| pdz |
| ID: | 1429814698 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 217 (214) | ||
| Sequences: | 2236 (1471.3) | ||
| Seq/Len: | 10.449 | ||
| Nf(neff/√len): | 100.6 |
HHblits Results: (2013_03)
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: 10.449).
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 |
| 39_G | 43_E | 3.646 | 1.00 |
| 176_D | 214_R | 2.761 | 1.00 |
| 172_L | 212_V | 2.750 | 1.00 |
| 163_E | 167_A | 2.709 | 1.00 |
| 157_I | 172_L | 2.547 | 1.00 |
| 47_V | 84_L | 2.304 | 1.00 |
| 55_A | 83_I | 2.258 | 1.00 |
| 66_Y | 70_T | 2.152 | 1.00 |
| 33_I | 47_V | 2.100 | 1.00 |
| 193_T | 197_H | 1.954 | 1.00 |
| 15_L | 18_M | 1.930 | 1.00 |
| 5_R | 86_T | 1.836 | 1.00 |
| 55_A | 58_Q | 1.805 | 1.00 |
| 47_V | 82_M | 1.796 | 1.00 |
| 162_P | 167_A | 1.767 | 1.00 |
| 54_L | 85_L | 1.698 | 1.00 |
| 180_D | 183_G | 1.621 | 1.00 |
| 196_V | 199_L | 1.611 | 1.00 |
| 38_E | 43_E | 1.542 | 1.00 |
| 191_M | 195_K | 1.536 | 1.00 |
| 33_I | 53_L | 1.535 | 1.00 |
| 180_D | 211_T | 1.530 | 1.00 |
| 138_P | 141_V | 1.513 | 1.00 |
| 159_H | 174_I | 1.504 | 1.00 |
| 64_S | 69_A | 1.493 | 1.00 |
| 21_Y | 66_Y | 1.445 | 1.00 |
| 69_A | 72_L | 1.428 | 1.00 |
| 166_V | 170_K | 1.414 | 1.00 |
| 192_T | 195_K | 1.384 | 0.99 |
| 135_E | 138_P | 1.368 | 0.99 |
| 155_C | 196_V | 1.360 | 0.99 |
| 193_T | 201_H | 1.351 | 0.99 |
| 42_A | 46_G | 1.332 | 0.99 |
| 172_L | 176_D | 1.316 | 0.99 |
| 144_C | 158_T | 1.310 | 0.99 |
| 198_Q | 201_H | 1.310 | 0.99 |
| 186_I | 191_M | 1.305 | 0.99 |
| 110_E | 114_P | 1.301 | 0.99 |
| 143_V | 193_T | 1.298 | 0.99 |
| 14_F | 17_I | 1.278 | 0.99 |
| 91_E | 95_A | 1.265 | 0.99 |
| 155_C | 181_I | 1.249 | 0.99 |
| 61_T | 69_A | 1.246 | 0.98 |
| 99_A | 103_K | 1.246 | 0.98 |
| 160_V | 174_I | 1.244 | 0.98 |
| 157_I | 176_D | 1.241 | 0.98 |
| 40_S | 45_A | 1.188 | 0.98 |
| 14_F | 41_N | 1.183 | 0.98 |
| 197_H | 200_F | 1.182 | 0.98 |
| 84_L | 93_I | 1.181 | 0.98 |
| 173_K | 214_R | 1.168 | 0.97 |
| 99_A | 102_K | 1.155 | 0.97 |
| 140_G | 143_V | 1.154 | 0.97 |
| 195_K | 198_Q | 1.148 | 0.97 |
| 22_G | 66_Y | 1.132 | 0.97 |
| 41_N | 45_A | 1.132 | 0.97 |
| 192_T | 196_V | 1.130 | 0.97 |
| 160_V | 172_L | 1.129 | 0.97 |
| 145_G | 193_T | 1.129 | 0.97 |
| 17_I | 154_G | 1.126 | 0.97 |
| 148_N | 151_V | 1.121 | 0.97 |
| 181_I | 193_T | 1.114 | 0.96 |
| 19_V | 22_G | 1.111 | 0.96 |
| 18_M | 21_Y | 1.104 | 0.96 |
| 108_K | 113_K | 1.101 | 0.96 |
| 37_R | 141_V | 1.095 | 0.96 |
| 66_Y | 141_V | 1.093 | 0.96 |
| 186_I | 196_V | 1.092 | 0.96 |
| 15_L | 139_M | 1.074 | 0.95 |
| 73_L | 76_A | 1.074 | 0.95 |
| 76_A | 157_I | 1.068 | 0.95 |
| 142_I | 159_H | 1.066 | 0.95 |
| 115_Q | 118_A | 1.064 | 0.95 |
| 20_I | 73_L | 1.062 | 0.95 |
| 189_G | 194_L | 1.059 | 0.95 |
| 9_V | 19_V | 1.058 | 0.95 |
| 120_A | 124_P | 1.057 | 0.95 |
| 173_K | 176_D | 1.055 | 0.95 |
| 198_Q | 202_T | 1.041 | 0.94 |
| 30_G | 154_G | 1.038 | 0.94 |
| 90_E | 94_K | 1.036 | 0.94 |
| 60_V | 63_E | 1.034 | 0.94 |
| 207_A | 212_V | 1.030 | 0.94 |
| 70_T | 73_L | 1.028 | 0.94 |
| 53_L | 61_T | 1.025 | 0.93 |
| 197_H | 201_H | 1.025 | 0.93 |
| 160_V | 164_G | 1.024 | 0.93 |
| 96_E | 111_E | 1.017 | 0.93 |
| 11_K | 15_L | 1.015 | 0.93 |
| 182_N | 210_L | 1.015 | 0.93 |
| 55_A | 60_V | 1.011 | 0.93 |
| 195_K | 200_F | 1.011 | 0.93 |
| 208_V | 212_V | 1.010 | 0.93 |
| 31_I | 64_S | 1.010 | 0.93 |
| 207_A | 211_T | 1.004 | 0.93 |
| 96_E | 115_Q | 1.002 | 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
- 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 | |
| 2xkxA | 2 | 0.9724 | 100 | 0.267 | Contact Map |
| 2qt5A | 2 | 0.8618 | 100 | 0.319 | Contact Map |
| 3gslA | 2 | 0.8341 | 100 | 0.416 | Contact Map |
| 3r0hA | 8 | 0.8111 | 100 | 0.416 | Contact Map |
| 1p1dA | 1 | 0.8525 | 100 | 0.434 | Contact Map |
| 3suzA | 1 | 0.4055 | 99.9 | 0.453 | Contact Map |
| 1w9eA | 2 | 0.7373 | 99.9 | 0.499 | Contact Map |
| 3rleA | 1 | 0.7419 | 99.9 | 0.509 | Contact Map |
| 4kfvA | 1 | 0.7143 | 99.9 | 0.51 | Contact Map |
| 1ky9A | 2 | 0.8157 | 99.9 | 0.531 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)