| SDH |
| ID: | 1502999525 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 278 (254) | ||
| Sequences: | 48767 (29307.4) | ||
| Seq/Len: | 191.996 | ||
| Nf(neff/√len): | 1838.9 |
HHblits Results: (2016_02)
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: 191.996).
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 |
| 119_K | 127_Y | 3.106 | 1.00 |
| 119_K | 123_D | 3.032 | 1.00 |
| 150_F | 178_T | 2.788 | 1.00 |
| 75_K | 78_D | 2.776 | 1.00 |
| 172_H | 176_G | 2.655 | 1.00 |
| 19_A | 95_I | 2.547 | 1.00 |
| 30_E | 34_K | 2.398 | 1.00 |
| 35_L | 238_D | 2.365 | 1.00 |
| 123_D | 127_Y | 2.282 | 1.00 |
| 87_I | 139_V | 2.233 | 1.00 |
| 80_R | 135_H | 2.213 | 1.00 |
| 147_S | 191_R | 2.176 | 1.00 |
| 98_G | 150_F | 2.125 | 1.00 |
| 201_A | 232_R | 2.070 | 1.00 |
| 133_A | 181_L | 2.025 | 1.00 |
| 18_V | 42_K | 2.018 | 1.00 |
| 178_T | 194_C | 1.983 | 1.00 |
| 50_D | 54_Q | 1.978 | 1.00 |
| 25_A | 47_D | 1.956 | 1.00 |
| 35_L | 39_Y | 1.953 | 1.00 |
| 83_V | 136_A | 1.939 | 1.00 |
| 196_S | 255_N | 1.922 | 1.00 |
| 30_E | 56_V | 1.893 | 1.00 |
| 42_K | 65_V | 1.890 | 1.00 |
| 152_A | 175_L | 1.876 | 1.00 |
| 76_D | 115_N | 1.846 | 1.00 |
| 137_A | 185_L | 1.841 | 1.00 |
| 95_I | 244_A | 1.816 | 1.00 |
| 125_N | 170_T | 1.793 | 1.00 |
| 35_L | 241_A | 1.791 | 1.00 |
| 46_A | 71_C | 1.770 | 1.00 |
| 30_E | 59_N | 1.757 | 1.00 |
| 34_K | 59_N | 1.751 | 1.00 |
| 24_G | 45_I | 1.750 | 1.00 |
| 71_C | 78_D | 1.748 | 1.00 |
| 141_I | 188_Y | 1.737 | 1.00 |
| 46_A | 82_L | 1.715 | 1.00 |
| 35_L | 38_R | 1.709 | 1.00 |
| 28_I | 200_V | 1.684 | 1.00 |
| 129_A | 174_V | 1.668 | 1.00 |
| 44_V | 86_T | 1.648 | 1.00 |
| 126_V | 173_A | 1.621 | 1.00 |
| 50_D | 70_H | 1.601 | 1.00 |
| 44_V | 90_H | 1.594 | 1.00 |
| 32_T | 240_V | 1.582 | 1.00 |
| 69_V | 85_T | 1.578 | 1.00 |
| 57_C | 61_G | 1.576 | 1.00 |
| 67_S | 89_K | 1.561 | 1.00 |
| 81_N | 85_T | 1.555 | 1.00 |
| 254_L | 257_V | 1.553 | 1.00 |
| 84_D | 88_A | 1.553 | 1.00 |
| 85_T | 89_K | 1.527 | 1.00 |
| 147_S | 193_N | 1.513 | 1.00 |
| 122_M | 126_V | 1.512 | 1.00 |
| 49_A | 52_H | 1.499 | 1.00 |
| 80_R | 84_D | 1.491 | 1.00 |
| 14_L | 41_A | 1.489 | 1.00 |
| 39_Y | 241_A | 1.486 | 1.00 |
| 57_C | 68_F | 1.476 | 1.00 |
| 18_V | 44_V | 1.467 | 1.00 |
| 96_M | 132_V | 1.464 | 1.00 |
| 114_G | 117_D | 1.454 | 1.00 |
| 19_A | 41_A | 1.449 | 1.00 |
| 53_G | 68_F | 1.444 | 1.00 |
| 78_D | 81_N | 1.431 | 1.00 |
| 16_D | 41_A | 1.424 | 1.00 |
| 133_A | 148_I | 1.421 | 1.00 |
| 31_T | 234_E | 1.412 | 1.00 |
| 97_F | 151_T | 1.410 | 1.00 |
| 239_A | 256_L | 1.393 | 0.99 |
| 76_D | 131_L | 1.389 | 0.99 |
| 19_A | 36_F | 1.383 | 0.99 |
| 115_N | 131_L | 1.378 | 0.99 |
| 18_V | 92_K | 1.377 | 0.99 |
