| het B2 |
| ID: | 1495615434 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 191 (191) | ||
| Sequences: | 3557 (2936.5) | ||
| Seq/Len: | 18.623 | ||
| Nf(neff/√len): | 212.5 |
HHblits Results: (2016_02)
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: 18.623).
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 |
| 28_T | 130_R | 4.131 | 1.00 |
| 60_A | 72_V | 3.551 | 1.00 |
| 104_C | 144_P | 3.223 | 1.00 |
| 5_N | 70_G | 3.219 | 1.00 |
| 177_C | 187_C | 3.119 | 1.00 |
| 87_L | 91_I | 2.817 | 1.00 |
| 23_A | 69_L | 2.791 | 1.00 |
| 67_N | 105_Y | 2.734 | 1.00 |
| 24_I | 101_A | 2.564 | 1.00 |
| 5_N | 12_E | 2.463 | 1.00 |
| 174_D | 191_Q | 2.277 | 1.00 |
| 23_A | 103_V | 2.273 | 1.00 |
| 57_I | 74_A | 2.257 | 1.00 |
| 63_R | 67_N | 2.139 | 1.00 |
| 27_H | 76_T | 2.100 | 1.00 |
| 108_L | 149_F | 2.096 | 1.00 |
| 24_I | 104_C | 2.070 | 1.00 |
| 23_A | 64_A | 2.014 | 1.00 |
| 69_L | 102_Q | 1.982 | 1.00 |
| 21_P | 102_Q | 1.978 | 1.00 |
| 59_A | 62_K | 1.969 | 1.00 |
| 106_V | 147_I | 1.935 | 1.00 |
| 80_D | 83_S | 1.831 | 1.00 |
| 3_L | 20_P | 1.797 | 1.00 |
| 27_H | 57_I | 1.747 | 1.00 |
| 164_A | 179_R | 1.743 | 1.00 |
| 111_V | 129_S | 1.642 | 1.00 |
| 131_W | 137_T | 1.592 | 1.00 |
| 6_V | 65_R | 1.585 | 1.00 |
| 7_S | 70_G | 1.580 | 1.00 |
| 106_V | 131_W | 1.568 | 1.00 |
| 168_R | 175_E | 1.562 | 1.00 |
| 80_D | 86_E | 1.545 | 1.00 |
| 94_M | 98_Y | 1.513 | 1.00 |
| 14_F | 20_P | 1.486 | 1.00 |
| 12_E | 71_Y | 1.480 | 1.00 |
| 63_R | 105_Y | 1.453 | 1.00 |
| 141_L | 149_F | 1.448 | 1.00 |
| 165_V | 175_E | 1.445 | 1.00 |
| 7_S | 65_R | 1.430 | 1.00 |
| 2_R | 86_E | 1.418 | 1.00 |
| 55_E | 58_Y | 1.404 | 0.99 |
| 62_K | 66_G | 1.365 | 0.99 |
| 184_V | 187_C | 1.361 | 0.99 |
| 103_V | 148_V | 1.336 | 0.99 |
| 122_V | 126_F | 1.332 | 0.99 |
| 39_W | 77_V | 1.327 | 0.99 |
| 101_A | 104_C | 1.315 | 0.99 |
| 37_Q | 82_T | 1.299 | 0.99 |
| 61_C | 72_V | 1.296 | 0.99 |
| 126_F | 129_S | 1.254 | 0.99 |
| 26_S | 29_W | 1.248 | 0.99 |
| 90_A | 97_W | 1.240 | 0.98 |
| 90_A | 93_S | 1.235 | 0.98 |
| 2_R | 11_I | 1.231 | 0.98 |
| 180_G | 183_R | 1.221 | 0.98 |
| 110_D | 115_S | 1.218 | 0.98 |
| 9_L | 58_Y | 1.189 | 0.98 |
| 24_I | 97_W | 1.187 | 0.98 |
| 187_C | 191_Q | 1.171 | 0.98 |
| 96_A | 100_N | 1.154 | 0.97 |
| 148_V | 156_Q | 1.154 | 0.97 |
| 154_W | 157_M | 1.153 | 0.97 |
| 33_E | 56_K | 1.123 | 0.97 |
| 151_T | 155_V | 1.117 | 0.96 |
| 39_W | 42_R | 1.115 | 0.96 |
| 64_A | 68_G | 1.111 | 0.96 |
| 130_R | 133_T | 1.106 | 0.96 |
| 143_A | 146_N | 1.098 | 0.96 |
| 110_D | 116_R | 1.098 | 0.96 |
| 127_R | 166_L | 1.097 | 0.96 |
| 94_M | 134_R | 1.092 | 0.96 |
| 174_D | 177_C | 1.089 | 0.96 |
| 5_N | 8_S | 1.084 | 0.96 |
| 175_E | 179_R | 1.082 | 0.96 |
| 63_R | 150_Y | 1.079 | 0.95 |
| 63_R | 66_G | 1.065 | 0.95 |
| 30_E | 109_S | 1.059 | 0.95 |
| 127_R | 169_E | 1.055 | 0.95 |
| 156_Q | 159_T | 1.042 | 0.94 |
| 55_E | 59_A | 1.040 | 0.94 |
| 36_F | 40_T | 1.014 | 0.93 |
| 64_A | 69_L | 1.006 | 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 | |
| 3venA | 1 | 0.4241 | 27.9 | 0.937 | Contact Map |
| 3woeB | 2 | 0.2461 | 3.8 | 0.958 | Contact Map |
| 4hrvA | 2 | 0.2461 | 3.5 | 0.959 | Contact Map |
| 4q2lA | 1 | 0.2565 | 3.2 | 0.959 | Contact Map |
| 2yi9A | 5 | 0.7696 | 3 | 0.96 | Contact Map |
| 2lvaA | 1 | 0.1623 | 2.4 | 0.962 | Contact Map |
| 3wofB | 12 | 0.2356 | 2.4 | 0.962 | Contact Map |
| 4mknA | 1 | 0.2513 | 2.3 | 0.962 | Contact Map |
| 3ha4A | 8 | 0.2147 | 2.2 | 0.962 | Contact Map |
| 2v0xA | 2 | 0.466 | 2.2 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)