| bioD |
| ID: | 1465559624 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 228 (213) | ||
| Sequences: | 16877 (9370.3) | ||
| Seq/Len: | 79.235 | ||
| Nf(neff/√len): | 642.0 |
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: 79.235).
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 |
| 20_A | 115_L | 4.238 | 1.00 |
| 27_A | 113_F | 3.746 | 1.00 |
| 32_L | 113_F | 3.189 | 1.00 |
| 35_A | 111_A | 3.045 | 1.00 |
| 3_P | 142_P | 2.869 | 1.00 |
| 178_I | 207_K | 2.803 | 1.00 |
| 33_S | 112_D | 2.506 | 1.00 |
| 19_I | 175_V | 2.430 | 1.00 |
| 7_I | 23_L | 2.387 | 1.00 |
| 6_F | 140_D | 2.285 | 1.00 |
| 24_L | 115_L | 2.276 | 1.00 |
| 191_A | 195_E | 2.225 | 1.00 |
| 75_V | 111_A | 2.126 | 1.00 |
| 20_A | 36_A | 2.066 | 1.00 |
| 201_C | 204_R | 2.019 | 1.00 |
| 27_A | 115_L | 1.964 | 1.00 |
| 4_A | 141_L | 1.943 | 1.00 |
| 142_P | 173_G | 1.937 | 1.00 |
| 148_G | 178_I | 1.885 | 1.00 |
| 24_L | 36_A | 1.884 | 1.00 |
| 17_T | 48_A | 1.867 | 1.00 |
| 192_T | 195_E | 1.854 | 1.00 |
| 26_A | 30_A | 1.836 | 1.00 |
| 6_F | 118_G | 1.805 | 1.00 |
| 192_T | 196_R | 1.753 | 1.00 |
| 147_V | 157_A | 1.751 | 1.00 |
| 143_V | 164_I | 1.750 | 1.00 |
| 21_A | 45_E | 1.722 | 1.00 |
| 19_I | 146_V | 1.721 | 1.00 |
| 191_A | 204_R | 1.703 | 1.00 |
| 7_I | 144_I | 1.702 | 1.00 |
| 147_V | 153_C | 1.702 | 1.00 |
| 71_E | 105_S | 1.633 | 1.00 |
| 11_D | 14_V | 1.627 | 1.00 |
| 162_E | 165_A | 1.592 | 1.00 |
| 21_A | 49_E | 1.580 | 1.00 |
| 22_G | 25_Y | 1.566 | 1.00 |
| 88_R | 128_G | 1.565 | 1.00 |
| 188_E | 191_A | 1.560 | 1.00 |
| 179_I | 204_R | 1.555 | 1.00 |
| 173_G | 202_L | 1.554 | 1.00 |
| 158_L | 196_R | 1.554 | 1.00 |
| 101_E | 105_S | 1.553 | 1.00 |
| 4_A | 103_M | 1.544 | 1.00 |
| 15_G | 177_N | 1.520 | 1.00 |
| 146_V | 177_N | 1.517 | 1.00 |
| 98_S | 101_E | 1.516 | 1.00 |
| 25_Y | 29_E | 1.511 | 1.00 |
| 4_A | 116_I | 1.497 | 1.00 |
| 36_A | 45_E | 1.489 | 1.00 |
| 142_P | 172_A | 1.452 | 1.00 |
| 19_I | 177_N | 1.443 | 1.00 |
| 24_L | 34_T | 1.433 | 1.00 |
| 140_D | 170_Q | 1.408 | 1.00 |
| 33_S | 111_A | 1.404 | 0.99 |
| 145_L | 160_T | 1.391 | 0.99 |
| 100_L | 104_R | 1.387 | 0.99 |
| 35_A | 114_T | 1.374 | 0.99 |
| 39_P | 116_I | 1.349 | 0.99 |
| 144_I | 202_L | 1.348 | 0.99 |
| 190_L | 194_A | 1.348 | 0.99 |
