| ctd |
| ID: | 1516142713 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 222 (194) | ||
| Sequences: | 1195 (862.1) | ||
| Seq/Len: | 6.160 | ||
| Nf(neff/√len): | 61.9 |
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: 6.160).
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 |
| 173_F | 190_Y | 3.618 | 1.00 |
| 165_L | 189_L | 3.179 | 1.00 |
| 133_E | 136_H | 3.011 | 1.00 |
| 32_E | 52_L | 2.719 | 1.00 |
| 101_A | 109_S | 2.609 | 1.00 |
| 110_M | 137_W | 2.605 | 1.00 |
| 24_H | 51_H | 2.553 | 1.00 |
| 185_R | 188_D | 2.445 | 1.00 |
| 118_D | 138_Y | 2.416 | 1.00 |
| 55_A | 63_A | 2.410 | 1.00 |
| 165_L | 196_A | 2.037 | 1.00 |
| 30_Y | 116_A | 1.949 | 1.00 |
| 193_A | 201_M | 1.924 | 1.00 |
| 25_L | 60_E | 1.886 | 1.00 |
| 47_S | 50_F | 1.863 | 1.00 |
| 110_M | 144_M | 1.837 | 1.00 |
| 56_A | 64_I | 1.765 | 1.00 |
| 133_E | 137_W | 1.656 | 1.00 |
| 176_G | 179_L | 1.653 | 1.00 |
| 166_A | 204_R | 1.646 | 1.00 |
| 27_M | 31_H | 1.602 | 0.99 |
| 203_G | 206_A | 1.524 | 0.99 |
| 72_S | 98_L | 1.521 | 0.99 |
| 189_L | 192_Q | 1.514 | 0.99 |
| 24_H | 58_L | 1.502 | 0.99 |
| 95_F | 123_L | 1.500 | 0.99 |
| 32_E | 66_G | 1.491 | 0.99 |
| 51_H | 137_W | 1.484 | 0.99 |
| 187_G | 209_Y | 1.464 | 0.99 |
| 70_M | 116_A | 1.446 | 0.99 |
| 139_N | 143_E | 1.425 | 0.99 |
| 157_Q | 160_P | 1.394 | 0.98 |
| 187_G | 205_L | 1.376 | 0.98 |
| 64_I | 202_K | 1.357 | 0.98 |
| 102_A | 194_A | 1.356 | 0.98 |
| 137_W | 140_T | 1.347 | 0.98 |
| 25_L | 166_A | 1.346 | 0.98 |
| 194_A | 202_K | 1.345 | 0.98 |
| 130_D | 133_E | 1.342 | 0.98 |
| 30_Y | 36_F | 1.337 | 0.98 |
| 34_G | 44_D | 1.327 | 0.97 |
| 159_E | 162_Y | 1.313 | 0.97 |
| 94_G | 98_L | 1.302 | 0.97 |
| 93_K | 97_Y | 1.302 | 0.97 |
| 56_A | 102_A | 1.287 | 0.97 |
| 99_L | 133_E | 1.283 | 0.97 |
| 169_A | 190_Y | 1.278 | 0.97 |
| 114_A | 138_Y | 1.275 | 0.97 |
| 28_V | 114_A | 1.271 | 0.96 |
| 134_A | 138_Y | 1.266 | 0.96 |
| 25_L | 63_A | 1.256 | 0.96 |
| 167_R | 170_E | 1.252 | 0.96 |
| 172_L | 185_R | 1.251 | 0.96 |
| 93_K | 96_D | 1.234 | 0.96 |
| 166_A | 198_M | 1.233 | 0.96 |
| 201_M | 205_L | 1.224 | 0.95 |
| 102_A | 110_M | 1.217 | 0.95 |
| 64_I | 97_Y | 1.209 | 0.95 |
| 49_V | 70_M | 1.196 | 0.94 |
| 57_N | 103_E | 1.188 | 0.94 |
| 113_V | 117_F | 1.181 | 0.94 |
| 98_L | 112_L | 1.180 | 0.94 |
| 199_E | 206_A | 1.178 | 0.94 |
| 99_L | 103_E | 1.176 | 0.94 |
| 189_L | 193_A | 1.175 | 0.94 |
| 44_D | 182_D | 1.167 | 0.93 |
| 168_E | 172_L | 1.151 | 0.93 |
| 142_L | 194_A | 1.149 | 0.93 |
| 55_A | 60_E | 1.133 | 0.92 |
| 64_I | 104_A | 1.122 | 0.92 |
| 117_F | 133_E | 1.117 | 0.91 |
| 170_E | 190_Y | 1.114 | 0.91 |
| 113_V | 137_W | 1.114 | 0.91 |
| 114_A | 169_A | 1.088 | 0.90 |
| 141_A | 149_E | 1.087 | 0.90 |
| 19_I | 23_V | 1.080 | 0.89 |
| 88_E | 180_E | 1.077 | 0.89 |
| 115_R | 138_Y | 1.076 | 0.89 |
| 53_E | 57_N | 1.070 | 0.89 |
| 138_Y | 162_Y | 1.065 | 0.89 |
| 16_G | 19_I | 1.061 | 0.88 |
| 169_A | 189_L | 1.059 | 0.88 |
| 101_A | 106_D | 1.058 | 0.88 |
| 49_V | 53_E | 1.053 | 0.88 |
| 157_Q | 162_Y | 1.051 | 0.88 |
| 102_A | 142_L | 1.047 | 0.87 |
| 111_I | 146_D | 1.046 | 0.87 |
| 56_A | 194_A | 1.037 | 0.87 |
| 51_H | 97_Y | 1.033 | 0.86 |
| 140_T | 192_Q | 1.025 | 0.86 |
| 66_G | 112_L | 1.024 | 0.86 |
| 137_W | 144_M | 1.022 | 0.86 |
| 81_D | 84_L | 1.015 | 0.85 |
| 77_H | 80_A | 1.013 | 0.85 |
| 186_S | 208_Q | 1.010 | 0.85 |
| 95_F | 99_L | 1.009 | 0.85 |
| 25_L | 66_G | 1.006 | 0.84 |
| 67_L | 71_Y | 1.002 | 0.84 |
| 182_D | 185_R | 1.002 | 0.84 |
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 | |
| 4bwrA | 1 | 0.9144 | 100 | 0.437 | Contact Map |
| 1ouvA | 1 | 0.8468 | 99.9 | 0.486 | Contact Map |
| 1klxA | 1 | 0.5991 | 99.8 | 0.591 | Contact Map |
| 3e4bA | 4 | 0.8333 | 99.8 | 0.614 | Contact Map |
| 3rjvA | 1 | 0.7883 | 99.6 | 0.684 | Contact Map |
| 2pziA | 2 | 0.7568 | 98.5 | 0.802 | Contact Map |
| 4ui9C | 2 | 0 | 98.4 | 0.806 | Contact Map |
| 4gpkA | 12 | 0.8153 | 98.3 | 0.81 | Contact Map |
| 4gywA | 2 | 0.7072 | 98.3 | 0.81 | Contact Map |
| 3ulqA | 1 | 0.8108 | 98.3 | 0.811 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)