| pa-pmrb |
| ID: | 1424758010 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 291 (271) | ||
| Sequences: | 27955 (21864) | ||
| Seq/Len: | 103.155 | ||
| Nf(neff/√len): | 1328.1 |
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: 103.155).
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 |
| 253_G | 266_Q | 3.131 | 1.00 |
| 127_V | 162_G | 3.117 | 1.00 |
| 204_R | 264_E | 3.061 | 1.00 |
| 242_K | 246_E | 2.906 | 1.00 |
| 76_A | 95_V | 2.704 | 1.00 |
| 202_R | 264_E | 2.677 | 1.00 |
| 205_D | 209_G | 2.561 | 1.00 |
| 191_R | 202_R | 2.452 | 1.00 |
| 126_P | 161_M | 2.343 | 1.00 |
| 162_G | 248_H | 2.341 | 1.00 |
| 152_S | 189_E | 2.315 | 1.00 |
| 182_T | 206_N | 2.258 | 1.00 |
| 202_R | 266_Q | 2.255 | 1.00 |
| 241_V | 252_I | 2.250 | 1.00 |
| 211_A | 214_E | 2.228 | 1.00 |
| 215_Q | 256_K | 2.207 | 1.00 |
| 80_L | 96_S | 2.204 | 1.00 |
| 126_P | 159_Y | 2.115 | 1.00 |
| 73_R | 100_E | 2.114 | 1.00 |
| 170_M | 245_V | 2.085 | 1.00 |
| 187_Q | 206_N | 2.046 | 1.00 |
| 254_L | 265_V | 1.992 | 1.00 |
| 189_E | 204_R | 1.981 | 1.00 |
| 191_R | 204_R | 1.962 | 1.00 |
| 257_G | 261_K | 1.954 | 1.00 |
| 73_R | 99_V | 1.951 | 1.00 |
| 154_H | 191_R | 1.935 | 1.00 |
| 215_Q | 254_L | 1.930 | 1.00 |
| 219_F | 252_I | 1.921 | 1.00 |
| 217_A | 223_Y | 1.892 | 1.00 |
| 103_S | 107_E | 1.887 | 1.00 |
| 73_R | 103_S | 1.853 | 1.00 |
| 125_H | 164_D | 1.843 | 1.00 |
| 140_L | 172_G | 1.831 | 1.00 |
| 214_E | 217_A | 1.828 | 1.00 |
| 128_N | 131_T | 1.822 | 1.00 |
| 135_D | 168_K | 1.813 | 1.00 |
| 255_G | 264_E | 1.812 | 1.00 |
| 245_V | 250_G | 1.793 | 1.00 |
| 255_G | 266_Q | 1.776 | 1.00 |
| 212_L | 215_Q | 1.743 | 1.00 |
| 170_M | 244_I | 1.737 | 1.00 |
| 152_S | 187_Q | 1.729 | 1.00 |
| 80_L | 93_L | 1.726 | 1.00 |
| 217_A | 220_T | 1.694 | 1.00 |
| 200_V | 268_F | 1.676 | 1.00 |
| 162_G | 167_L | 1.673 | 1.00 |
| 245_V | 267_V | 1.665 | 1.00 |
| 124_F | 161_M | 1.636 | 1.00 |
| 214_E | 225_S | 1.631 | 1.00 |
| 251_S | 268_F | 1.600 | 1.00 |
| 210_V | 218_I | 1.600 | 1.00 |
| 85_P | 88_H | 1.598 | 1.00 |
| 150_E | 187_Q | 1.593 | 1.00 |
| 176_G | 180_R | 1.564 | 1.00 |
| 170_M | 241_V | 1.533 | 1.00 |
| 193_E | 202_R | 1.528 | 1.00 |
| 144_A | 179_L | 1.518 | 1.00 |
| 77_Q | 96_S | 1.513 | 1.00 |
| 72_L | 99_V | 1.511 | 1.00 |
| 51_L | 54_E | 1.502 | 1.00 |
| 253_G | 268_F | 1.501 | 1.00 |
| 182_T | 186_G | 1.493 | 1.00 |
| 198_H | 268_F | 1.470 | 1.00 |
| 214_E | 223_Y | 1.457 | 1.00 |
| 211_A | 258_L | 1.456 | 1.00 |
| 154_H | 189_E | 1.434 | 1.00 |
| 84_D | 88_H | 1.426 | 1.00 |
| 193_E | 200_V | 1.422 | 1.00 |
| 194_N | 271_K | 1.405 | 0.99 |
| 96_S | 100_E | 1.401 | 0.99 |
| 56_R | 60_D | 1.397 | 0.99 |
