.99 |
| 151_E | 199_S | 1.607 | 0.99 |
| 55_S | 236_H | 1.601 | 0.99 |
| 155_R | 207_F | 1.587 | 0.99 |
| 158_L | 209_T | 1.520 | 0.99 |
| 111_R | 157_L | 1.509 | 0.99 |
| 158_L | 172_L | 1.507 | 0.99 |
| 243_Q | 247_N | 1.472 | 0.98 |
| 49_I | 97_I | 1.423 | 0.98 |
| 54_D | 57_T | 1.366 | 0.97 |
| 214_F | 245_M | 1.362 | 0.97 |
| 107_V | 154_L | 1.353 | 0.97 |
| 115_E | 160_Y | 1.343 | 0.97 |
| 150_Y | 196_F | 1.338 | 0.96 |
| 150_Y | 200_A | 1.334 | 0.96 |
| 85_Q | 250_M | 1.319 | 0.96 |
| 81_F | 243_Q | 1.298 | 0.96 |
| 129_L | 132_V | 1.293 | 0.96 |
| 81_F | 239_L | 1.283 | 0.95 |
| 101_G | 218_F | 1.279 | 0.95 |
| 49_I | 125_V | 1.279 | 0.95 |
| 197_R | 200_A | 1.272 | 0.95 |
| 237_P | 242_R | 1.271 | 0.95 |
| 165_L | 168_T | 1.270 | 0.95 |
| 107_V | 157_L | 1.244 | 0.94 |
| 132_V | 238_D | 1.238 | 0.94 |
| 61_R | 132_V | 1.219 | 0.93 |
| 155_R | 159_K | 1.214 | 0.93 |
| 56_I | 136_W | 1.188 | 0.92 |
| 111_R | 153_D | 1.184 | 0.92 |
| 125_V | 171_V | 1.181 | 0.92 |
| 150_Y | 154_L | 1.181 | 0.92 |
| 78_Y | 129_L | 1.178 | 0.92 |
| 172_L | 209_T | 1.170 | 0.91 |
| 52_Q | 100_R | 1.155 | 0.91 |
| 154_L | 200_A | 1.148 | 0.90 |
| 172_L | 200_A | 1.148 | 0.90 |
| 193_F | 197_R | 1.148 | 0.90 |
| 125_V | 169_Q | 1.145 | 0.90 |
| 56_I | 175_P | 1.143 | 0.90 |
| 169_Q | 253_T | 1.137 | 0.90 |
| 199_S | 202_K | 1.135 | 0.90 |
| 172_L | 246_A | 1.126 | 0.89 |
| 106_K | 137_H | 1.125 | 0.89 |
| 202_K | 206_E | 1.122 | 0.89 |
| 52_Q | 110_L | 1.118 | 0.89 |
| 59_C | 132_V | 1.115 | 0.88 |
| 171_V | 210_I | 1.110 | 0.88 |
| 64_N | 70_T | 1.108 | 0.88 |
| 104_G | 134_D | 1.106 | 0.88 |
| 248_M | 251_E | 1.104 | 0.88 |
| 172_L | 203_L | 1.103 | 0.88 |
| 198_K | 202_K | 1.102 | 0.88 |
| 107_V | 150_Y | 1.102 | 0.88 |
| 151_E | 155_R | 1.091 | 0.87 |
| 200_A | 211_F | 1.083 | 0.86 |
| 54_D | 134_D | 1.079 | 0.86 |
| 204_S | 209_T | 1.075 | 0.86 |
| 85_Q | 247_N | 1.073 | 0.86 |
| 161_T | 168_T | 1.072 | 0.86 |
| 52_Q | 114_W | 1.069 | 0.85 |
| 51_F | 79_V | 1.068 | 0.85 |
| 134_D | 233_D | 1.062 | 0.85 |
| 78_Y | 117_D | 1.053 | 0.84 |
| 123_P | 165_L | 1.051 | 0.84 |
| 51_F | 127_S | 1.049 | 0.84 |
| 161_T | 170_I | 1.046 | 0.84 |
| 54_D | 197_R | 1.043 | 0.83 |
| 58_D | 101_G | 1.042 | 0.83 |
| 109_Q | 235_V | 1.039 | 0.83 |
| 78_Y | 101_G | 1.030 | 0.82 |
| 150_Y | 199_S | 1.023 | 0.82 |
| 100_R | 118_C | 1.022 | 0.82 |
| 58_D | 103_S | 1.015 | 0.81 |
| 155_R | 203_L | 1.013 | 0.81 |
| 47_C | 166_P | 1.013 | 0.81 |
| 52_Q | 161_T | 1.009 | 0.81 |
| 212_V | 249_W | 1.006 | 0.80 |
| 135_Y | 196_F | 1.002 | 0.80 |
| 51_F | 78_Y | 1.000 | 0.80 |
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 | |
| 4jhlA | 2 | 0.8203 | 100 | 0.436 | Contact Map |
| 3rjtA | 2 | 0.8164 | 100 | 0.445 | Contact Map |
| 4hyqA | 1 | 0.7891 | 100 | 0.476 | Contact Map |
| 1escA | 1 | 0.8125 | 100 | 0.481 | Contact Map |
| 4jggA | 2 | 0.6992 | 100 | 0.481 | Contact Map |
| 1vjgA | 1 | 0.7578 | 100 | 0.486 | Contact Map |
| 2q0qA | 8 | 0.7539 | 100 | 0.497 | Contact Map |
| 3dciA | 3 | 0.7383 | 100 | 0.497 | Contact Map |
| 3bzwA | 6 | 0.7891 | 100 | 0.501 | Contact Map |
| 3dc7A | 3 | 0.7578 | 100 | 0.507 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)