| Amy Keating |
| ID: | 1504911862 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 189 (183) | ||
| Sequences: | 260 (177.9) | ||
| Seq/Len: | 1.421 | ||
| Nf(neff/√len): | 13.2 |
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: 1.421).
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 |
| 82_F | 141_Y | 4.396 | 1.00 |
| 19_L | 152_V | 3.614 | 1.00 |
| 11_A | 92_D | 2.684 | 1.00 |
| 47_D | 161_R | 2.574 | 1.00 |
| 82_F | 130_A | 2.081 | 0.98 |
| 37_E | 63_E | 1.826 | 0.96 |
| 77_G | 163_I | 1.778 | 0.95 |
| 59_A | 62_E | 1.746 | 0.94 |
| 54_D | 63_E | 1.715 | 0.93 |
| 64_Y | 70_Q | 1.631 | 0.91 |
| 82_F | 90_F | 1.559 | 0.88 |
| 87_T | 129_Q | 1.558 | 0.88 |
| 19_L | 81_V | 1.499 | 0.85 |
| 61_Q | 70_Q | 1.447 | 0.82 |
| 115_G | 130_A | 1.430 | 0.81 |
| 86_N | 124_T | 1.418 | 0.80 |
| 118_C | 150_Q | 1.414 | 0.80 |
| 54_D | 64_Y | 1.387 | 0.78 |
| 22_Q | 26_N | 1.374 | 0.77 |
| 115_G | 143_E | 1.364 | 0.77 |
| 113_L | 139_I | 1.354 | 0.76 |
| 63_E | 70_Q | 1.335 | 0.74 |
| 55_I | 76_E | 1.306 | 0.72 |
| 46_I | 161_R | 1.301 | 0.72 |
| 144_T | 147_K | 1.297 | 0.71 |
| 56_L | 63_E | 1.283 | 0.70 |
| 92_D | 129_Q | 1.273 | 0.69 |
| 28_F | 59_A | 1.270 | 0.69 |
| 17_S | 24_I | 1.262 | 0.68 |
| 7_V | 25_Q | 1.259 | 0.68 |
| 14_V | 146_A | 1.255 | 0.68 |
| 175_D | 178_G | 1.244 | 0.67 |
| 63_E | 96_Y | 1.234 | 0.66 |
| 89_S | 114_V | 1.225 | 0.65 |
| 14_V | 117_K | 1.224 | 0.65 |
| 14_V | 145_S | 1.220 | 0.65 |
| 20_T | 68_R | 1.215 | 0.64 |
| 34_P | 63_E | 1.210 | 0.64 |
| 32_Y | 125_V | 1.209 | 0.64 |
| 8_V | 19_L | 1.205 | 0.63 |
| 17_S | 120_L | 1.203 | 0.63 |
| 143_E | 151_G | 1.191 | 0.62 |
| 117_K | 145_S | 1.184 | 0.61 |
| 12_G | 78_F | 1.183 | 0.61 |
| 37_E | 83_A | 1.149 | 0.58 |
| 12_G | 32_Y | 1.144 | 0.57 |
| 26_N | 77_G | 1.144 | 0.57 |
| 12_G | 37_E | 1.140 | 0.57 |
| 113_L | 134_A | 1.134 | 0.56 |
| 61_Q | 64_Y | 1.132 | 0.56 |
| 18_A | 28_F | 1.131 | 0.56 |
| 94_H | 149_R | 1.115 | 0.54 |
| 23_L | 26_N | 1.115 | 0.54 |
| 28_F | 147_K | 1.115 | 0.54 |
| 127_S | 134_A | 1.111 | 0.54 |
| 9_V | 72_M | 1.107 | 0.53 |
| 130_A | 141_Y | 1.103 | 0.53 |
| 93_I | 162_E | 1.102 | 0.53 |
| 56_L | 160_V | 1.097 | 0.52 |
| 83_A | 96_Y | 1.097 | 0.52 |
| 26_N | 64_Y | 1.097 | 0.52 |
| 68_R | 75_G | 1.097 | 0.52 |
| 62_E | 90_F | 1.095 | 0.52 |
| 19_L | 93_I | 1.091 | 0.52 |
| 79_L | 105_D | 1.085 | 0.51 |
| 31_E | 79_L | 1.081 | 0.51 |
| 62_E | 71_Y | 1.079 | 0.51 |
| 38_D | 42_K | 1.079 | 0.51 |
| 80_C | 159_L | 1.070 | 0.50 |
| 112_V | 155_A | 1.067 | 0.49 |
| 128_R | 131_Q | 1.064 | 0.49 |
| 33_D | 72_M | 1.060 | 0.49 |
| 84_I | 107_D | 1.057 | 0.48 |
| 32_Y | 37_E | 1.057 | 0.48 |
| 25_Q | 67_M | 1.051 | 0.48 |
| 80_C | 93_I | 1.047 | 0.47 |
| 22_Q | 66_A | 1.041 | 0.47 |
| 61_Q | 73_R | 1.038 | 0.46 |
| 130_A | 143_E | 1.033 | 0.46 |
| 114_V | 155_A | 1.032 | 0.46 |
| 82_F | 151_G | 1.031 | 0.46 |
| 37_E | 56_L | 1.025 | 0.45 |
| 76_E | 99_Q | 1.023 | 0.45 |
| 109_V | 180_G | 1.020 | 0.45 |
| 20_T | 33_D | 1.019 | 0.45 |
| 35_T | 60_G | 1.019 | 0.45 |
| 144_T | 166_H | 1.016 | 0.44 |
| 57_D | 60_G | 1.015 | 0.44 |
| 22_Q | 29_V | 1.013 | 0.44 |
| 34_P | 37_E | 1.013 | 0.44 |
| 12_G | 75_G | 1.011 | 0.44 |
| 117_K | 146_A | 1.010 | 0.44 |
| 178_G | 181_C | 1.009 | 0.44 |
| 63_E | 83_A | 1.009 | 0.44 |
| 37_E | 96_Y | 1.008 | 0.43 |
| 4_Y | 141_Y | 1.007 | 0.43 |
| 51_C | 113_L | 1.006 | 0.43 |
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 | |
| 2j0vA | 4 | 0.8836 | 100 | 0.44 | Contact Map |
| 2gf0A | 4 | 0.9048 | 100 | 0.444 | Contact Map |
| 2iwrA | 1 | 0.8677 | 100 | 0.447 | Contact Map |
| 1m7bA | 1 | 0.8624 | 100 | 0.449 | Contact Map |
| 4dsuA | 1 | 0.9365 | 100 | 0.451 | Contact Map |
| 3ihwA | 1 | 0.8519 | 100 | 0.454 | Contact Map |
| 3regA | 2 | 0.8783 | 100 | 0.456 | Contact Map |
| 2bovA | 1 | 0.9048 | 100 | 0.456 | Contact Map |
| 3conA | 1 | 0.8254 | 100 | 0.458 | Contact Map |
| 4klzA | 1 | 0.8201 | 100 | 0.459 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)