| T0806 |
| ID: | 1435255063 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 258 (256) | ||
| Sequences: | 2251 (1551.3) | ||
| Seq/Len: | 8.793 | ||
| Nf(neff/√len): | 97.0 |
Jackhmmer Results: (2015_01_07)
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: 8.793).
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 |
| 30_N | 150_I | 4.021 | 1.00 |
| 52_I | 56_L | 3.133 | 1.00 |
| 92_Q | 95_T | 3.071 | 1.00 |
| 241_D | 244_S | 2.843 | 1.00 |
| 142_D | 145_Q | 2.773 | 1.00 |
| 100_D | 221_E | 2.597 | 1.00 |
| 81_L | 101_F | 2.540 | 1.00 |
| 60_N | 63_R | 2.526 | 1.00 |
| 149_D | 153_N | 2.453 | 1.00 |
| 97_S | 100_D | 2.447 | 1.00 |
| 104_A | 220_I | 2.349 | 1.00 |
| 3_I | 219_I | 2.323 | 1.00 |
| 4_L | 167_V | 2.279 | 1.00 |
| 217_R | 221_E | 2.275 | 1.00 |
| 10_T | 84_K | 2.241 | 1.00 |
| 47_S | 54_D | 2.203 | 1.00 |
| 168_I | 219_I | 2.191 | 1.00 |
| 17_L | 77_R | 2.173 | 1.00 |
| 226_K | 229_Q | 2.150 | 1.00 |
| 100_D | 223_R | 2.127 | 1.00 |
| 244_S | 253_K | 2.078 | 1.00 |
| 246_S | 249_E | 2.059 | 1.00 |
| 196_E | 255_Y | 2.028 | 1.00 |
| 241_D | 253_K | 2.024 | 1.00 |
| 96_F | 217_R | 1.991 | 1.00 |
| 187_E | 248_G | 1.946 | 1.00 |
| 96_F | 100_D | 1.917 | 1.00 |
| 192_V | 249_E | 1.879 | 1.00 |
| 137_N | 140_G | 1.874 | 1.00 |
| 151_I | 178_S | 1.842 | 1.00 |
| 103_F | 107_H | 1.840 | 1.00 |
| 13_Y | 82_A | 1.820 | 1.00 |
| 26_E | 154_K | 1.799 | 1.00 |
| 38_A | 64_F | 1.764 | 1.00 |
| 228_E | 231_T | 1.743 | 1.00 |
| 131_M | 178_S | 1.733 | 1.00 |
| 61_A | 65_H | 1.724 | 1.00 |
| 5_I | 216_S | 1.720 | 1.00 |
| 26_E | 158_A | 1.688 | 1.00 |
| 109_R | 158_A | 1.597 | 1.00 |
| 105_Q | 121_L | 1.587 | 1.00 |
| 141_K | 145_Q | 1.548 | 1.00 |
| 227_P | 250_L | 1.548 | 1.00 |
| 100_D | 220_I | 1.544 | 1.00 |
| 31_S | 67_W | 1.544 | 1.00 |
| 214_L | 236_E | 1.539 | 1.00 |
| 194_L | 253_K | 1.534 | 1.00 |
| 5_I | 108_L | 1.533 | 1.00 |
| 103_F | 220_I | 1.533 | 1.00 |
| 15_S | 77_R | 1.529 | 1.00 |
| 231_T | 250_L | 1.485 | 1.00 |
| 37_E | 135_L | 1.478 | 1.00 |
| 5_I | 87_V | 1.465 | 1.00 |
| 58_G | 62_A | 1.463 | 1.00 |
| 84_K | 94_E | 1.451 | 0.99 |
| 62_A | 66_D | 1.446 | 0.99 |
| 219_I | 224_L | 1.440 | 0.99 |
| 219_I | 230_L | 1.413 | 0.99 |
| 86_D | 206_F | 1.395 | 0.99 |
| 224_L | 229_Q | 1.387 | 0.99 |
| 96_F | 104_A | 1.370 | 0.99 |
| 8_A | 11_L | 1.367 | 0.99 |
| 191_P | 250_L | 1.348 | 0.99 |
| 59_I | 63_R | 1.331 | 0.99 |
| 208_A | 212_R | 1.310 | 0.99 |
| 104_A | 216_S | 1.305 | 0.99 |
| 154_K | 157_E | 1.304 | 0.99 |