| 31_T | 34_K | 1.373 | 0.99 |
| 195_V | 240_V | 1.369 | 0.99 |
| 41_A | 95_I | 1.364 | 0.99 |
| 36_F | 244_A | 1.350 | 0.99 |
| 26_G | 203_P | 1.347 | 0.99 |
| 98_G | 133_A | 1.346 | 0.99 |
| 36_F | 41_A | 1.307 | 0.99 |
| 76_D | 80_R | 1.303 | 0.99 |
| 85_T | 88_A | 1.296 | 0.99 |
| 32_T | 237_A | 1.280 | 0.99 |
| 79_V | 132_V | 1.259 | 0.99 |
| 47_D | 53_G | 1.257 | 0.99 |
| 20_I | 82_L | 1.235 | 0.98 |
| 127_Y | 131_L | 1.235 | 0.98 |
| 71_C | 82_L | 1.232 | 0.98 |
| 33_A | 45_I | 1.230 | 0.98 |
| 130_F | 177_L | 1.220 | 0.98 |
| 35_L | 237_A | 1.218 | 0.98 |
| 178_T | 192_V | 1.204 | 0.98 |
| 74_T | 120_R | 1.199 | 0.98 |
| 42_K | 64_D | 1.194 | 0.98 |
| 102_V | 124_I | 1.185 | 0.98 |
| 54_Q | 58_N | 1.156 | 0.97 |
| 133_A | 177_L | 1.145 | 0.97 |
| 13_R | 247_E | 1.144 | 0.97 |
| 200_V | 231_L | 1.143 | 0.97 |
| 238_D | 247_E | 1.138 | 0.97 |
| 34_K | 38_R | 1.135 | 0.97 |
| 122_M | 127_Y | 1.131 | 0.97 |
| 67_S | 90_H | 1.130 | 0.97 |
| 17_K | 94_D | 1.125 | 0.97 |
| 42_K | 67_S | 1.123 | 0.97 |
| 69_V | 82_L | 1.120 | 0.96 |
| 152_A | 194_C | 1.117 | 0.96 |
| 167_Y | 171_K | 1.112 | 0.96 |
| 54_Q | 57_C | 1.110 | 0.96 |
| 77_E | 81_N | 1.100 | 0.96 |
| 239_A | 258_I | 1.099 | 0.96 |
| 36_F | 241_A | 1.095 | 0.96 |
| 116_E | 120_R | 1.094 | 0.96 |
| 111_L | 141_I | 1.086 | 0.96 |
| 32_T | 97_F | 1.082 | 0.96 |
| 58_N | 61_G | 1.077 | 0.95 |
| 35_L | 234_E | 1.073 | 0.95 |
| 58_N | 62_S | 1.070 | 0.95 |
| 104_S | 120_R | 1.066 | 0.95 |
| 151_T | 240_V | 1.054 | 0.95 |
| 44_V | 67_S | 1.053 | 0.95 |
| 93_L | 136_A | 1.048 | 0.94 |
| 99_N | 151_T | 1.042 | 0.94 |
| 81_N | 84_D | 1.040 | 0.94 |
| 18_V | 90_H | 1.038 | 0.94 |
| 201_A | 206_T | 1.035 | 0.94 |
| 232_R | 235_D | 1.035 | 0.94 |
| 39_Y | 245_G | 1.034 | 0.94 |
| 26_G | 52_H | 1.033 | 0.94 |
| 45_I | 66_I | 1.032 | 0.94 |
| 55_K | 59_N | 1.030 | 0.94 |
| 31_T | 233_A | 1.025 | 0.93 |
| 109_S | 112_E | 1.023 | 0.93 |
| 13_R | 39_Y | 1.022 | 0.93 |
| 118_F | 127_Y | 1.018 | 0.93 |
| 129_A | 150_F | 1.017 | 0.93 |
| 44_V | 69_V | 1.014 | 0.93 |
| 30_E | 55_K | 1.011 | 0.93 |
| 37_V | 60_I | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2bgkA | 2 | 0.9568 | 100 | 0.123 | Contact Map |
| 3lf2A | 4 | 0.9101 | 100 | 0.181 | Contact Map |
| 1iy8A | 8 | 0.9029 | 100 | 0.181 | Contact Map |
| 2z1nA | 2 | 0.8633 | 100 | 0.183 | Contact Map |
| 3rihA | 4 | 0.9245 | 100 | 0.183 | Contact Map |
| 1vl8A | 2 | 0.8957 | 100 | 0.183 | Contact Map |
| 3wtcA | 2 | 0.8993 | 100 | 0.184 | Contact Map |
| 4j2hA | 1 | 0.9029 | 100 | 0.186 | Contact Map |
| 1zemA | 8 | 0.8885 | 100 | 0.187 | Contact Map |
| 3sjuA | 2 | 0.8813 | 100 | 0.188 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)