| ab-pmrb |
| ID: | 1424758054 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 283 (271) | ||
| Sequences: | 35780 (27777.5) | ||
| Seq/Len: | 132.030 | ||
| Nf(neff/√len): | 1687.4 |
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: 132.030).
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 |
| 129_F | 165_S | 3.074 | 1.00 |
| 256_T | 269_L | 3.040 | 1.00 |
| 208_E | 267_S | 2.957 | 1.00 |
| 245_D | 249_Q | 2.815 | 1.00 |
| 209_D | 213_G | 2.714 | 1.00 |
| 80_T | 96_L | 2.661 | 1.00 |
| 206_Q | 267_S | 2.506 | 1.00 |
| 201_H | 271_K | 2.431 | 1.00 |
| 165_S | 251_L | 2.424 | 1.00 |
| 194_S | 206_Q | 2.338 | 1.00 |
| 185_T | 210_S | 2.321 | 1.00 |
| 128_Y | 164_H | 2.293 | 1.00 |
| 204_C | 271_K | 2.235 | 1.00 |
| 154_G | 192_N | 2.224 | 1.00 |
| 84_L | 97_S | 2.207 | 1.00 |
| 219_Y | 259_K | 2.172 | 1.00 |
| 206_Q | 269_L | 2.168 | 1.00 |
| 215_D | 218_N | 2.154 | 1.00 |
| 197_T | 274_K | 2.068 | 1.00 |
| 77_N | 101_A | 2.064 | 1.00 |
| 204_C | 269_L | 2.046 | 1.00 |
| 244_V | 255_L | 2.045 | 1.00 |
| 260_S | 264_G | 2.039 | 1.00 |
| 219_Y | 257_L | 2.008 | 1.00 |
| 173_I | 248_T | 2.005 | 1.00 |
| 257_L | 268_V | 2.000 | 1.00 |
| 192_N | 208_E | 1.959 | 1.00 |
| 127_G | 167_E | 1.955 | 1.00 |
| 190_V | 210_S | 1.947 | 1.00 |
| 77_N | 100_L | 1.932 | 1.00 |
| 221_K | 227_Y | 1.930 | 1.00 |
| 194_S | 208_E | 1.923 | 1.00 |
| 128_Y | 162_E | 1.919 | 1.00 |
| 223_L | 255_L | 1.906 | 1.00 |
| 156_V | 194_S | 1.905 | 1.00 |
| 84_L | 94_Q | 1.877 | 1.00 |
| 137_N | 171_H | 1.833 | 1.00 |
| 258_D | 267_S | 1.827 | 1.00 |
| 248_T | 253_G | 1.810 | 1.00 |
| 218_N | 221_K | 1.793 | 1.00 |
| 196_Y | 204_C | 1.790 | 1.00 |
| 130_Q | 133_D | 1.771 | 1.00 |
| 104_Q | 108_T | 1.770 | 1.00 |
| 86_Q | 89_E | 1.769 | 1.00 |
| 142_L | 175_F | 1.765 | 1.00 |
| 216_P | 219_Y | 1.760 | 1.00 |
| 154_G | 190_V | 1.736 | 1.00 |
| 258_D | 269_L | 1.707 | 1.00 |
| 173_I | 247_A | 1.692 | 1.00 |
| 196_Y | 206_Q | 1.685 | 1.00 |
| 248_T | 270_V | 1.667 | 1.00 |
| 254_T | 271_K | 1.654 | 1.00 |
| 165_S | 170_V | 1.649 | 1.00 |
| 77_N | 104_Q | 1.644 | 1.00 |
| 214_I | 222_V | 1.618 | 1.00 |
| 152_D | 190_V | 1.596 | 1.00 |
| 221_K | 224_K | 1.586 | 1.00 |
| 173_I | 244_V | 1.578 | 1.00 |
| 218_N | 229_V | 1.574 | 1.00 |
| 198_D | 204_C | 1.574 | 1.00 |
| 126_T | 164_H | 1.551 | 1.00 |
| 81_K | 97_S | 1.512 | 1.00 |
| 179_D | 183_K | 1.507 | 1.00 |
| 76_L | 100_L | 1.497 | 1.00 |
| 156_V | 192_N | 1.493 | 1.00 |
| 146_A | 182_I | 1.486 | 1.00 |
| 85_S | 89_E | 1.483 | 1.00 |
| 259_K | 266_L | 1.452 | 1.00 |
| 249_Q | 254_T | 1.414 | 1.00 |
| 218_N | 227_Y | 1.406 | 0.99 |
| 80_T | 97_S | 1.405 | 0.99 |