| 207_Y | 254_R | 1.302 | 0.99 |
| 90_G | 210_K | 1.302 | 0.99 |
| 46_I | 52_I | 1.301 | 0.99 |
| 151_I | 179_V | 1.299 | 0.99 |
| 75_N | 125_Q | 1.283 | 0.98 |
| 72_T | 75_N | 1.269 | 0.98 |
| 96_F | 101_F | 1.252 | 0.98 |
| 196_E | 201_F | 1.245 | 0.98 |
| 118_L | 124_M | 1.244 | 0.98 |
| 148_G | 180_K | 1.241 | 0.98 |
| 2_L | 109_R | 1.240 | 0.98 |
| 4_L | 155_L | 1.239 | 0.98 |
| 240_F | 250_L | 1.237 | 0.98 |
| 91_L | 216_S | 1.231 | 0.98 |
| 27_L | 154_K | 1.217 | 0.98 |
| 117_V | 154_K | 1.215 | 0.98 |
| 113_G | 131_M | 1.213 | 0.98 |
| 33_Q | 146_F | 1.212 | 0.98 |
| 95_T | 217_R | 1.208 | 0.97 |
| 96_F | 221_E | 1.207 | 0.97 |
| 99_D | 223_R | 1.200 | 0.97 |
| 77_R | 82_A | 1.199 | 0.97 |
| 12_D | 84_K | 1.190 | 0.97 |
| 37_E | 41_L | 1.189 | 0.97 |
| 225_T | 229_Q | 1.177 | 0.97 |
| 168_I | 191_P | 1.175 | 0.97 |
| 2_L | 165_N | 1.168 | 0.97 |
| 30_N | 146_F | 1.167 | 0.97 |
| 76_A | 123_L | 1.160 | 0.97 |
| 32_Q | 36_H | 1.154 | 0.96 |
| 80_I | 91_L | 1.149 | 0.96 |
| 52_I | 57_A | 1.148 | 0.96 |
| 34_L | 137_N | 1.143 | 0.96 |
| 47_S | 57_A | 1.132 | 0.96 |
| 13_Y | 124_M | 1.125 | 0.96 |
| 229_Q | 232_G | 1.120 | 0.96 |
| 159_L | 186_A | 1.100 | 0.95 |
| 239_F | 255_Y | 1.097 | 0.95 |
| 221_E | 235_S | 1.094 | 0.95 |
| 166_V | 187_E | 1.091 | 0.95 |
| 168_I | 230_L | 1.083 | 0.94 |
| 18_T | 81_L | 1.083 | 0.94 |
| 33_Q | 37_E | 1.064 | 0.94 |
| 134_R | 142_D | 1.052 | 0.93 |
| 247_N | 250_L | 1.051 | 0.93 |
| 95_T | 221_E | 1.044 | 0.93 |
| 131_M | 174_E | 1.044 | 0.93 |
| 30_N | 139_R | 1.040 | 0.93 |
| 144_Y | 177_K | 1.039 | 0.93 |
| 43_P | 58_G | 1.033 | 0.92 |
| 47_S | 52_I | 1.030 | 0.92 |
| 53_S | 56_L | 1.028 | 0.92 |
| 195_D | 205_S | 1.026 | 0.92 |
| 37_E | 138_A | 1.026 | 0.92 |
| 80_I | 120_P | 1.026 | 0.92 |
| 43_P | 61_A | 1.020 | 0.92 |
| 12_D | 77_R | 1.018 | 0.92 |
| 216_S | 220_I | 1.010 | 0.91 |
| 101_F | 121_L | 1.004 | 0.91 |
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 | |
| 3c65A | 1 | 0.0349 | 23.5 | 0.962 | Contact Map |
| 4ou0A | 1 | 0.2287 | 21 | 0.963 | Contact Map |
| 4glxA | 1 | 0.3256 | 8.1 | 0.969 | Contact Map |
| 2yfvC | 1 | 0.2209 | 7.8 | 0.969 | Contact Map |
| 4pj0U | 2 | 0.3566 | 7.3 | 0.969 | Contact Map |
| 2vqeB | 1 | 0.4729 | 7 | 0.97 | Contact Map |
| 4e1pA | 2 | 0.1589 | 6.4 | 0.97 | Contact Map |
| 2k9lA | 1 | 0.2636 | 6.3 | 0.97 | Contact Map |
| 3sgiA | 1 | 0 | 6.1 | 0.97 | Contact Map |
| 3eyiA | 2 | 0.2403 | 6 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)