| se-pmrb |
| ID: | 1424757949 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 270 (266) | ||
| Sequences: | 42817 (32911.9) | ||
| Seq/Len: | 160.966 | ||
| Nf(neff/√len): | 2018.0 |
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: 160.966).
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 |
| 125_V | 163_G | 3.093 | 1.00 |
| 204_E | 262_R | 3.061 | 1.00 |
| 251_F | 264_W | 3.041 | 1.00 |
| 240_S | 244_Q | 2.900 | 1.00 |
| 205_D | 209_G | 2.715 | 1.00 |
| 198_D | 266_L | 2.519 | 1.00 |
| 163_G | 246_H | 2.512 | 1.00 |
| 202_A | 262_R | 2.511 | 1.00 |
| 183_S | 206_E | 2.473 | 1.00 |
| 211_D | 214_K | 2.416 | 1.00 |
| 192_H | 202_A | 2.352 | 1.00 |
| 79_L | 93_L | 2.327 | 1.00 |
| 215_C | 254_N | 2.305 | 1.00 |
| 200_I | 266_L | 2.299 | 1.00 |
| 124_E | 162_R | 2.289 | 1.00 |
| 151_L | 190_T | 2.249 | 1.00 |
| 202_A | 264_W | 2.218 | 1.00 |
| 200_I | 264_W | 2.194 | 1.00 |
| 76_R | 98_D | 2.167 | 1.00 |
| 255_R | 259_T | 2.135 | 1.00 |
| 76_R | 97_L | 2.097 | 1.00 |
| 83_S | 94_I | 2.084 | 1.00 |
| 171_L | 243_T | 2.071 | 1.00 |
| 239_V | 250_F | 2.067 | 1.00 |
| 252_L | 263_A | 2.064 | 1.00 |
| 215_C | 252_L | 2.043 | 1.00 |
| 123_Q | 165_A | 1.993 | 1.00 |
| 190_T | 204_E | 1.991 | 1.00 |
| 192_H | 204_E | 1.973 | 1.00 |
| 153_P | 192_H | 1.971 | 1.00 |
| 195_A | 269_K | 1.953 | 1.00 |
| 219_S | 250_F | 1.929 | 1.00 |
| 217_K | 223_V | 1.900 | 1.00 |
| 151_L | 188_H | 1.894 | 1.00 |
| 188_H | 206_E | 1.884 | 1.00 |
| 124_E | 160_V | 1.874 | 1.00 |
| 243_T | 248_G | 1.873 | 1.00 |
| 194_S | 200_I | 1.872 | 1.00 |
| 134_P | 169_R | 1.871 | 1.00 |
| 253_Q | 262_R | 1.861 | 1.00 |
| 253_Q | 264_W | 1.851 | 1.00 |
| 212_E | 215_C | 1.843 | 1.00 |
| 214_K | 217_K | 1.775 | 1.00 |
| 126_K | 130_D | 1.765 | 1.00 |
| 194_S | 202_A | 1.754 | 1.00 |
| 171_L | 242_I | 1.747 | 1.00 |
| 249_Q | 266_L | 1.742 | 1.00 |
| 139_L | 173_R | 1.731 | 1.00 |
| 83_S | 91_A | 1.728 | 1.00 |
| 101_M | 105_S | 1.725 | 1.00 |
| 210_I | 218_L | 1.717 | 1.00 |
| 149_T | 188_H | 1.702 | 1.00 |
| 243_T | 265_V | 1.687 | 1.00 |
| 210_I | 214_K | 1.675 | 1.00 |
| 163_G | 168_L | 1.674 | 1.00 |
| 171_L | 239_V | 1.665 | 1.00 |
| 217_K | 220_E | 1.638 | 1.00 |
| 76_R | 101_M | 1.595 | 1.00 |
| 254_N | 261_T | 1.580 | 1.00 |
| 153_P | 190_T | 1.558 | 1.00 |
| 177_E | 181_R | 1.543 | 1.00 |
| 214_K | 223_V | 1.506 | 1.00 |
| 122_Y | 162_R | 1.503 | 1.00 |
| 143_L | 180_H | 1.499 | 1.00 |
| 75_V | 97_L | 1.494 | 1.00 |
| 244_Q | 249_Q | 1.488 | 1.00 |
| 251_F | 266_L | 1.477 | 1.00 |
| 183_S | 187_T | 1.477 | 1.00 |
