| 2x6u |
| ID: | 1453971974 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 203 (192) | ||
| Sequences: | 636 (430.2) | ||
| Seq/Len: | 3.312 | ||
| Nf(neff/√len): | 31.0 |
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: 3.312).
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 |
| 175_T | 179_I | 2.209 | 1.00 |
| 13_R | 17_L | 2.169 | 1.00 |
| 29_T | 32_G | 2.117 | 1.00 |
| 25_E | 32_G | 2.050 | 1.00 |
| 178_K | 182_N | 2.038 | 1.00 |
| 182_N | 185_A | 1.995 | 1.00 |
| 50_T | 139_K | 1.960 | 1.00 |
| 26_M | 32_G | 1.943 | 1.00 |
| 26_M | 30_K | 1.923 | 1.00 |
| 8_V | 43_V | 1.837 | 0.99 |
| 125_L | 165_A | 1.831 | 0.99 |
| 26_M | 29_T | 1.808 | 0.99 |
| 43_V | 54_L | 1.798 | 0.99 |
| 179_I | 188_F | 1.797 | 0.99 |
| 27_I | 30_K | 1.736 | 0.99 |
| 178_K | 185_A | 1.629 | 0.98 |
| 185_A | 188_F | 1.603 | 0.98 |
| 19_F | 24_T | 1.574 | 0.98 |
| 95_A | 100_W | 1.570 | 0.97 |
| 136_H | 155_T | 1.537 | 0.97 |
| 97_G | 101_M | 1.535 | 0.97 |
| 182_N | 186_K | 1.526 | 0.97 |
| 54_L | 135_L | 1.523 | 0.97 |
| 129_H | 133_P | 1.516 | 0.97 |
| 127_S | 167_T | 1.504 | 0.96 |
| 174_I | 178_K | 1.465 | 0.96 |
| 167_T | 170_Q | 1.446 | 0.95 |
| 15_L | 19_F | 1.442 | 0.95 |
| 27_I | 32_G | 1.426 | 0.95 |
| 125_L | 129_H | 1.418 | 0.95 |
| 90_H | 93_S | 1.417 | 0.95 |
| 175_T | 186_K | 1.409 | 0.94 |
| 118_D | 122_H | 1.408 | 0.94 |
| 16_W | 26_M | 1.383 | 0.94 |
| 183_P | 186_K | 1.373 | 0.93 |
| 178_K | 186_K | 1.364 | 0.93 |
| 177_L | 183_P | 1.361 | 0.93 |
| 178_K | 184_F | 1.358 | 0.93 |
| 175_T | 188_F | 1.349 | 0.93 |
| 184_F | 188_F | 1.346 | 0.92 |
| 9_F | 42_K | 1.345 | 0.92 |
| 39_Y | 68_F | 1.339 | 0.92 |
| 25_E | 30_K | 1.328 | 0.92 |
| 90_H | 107_F | 1.325 | 0.92 |
| 179_I | 183_P | 1.320 | 0.91 |
| 166_V | 170_Q | 1.315 | 0.91 |
| 179_I | 185_A | 1.312 | 0.91 |
| 179_I | 186_K | 1.310 | 0.91 |
| 117_L | 122_H | 1.305 | 0.91 |
| 56_M | 110_L | 1.266 | 0.89 |
| 166_V | 169_Y | 1.260 | 0.89 |
| 183_P | 188_F | 1.257 | 0.89 |
| 100_W | 107_F | 1.249 | 0.88 |
| 19_F | 26_M | 1.243 | 0.88 |
| 91_P | 94_P | 1.231 | 0.87 |
| 25_E | 29_T | 1.214 | 0.86 |
| 130_K | 164_I | 1.210 | 0.86 |
| 177_L | 188_F | 1.205 | 0.86 |
| 86_R | 118_D | 1.188 | 0.85 |
| 88_Y | 91_P | 1.188 | 0.85 |
| 55_L | 138_V | 1.183 | 0.84 |
| 163_F | 166_V | 1.180 | 0.84 |
| 15_L | 32_G | 1.178 | 0.84 |
| 16_W | 25_E | 1.172 | 0.83 |
| 68_F | 73_W | 1.169 | 0.83 |
| 182_N | 189_R | 1.154 | 0.82 |
| 41_V | 135_L | 1.153 | 0.82 |
| 47_N | 101_M | 1.134 | 0.81 |
| 179_I | 184_F | 1.123 | 0.80 |
| 182_N | 188_F | 1.123 | 0.80 |
| 24_T | 32_G | 1.113 | 0.79 |
| 179_I | 189_R | 1.108 | 0.78 |
| 64_H | 181_N | 1.102 | 0.78 |
| 128_M | 168_S | 1.100 | 0.78 |
| 111_K | 114_N | 1.095 | 0.77 |
| 167_T | 171_N | 1.081 | 0.76 |
| 175_T | 189_R | 1.077 | 0.76 |
| 40_K | 51_K | 1.060 | 0.74 |
| 19_F | 29_T | 1.052 | 0.73 |
| 177_L | 185_A | 1.042 | 0.72 |
| 19_F | 30_K | 1.040 | 0.72 |
| 39_Y | 135_L | 1.039 | 0.72 |
| 15_L | 29_T | 1.038 | 0.72 |
| 175_T | 178_K | 1.033 | 0.71 |
| 41_V | 57_D | 1.029 | 0.71 |
| 64_H | 67_K | 1.027 | 0.71 |
| 16_W | 32_G | 1.020 | 0.70 |
| 163_F | 171_N | 1.020 | 0.70 |
| 71_N | 174_I | 1.017 | 0.70 |
| 177_L | 182_N | 1.016 | 0.69 |
| 174_I | 179_I | 1.015 | 0.69 |
| 137_I | 144_N | 1.014 | 0.69 |
| 175_T | 184_F | 1.014 | 0.69 |
| 37_P | 52_Y | 1.009 | 0.69 |
| 175_T | 185_A | 1.001 | 0.68 |
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 | |
| 2x6uA | 1 | 0.867 | 100 | -0.011 | Contact Map |
| 1h6fA | 2 | 0.9163 | 100 | 0.035 | Contact Map |
| 4a04A | 2 | 0.9212 | 100 | 0.046 | Contact Map |
| 1xbrA | 2 | 0.9064 | 100 | 0.05 | Contact Map |
| 2xn2A | 1 | 0.4483 | 18.7 | 0.958 | Contact Map |
| 3mi6A | 4 | 0.5074 | 16.9 | 0.959 | Contact Map |
| 2yfoA | 1 | 0.4433 | 10.7 | 0.963 | Contact Map |
| 1uemA | 1 | 0.3498 | 10 | 0.963 | Contact Map |
| 4hwbA | 1 | 0.3842 | 9 | 0.964 | Contact Map |
| 2yuwA | 1 | 0.3547 | 7.9 | 0.965 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)