| 246_E | 251_S | 1.396 | 0.99 |
| 210_V | 263_L | 1.372 | 0.99 |
| 76_A | 96_S | 1.371 | 0.99 |
| 210_V | 214_E | 1.368 | 0.99 |
| 200_V | 266_Q | 1.366 | 0.99 |
| 64_E | 169_A | 1.347 | 0.99 |
| 171_V | 201_L | 1.341 | 0.99 |
| 166_W | 169_A | 1.326 | 0.99 |
| 139_E | 168_K | 1.323 | 0.99 |
| 31_L | 34_R | 1.320 | 0.99 |
| 244_I | 248_H | 1.312 | 0.99 |
| 173_N | 241_V | 1.309 | 0.99 |
| 219_F | 254_L | 1.306 | 0.99 |
| 163_I | 166_W | 1.299 | 0.99 |
| 141_A | 145_I | 1.294 | 0.99 |
| 256_K | 263_L | 1.291 | 0.99 |
| 56_R | 221_R | 1.283 | 0.99 |
| 195_R | 200_V | 1.281 | 0.99 |
| 73_R | 96_S | 1.281 | 0.99 |
| 186_G | 206_N | 1.279 | 0.99 |
| 189_E | 206_N | 1.264 | 0.99 |
| 220_T | 223_Y | 1.252 | 0.99 |
| 71_S | 98_S | 1.232 | 0.98 |
| 250_G | 269_L | 1.228 | 0.98 |
| 79_A | 92_L | 1.220 | 0.98 |
| 66_R | 107_E | 1.220 | 0.98 |
| 130_A | 134_E | 1.220 | 0.98 |
| 15_Q | 20_H | 1.210 | 0.98 |
| 75_H | 94_Q | 1.204 | 0.98 |
| 128_N | 159_Y | 1.180 | 0.98 |
| 201_L | 267_V | 1.180 | 0.98 |
| 75_H | 91_G | 1.180 | 0.98 |
| 29_V | 34_R | 1.167 | 0.97 |
| 104_T | 165_L | 1.164 | 0.97 |
| 205_D | 262_G | 1.153 | 0.97 |
| 72_L | 95_V | 1.150 | 0.97 |
| 245_V | 252_I | 1.138 | 0.97 |
| 60_D | 221_R | 1.130 | 0.97 |
| 98_S | 101_R | 1.121 | 0.97 |
| 164_D | 168_K | 1.120 | 0.96 |
| 10_Q | 35_G | 1.105 | 0.96 |
| 135_D | 164_D | 1.096 | 0.96 |
| 52_E | 56_R | 1.091 | 0.96 |
| 170_M | 267_V | 1.081 | 0.95 |
| 82_S | 88_H | 1.079 | 0.95 |
| 167_L | 248_H | 1.078 | 0.95 |
| 166_W | 247_L | 1.075 | 0.95 |
| 166_W | 244_I | 1.070 | 0.95 |
| 16_R | 44_L | 1.070 | 0.95 |
| 80_L | 89_A | 1.062 | 0.95 |
| 210_V | 215_Q | 1.056 | 0.95 |
| 243_R | 246_E | 1.050 | 0.94 |
| 94_Q | 98_S | 1.046 | 0.94 |
| 130_A | 157_T | 1.040 | 0.94 |
| 90_R | 94_Q | 1.038 | 0.94 |
| 71_S | 75_H | 1.028 | 0.94 |
| 112_L | 239_P | 1.024 | 0.93 |
| 143_Q | 146_D | 1.020 | 0.93 |
| 218_I | 254_L | 1.020 | 0.93 |
| 48_R | 52_E | 1.019 | 0.93 |
| 122_E | 163_I | 1.019 | 0.93 |
| 136_V | 168_K | 1.016 | 0.93 |
| 127_V | 132_L | 1.011 | 0.93 |
| 168_K | 172_G | 1.008 | 0.93 |
| 54_E | 58_T | 1.003 | 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 | 0.89 | 100 | 0.313 | Contact Map |
| 4i5sA | 2 | 0.9038 | 100 | 0.321 | Contact Map |
| 4bixA | 2 | 0.7801 | 100 | 0.335 | Contact Map |
| 4ctiA | 4 | 0.7835 | 100 | 0.352 | Contact Map |
| 4e01A | 1 | 0.9003 | 100 | 0.391 | Contact Map |
| 4q20A | 2 | 0.7869 | 100 | 0.397 | Contact Map |
| 4mpcA | 1 | 0.921 | 100 | 0.399 | Contact Map |
| 3jz3A | 2 | 0.5464 | 100 | 0.403 | Contact Map |
| 4gczA | 2 | 0.9313 | 100 | 0.412 | Contact Map |
| 2e0aA | 2 | 0.9725 | 100 | 0.414 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)