| 214_K | 225_M | 1.461 | 1.00 |
| 80_E | 94_I | 1.410 | 1.00 |
| 187_T | 206_E | 1.392 | 0.99 |
| 172_L | 201_M | 1.370 | 0.99 |
| 210_I | 261_T | 1.348 | 0.99 |
| 167_L | 170_M | 1.343 | 0.99 |
| 242_I | 246_H | 1.334 | 0.99 |
| 201_M | 265_V | 1.321 | 0.99 |
| 79_L | 94_I | 1.319 | 0.99 |
| 67_E | 170_M | 1.303 | 0.99 |
| 140_N | 144_E | 1.294 | 0.99 |
| 59_L | 63_D | 1.292 | 0.99 |
| 128_L | 193_I | 1.290 | 0.99 |
| 220_E | 223_V | 1.278 | 0.99 |
| 34_L | 37_E | 1.275 | 0.99 |
| 164_D | 167_L | 1.273 | 0.99 |
| 219_S | 252_L | 1.266 | 0.99 |
| 94_I | 98_D | 1.239 | 0.98 |
| 69_R | 105_S | 1.222 | 0.98 |
| 190_T | 206_E | 1.195 | 0.98 |
| 63_D | 221_A | 1.194 | 0.98 |
| 248_G | 267_L | 1.194 | 0.98 |
| 102_D | 166_T | 1.191 | 0.98 |
| 183_S | 189_I | 1.189 | 0.98 |
| 198_D | 249_Q | 1.188 | 0.98 |
| 126_K | 160_V | 1.178 | 0.98 |
| 18_A | 23_N | 1.172 | 0.98 |
| 174_N | 239_V | 1.171 | 0.98 |
| 218_L | 252_L | 1.164 | 0.97 |
| 74_G | 78_H | 1.138 | 0.97 |
| 93_L | 97_L | 1.132 | 0.97 |
| 211_D | 256_T | 1.126 | 0.97 |
| 134_P | 165_A | 1.124 | 0.97 |
| 138_E | 169_R | 1.116 | 0.96 |
| 76_R | 94_I | 1.116 | 0.96 |
| 165_A | 169_R | 1.113 | 0.96 |
| 254_N | 259_T | 1.112 | 0.96 |
| 205_D | 260_G | 1.104 | 0.96 |
| 167_L | 245_L | 1.098 | 0.96 |
| 92_P | 96_R | 1.096 | 0.96 |
| 74_G | 96_R | 1.096 | 0.96 |
| 167_L | 242_I | 1.095 | 0.96 |
| 171_L | 265_V | 1.091 | 0.96 |
| 57_E | 61_T | 1.088 | 0.96 |
| 205_D | 261_T | 1.085 | 0.96 |
| 54_L | 57_E | 1.085 | 0.96 |
| 241_R | 244_Q | 1.081 | 0.95 |
| 126_K | 158_D | 1.075 | 0.95 |
| 199_A | 269_K | 1.071 | 0.95 |
| 79_L | 97_L | 1.069 | 0.95 |
| 128_L | 133_L | 1.063 | 0.95 |
| 135_S | 169_R | 1.062 | 0.95 |
| 243_T | 250_F | 1.061 | 0.95 |
| 78_H | 92_P | 1.054 | 0.95 |
| 122_Y | 246_H | 1.036 | 0.94 |
| 120_G | 164_D | 1.023 | 0.93 |
| 154_E | 193_I | 1.021 | 0.93 |
| 142_M | 145_T | 1.016 | 0.93 |
| 125_V | 131_V | 1.007 | 0.93 |
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 | |
| 3a0rA | 1 | 0.9407 | 100 | 0.211 | Contact Map |
| 4i5sA | 2 | 0.9667 | 100 | 0.226 | Contact Map |
| 4bixA | 2 | 0.8296 | 100 | 0.23 | Contact Map |
| 4ctiA | 4 | 0.8407 | 100 | 0.254 | Contact Map |
| 3jz3A | 2 | 0.5852 | 100 | 0.307 | Contact Map |
| 4q20A | 2 | 0.8333 | 100 | 0.312 | Contact Map |
| 4mpcA | 1 | 0.9185 | 100 | 0.319 | Contact Map |
| 4e01A | 1 | 0.9593 | 100 | 0.324 | Contact Map |
| 4gczA | 2 | 0.9704 | 100 | 0.333 | Contact Map |
| 2c2aA | 1 | 0.837 | 100 | 0.351 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)