| 214_I | 218_N | 1.398 | 0.99 |
| 256_T | 271_K | 1.375 | 0.99 |
| 97_S | 101_A | 1.368 | 0.99 |
| 185_T | 189_G | 1.353 | 0.99 |
| 60_Q | 64_D | 1.344 | 0.99 |
| 169_T | 172_S | 1.328 | 0.99 |
| 215_D | 261_L | 1.328 | 0.99 |
| 214_I | 266_L | 1.308 | 0.99 |
| 189_G | 210_S | 1.304 | 0.99 |
| 143_V | 147_M | 1.297 | 0.99 |
| 224_K | 227_Y | 1.294 | 0.99 |
| 174_I | 205_I | 1.290 | 0.99 |
| 205_I | 270_V | 1.281 | 0.99 |
| 166_I | 169_T | 1.281 | 0.99 |
| 68_E | 172_S | 1.275 | 0.99 |
| 223_L | 257_L | 1.235 | 0.98 |
| 79_Q | 92_S | 1.232 | 0.98 |
| 56_N | 60_Q | 1.232 | 0.98 |
| 35_Q | 38_L | 1.210 | 0.98 |
| 176_N | 244_V | 1.209 | 0.98 |
| 77_N | 97_S | 1.207 | 0.98 |
| 247_A | 251_L | 1.204 | 0.98 |
| 192_N | 210_S | 1.201 | 0.98 |
| 83_L | 93_L | 1.193 | 0.98 |
| 75_A | 99_G | 1.192 | 0.98 |
| 33_Y | 38_L | 1.180 | 0.98 |
| 260_S | 263_L | 1.179 | 0.98 |
| 105_H | 168_P | 1.179 | 0.98 |
| 79_Q | 95_N | 1.177 | 0.98 |
| 55_Q | 58_Q | 1.173 | 0.98 |
| 132_N | 136_L | 1.172 | 0.98 |
| 141_Q | 171_H | 1.170 | 0.97 |
| 253_G | 272_L | 1.169 | 0.97 |
| 64_D | 225_R | 1.145 | 0.97 |
| 130_Q | 162_E | 1.138 | 0.97 |
| 84_L | 90_H | 1.137 | 0.97 |
| 70_R | 108_T | 1.133 | 0.97 |
| 19_E | 24_E | 1.132 | 0.97 |
| 76_L | 96_L | 1.125 | 0.97 |
| 124_E | 166_I | 1.121 | 0.97 |
| 60_Q | 225_R | 1.118 | 0.96 |
| 58_Q | 62_I | 1.112 | 0.96 |
| 167_E | 171_H | 1.111 | 0.96 |
| 201_H | 204_C | 1.109 | 0.96 |
| 137_N | 167_E | 1.108 | 0.96 |
| 209_D | 265_G | 1.097 | 0.96 |
| 169_T | 247_A | 1.094 | 0.96 |
| 80_T | 100_L | 1.087 | 0.96 |
| 259_K | 264_G | 1.083 | 0.96 |
| 203_A | 274_K | 1.081 | 0.95 |
| 173_I | 270_V | 1.073 | 0.95 |
| 209_D | 266_L | 1.063 | 0.95 |
| 246_R | 249_Q | 1.053 | 0.95 |
| 75_A | 79_Q | 1.049 | 0.94 |
| 201_H | 254_T | 1.049 | 0.94 |
| 248_T | 255_L | 1.048 | 0.94 |
| 138_C | 171_H | 1.045 | 0.94 |
| 83_L | 89_E | 1.022 | 0.93 |
| 222_V | 257_L | 1.016 | 0.93 |
| 132_N | 195_V | 1.015 | 0.93 |
| 139_V | 155_F | 1.011 | 0.93 |
| 126_T | 251_L | 1.005 | 0.93 |
| 45_N | 48_F | 1.000 | 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 | |
| 4bixA | 2 | 0.8057 | 100 | 0.24 | Contact Map |
| 3a0rA | 1 | 0.8834 | 100 | 0.242 | Contact Map |
| 4i5sA | 2 | 0.9329 | 100 | 0.255 | Contact Map |
| 4ctiA | 4 | 0.8057 | 100 | 0.297 | Contact Map |
| 4q20A | 2 | 0.8057 | 100 | 0.337 | Contact Map |
| 3jz3A | 2 | 0.5548 | 100 | 0.35 | Contact Map |
| 4e01A | 1 | 0.9364 | 100 | 0.351 | Contact Map |
| 4mpcA | 1 | 0.9152 | 100 | 0.358 | Contact Map |
| 4gczA | 2 | 0.9293 | 100 | 0.361 | Contact Map |
| 2e0aA | 2 | 0.9717 | 100 | 0.372 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)