| 5_Y | 113_F | 1.340 | 0.99 |
| 187_E | 191_A | 1.287 | 0.99 |
| 32_L | 112_D | 1.276 | 0.99 |
| 193_L | 197_L | 1.270 | 0.99 |
| 162_E | 166_R | 1.269 | 0.99 |
| 95_T | 98_S | 1.258 | 0.99 |
| 26_A | 29_E | 1.248 | 0.99 |
| 48_A | 152_G | 1.242 | 0.98 |
| 194_A | 201_C | 1.229 | 0.98 |
| 100_L | 138_A | 1.220 | 0.98 |
| 161_A | 199_A | 1.217 | 0.98 |
| 3_P | 141_L | 1.198 | 0.98 |
| 161_A | 165_A | 1.195 | 0.98 |
| 135_L | 139_L | 1.193 | 0.98 |
| 158_L | 162_E | 1.173 | 0.98 |
| 27_A | 34_T | 1.164 | 0.97 |
| 19_I | 205_V | 1.162 | 0.97 |
| 7_I | 20_A | 1.151 | 0.97 |
| 21_A | 48_A | 1.144 | 0.97 |
| 149_V | 176_A | 1.143 | 0.97 |
| 194_A | 200_P | 1.140 | 0.97 |
| 11_D | 156_H | 1.135 | 0.97 |
| 161_A | 171_L | 1.134 | 0.97 |
| 79_P | 89_E | 1.131 | 0.97 |
| 47_T | 155_S | 1.125 | 0.97 |
| 111_A | 114_T | 1.118 | 0.96 |
| 102_P | 105_S | 1.116 | 0.96 |
| 22_G | 26_A | 1.113 | 0.96 |
| 37_G | 114_T | 1.111 | 0.96 |
| 144_I | 175_V | 1.106 | 0.96 |
| 145_L | 161_A | 1.096 | 0.96 |
| 9_G | 14_V | 1.094 | 0.96 |
| 148_G | 153_C | 1.090 | 0.96 |
| 184_S | 187_E | 1.082 | 0.96 |
| 37_G | 103_M | 1.079 | 0.95 |
| 188_E | 192_T | 1.076 | 0.95 |
| 173_G | 200_P | 1.065 | 0.95 |
| 161_A | 174_W | 1.058 | 0.95 |
| 6_F | 136_A | 1.058 | 0.95 |
| 190_L | 204_R | 1.057 | 0.95 |
| 173_G | 203_G | 1.053 | 0.95 |
| 34_T | 113_F | 1.046 | 0.94 |
| 18_T | 211_A | 1.039 | 0.94 |
| 191_A | 194_A | 1.039 | 0.94 |
| 5_Y | 172_A | 1.034 | 0.94 |
| 37_G | 102_P | 1.030 | 0.94 |
| 78_E | 90_A | 1.030 | 0.94 |
| 44_C | 76_A | 1.027 | 0.94 |
| 3_P | 113_F | 1.021 | 0.93 |
| 28_R | 34_T | 1.012 | 0.93 |
| 176_A | 179_I | 1.004 | 0.93 |
| 158_L | 197_L | 1.002 | 0.92 |
| 8_T | 143_V | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1byiA | 1 | 0.9781 | 100 | 0.255 | Contact Map |
| 3of5A | 2 | 0.9605 | 100 | 0.266 | Contact Map |
| 3fgnA | 4 | 0.9518 | 100 | 0.304 | Contact Map |
| 4v03A | 2 | 0.8816 | 100 | 0.326 | Contact Map |
| 1g3qA | 1 | 0.9298 | 99.9 | 0.331 | Contact Map |
| 1hyqA | 1 | 0.9123 | 99.9 | 0.338 | Contact Map |
| 3q9lA | 2 | 0.9211 | 99.9 | 0.342 | Contact Map |
| 3qxcA | 1 | 0.9342 | 99.9 | 0.358 | Contact Map |
| 4pfsA | 2 | 0.8904 | 99.9 | 0.36 | Contact Map |
| 3ea0A | 2 | 0.9123 | 99.9 | 0.361 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)