| 1w2u |
| ID: | 1452700743 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 224 (220) | ||
| Sequences: | 597 (432.1) | ||
| Seq/Len: | 2.714 | ||
| Nf(neff/√len): | 29.1 |
HHblits Results: (2015_06)
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: 2.714).
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 |
| 7_E | 10_G | 5.207 | 1.00 |
| 85_T | 102_Y | 3.546 | 1.00 |
| 6_C | 35_C | 3.217 | 1.00 |
| 39_D | 49_S | 2.864 | 1.00 |
| 106_T | 195_Q | 2.780 | 1.00 |
| 178_K | 182_N | 2.648 | 1.00 |
| 19_L | 38_L | 2.270 | 1.00 |
| 50_T | 65_P | 2.170 | 1.00 |
| 87_V | 216_C | 2.156 | 1.00 |
| 200_Y | 221_A | 1.945 | 0.99 |
| 153_G | 160_V | 1.941 | 0.99 |
| 37_Y | 49_S | 1.933 | 0.99 |
| 87_V | 202_V | 1.907 | 0.99 |
| 132_Y | 151_W | 1.905 | 0.99 |
| 153_G | 162_S | 1.852 | 0.99 |
| 76_K | 79_D | 1.849 | 0.99 |
| 103_D | 122_M | 1.840 | 0.99 |
| 149_D | 166_P | 1.740 | 0.98 |
| 28_T | 60_N | 1.735 | 0.98 |
| 163_F | 180_F | 1.715 | 0.98 |
| 152_T | 159_R | 1.651 | 0.97 |
| 163_F | 183_Y | 1.608 | 0.97 |
| 200_Y | 223_L | 1.558 | 0.96 |
| 150_L | 161_Y | 1.555 | 0.96 |
| 23_L | 65_P | 1.484 | 0.94 |
| 103_D | 124_W | 1.462 | 0.94 |
| 29_A | 55_Q | 1.443 | 0.93 |
| 64_Y | 88_S | 1.436 | 0.93 |
| 24_W | 122_M | 1.435 | 0.93 |
| 8_L | 26_K | 1.429 | 0.93 |
| 4_S | 37_Y | 1.423 | 0.93 |
| 20_L | 66_Y | 1.423 | 0.93 |
| 97_R | 131_I | 1.422 | 0.93 |
| 202_V | 219_F | 1.409 | 0.92 |
| 83_M | 200_Y | 1.398 | 0.92 |
| 68_G | 201_Q | 1.378 | 0.91 |
| 85_T | 177_I | 1.375 | 0.91 |
| 4_S | 49_S | 1.365 | 0.90 |
| 123_I | 177_I | 1.323 | 0.88 |
| 123_I | 216_C | 1.321 | 0.88 |
| 105_F | 175_C | 1.316 | 0.88 |
| 105_F | 199_V | 1.316 | 0.88 |
| 122_M | 205_E | 1.313 | 0.88 |
| 3_R | 37_Y | 1.296 | 0.87 |
| 134_I | 155_N | 1.288 | 0.87 |
| 52_W | 96_I | 1.268 | 0.85 |
| 105_F | 158_M | 1.258 | 0.85 |
| 144_A | 175_C | 1.252 | 0.84 |
| 5_L | 21_N | 1.236 | 0.83 |
| 134_I | 160_V | 1.235 | 0.83 |
| 144_A | 179_D | 1.229 | 0.83 |
| 182_N | 185_E | 1.226 | 0.83 |
| 140_Q | 147_T | 1.215 | 0.82 |
| 61_V | 122_M | 1.215 | 0.82 |
| 22_N | 99_N | 1.212 | 0.82 |
| 103_D | 153_G | 1.209 | 0.82 |
| 155_N | 158_M | 1.203 | 0.81 |
| 76_K | 196_N | 1.156 | 0.77 |
| 219_F | 223_L | 1.153 | 0.77 |
| 21_N | 36_T | 1.137 | 0.76 |
| 204_T | 207_F | 1.132 | 0.75 |
| 51_A | 213_R | 1.132 | 0.75 |
| 85_T | 179_D | 1.121 | 0.74 |
| 77_I | 190_Y | 1.116 | 0.74 |
| 39_D | 47_Q | 1.110 | 0.73 |
| 36_T | 65_P | 1.105 | 0.73 |
| 184_L | 196_N | 1.098 | 0.72 |
| 117_G | 158_M | 1.095 | 0.72 |
| 23_L | 206_C | 1.089 | 0.71 |
| 211_P | 214_F | 1.082 | 0.70 |
| 53_E | 210_G | 1.081 | 0.70 |
| 72_Q | 196_N | 1.075 | 0.70 |
| 52_W | 61_V | 1.068 | 0.69 |
| 48_W | 85_T | 1.066 | 0.69 |
| 108_R | 118_D | 1.066 | 0.69 |
| 89_W | 214_F | 1.063 | 0.68 |
| 202_V | 216_C | 1.061 | 0.68 |
| 34_Q | 63_S | 1.056 | 0.68 |
| 30_T | 55_Q | 1.052 | 0.67 |
| 93_R | 212_A | 1.052 | 0.67 |
| 135_G | 158_M | 1.044 | 0.66 |
| 45_G | 88_S | 1.043 | 0.66 |
| 147_T | 166_P | 1.042 | 0.66 |
| 176_D | 179_D | 1.041 | 0.66 |
| 77_I | 152_T | 1.029 | 0.65 |
| 140_Q | 149_D | 1.027 | 0.65 |
| 34_Q | 50_T | 1.022 | 0.64 |
| 109_D | 202_V | 1.016 | 0.63 |
| 18_E | 70_Q | 1.015 | 0.63 |
| 76_K | 171_R | 1.013 | 0.63 |
| 165_P | 170_I | 1.008 | 0.62 |
| 147_T | 179_D | 1.007 | 0.62 |
| 59_D | 208_T | 1.005 | 0.62 |
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 | |
| 1olrA | 1 | 0.9911 | 100 | 0.021 | Contact Map |
| 4nprA | 2 | 0.9732 | 100 | 0.053 | Contact Map |
| 1ks5A | 1 | 0.9777 | 100 | 0.054 | Contact Map |
| 1oa2A | 6 | 0.9643 | 100 | 0.057 | Contact Map |
| 3vl9A | 2 | 0.9688 | 100 | 0.061 | Contact Map |
| 2jenA | 1 | 0.9509 | 100 | 0.117 | Contact Map |
| 2nlrA | 1 | 0.9375 | 100 | 0.122 | Contact Map |
| 1h0bA | 2 | 0.9375 | 100 | 0.123 | Contact Map |
| 2bw8A | 2 | 0.9375 | 100 | 0.123 | Contact Map |
| 3vgiA | 1 | 0.9688 | 100 | 0.185 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)