| 3lfy |
| ID: | 1511347317 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 212 (208) | ||
| Sequences: | 4998 (3544.7) | ||
| Seq/Len: | 24.029 | ||
| Nf(neff/√len): | 245.8 |
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: 24.029).
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 |
| 183_E | 188_R | 4.530 | 1.00 |
| 8_R | 172_L | 2.876 | 1.00 |
| 12_A | 39_K | 2.844 | 1.00 |
| 172_L | 188_R | 2.457 | 1.00 |
| 121_L | 130_V | 2.454 | 1.00 |
| 32_V | 162_A | 2.445 | 1.00 |
| 173_I | 187_I | 2.441 | 1.00 |
| 57_D | 60_S | 2.399 | 1.00 |
| 29_S | 131_S | 2.327 | 1.00 |
| 25_C | 159_H | 2.304 | 1.00 |
| 162_A | 174_K | 2.224 | 1.00 |
| 167_G | 170_Y | 2.114 | 1.00 |
| 22_C | 63_C | 1.916 | 1.00 |
| 69_W | 112_Q | 1.911 | 1.00 |
| 26_W | 71_A | 1.869 | 1.00 |
| 150_V | 190_K | 1.862 | 1.00 |
| 133_V | 160_A | 1.847 | 1.00 |
| 132_V | 161_V | 1.830 | 1.00 |
| 163_A | 173_I | 1.791 | 1.00 |
| 14_T | 174_K | 1.777 | 1.00 |
| 31_V | 80_I | 1.766 | 1.00 |
| 24_S | 88_Y | 1.751 | 1.00 |
| 134_L | 187_I | 1.750 | 1.00 |
| 29_S | 160_A | 1.739 | 1.00 |
| 174_K | 186_Y | 1.714 | 1.00 |
| 164_V | 186_Y | 1.685 | 1.00 |
| 140_D | 149_F | 1.670 | 1.00 |
| 117_N | 120_A | 1.663 | 1.00 |
| 3_E | 168_P | 1.655 | 1.00 |
| 190_K | 193_T | 1.601 | 1.00 |
| 122_L | 191_R | 1.599 | 1.00 |
| 136_A | 158_D | 1.592 | 1.00 |
| 52_E | 74_L | 1.512 | 1.00 |
| 68_P | 160_A | 1.502 | 1.00 |
| 17_K | 50_E | 1.490 | 1.00 |
| 5_V | 166_Y | 1.489 | 1.00 |
| 68_P | 133_V | 1.489 | 1.00 |
| 38_I | 48_Y | 1.486 | 1.00 |
| 51_Q | 55_D | 1.485 | 1.00 |
| 170_Y | 188_R | 1.477 | 1.00 |
| 190_K | 199_V | 1.475 | 1.00 |
| 132_V | 163_A | 1.451 | 1.00 |
| 23_G | 65_G | 1.440 | 1.00 |
| 34_I | 75_V | 1.434 | 1.00 |
| 19_Q | 25_C | 1.350 | 0.99 |
| 72_L | 131_S | 1.346 | 0.99 |
| 161_V | 173_I | 1.335 | 0.99 |
| 26_W | 53_L | 1.331 | 0.99 |
| 1_I | 122_L | 1.321 | 0.99 |
| 24_S | 54_L | 1.321 | 0.99 |
| 4_Y | 9_Q | 1.295 | 0.99 |
| 16_V | 174_K | 1.273 | 0.99 |
| 182_G | 185_G | 1.271 | 0.99 |
| 119_G | 122_L | 1.268 | 0.99 |
| 89_E | 96_R | 1.266 | 0.99 |
| 37_I | 128_Q | 1.263 | 0.99 |
| 168_P | 191_R | 1.251 | 0.99 |
| 32_V | 35_E | 1.251 | 0.99 |
| 134_L | 161_V | 1.248 | 0.99 |
| 55_D | 86_Y | 1.246 | 0.98 |
| 81_H | 85_T | 1.233 | 0.98 |
| 134_L | 141_F | 1.225 | 0.98 |
| 120_A | 123_Y | 1.222 | 0.98 |
| 167_G | 191_R | 1.221 | 0.98 |
| 132_V | 202_L | 1.217 | 0.98 |
| 52_E | 81_H | 1.212 | 0.98 |
| 18_N | 178_G | 1.210 | 0.98 |
| 121_L | 124_S | 1.209 | 0.98 |
| 179_T | 184_N | 1.205 | 0.98 |
| 47_E | 50_E | 1.196 | 0.98 |
| 5_V | 126_A | 1.194 | 0.98 |
| 38_I | 105_A | 1.193 | 0.98 |
| 33_T | 162_A | 1.193 | 0.98 |
| 56_C | 95_C | 1.190 | 0.98 |
| 173_I | 202_L | 1.188 | 0.98 |
| 17_K | 28_F | 1.188 | 0.98 |
| 16_V | 19_Q | 1.160 | 0.97 |
| 12_A | 40_I | 1.156 | 0.97 |
| 31_V | 53_L | 1.147 | 0.97 |
| 17_K | 47_E | 1.142 | 0.97 |
| 28_F | 50_E | 1.142 | 0.97 |
| 13_V | 36_G | 1.140 | 0.97 |
| 73_Q | 77_Q | 1.139 | 0.97 |
| 163_A | 171_I | 1.138 | 0.97 |
| 51_Q | 89_E | 1.133 | 0.97 |
| 164_V | 172_L | 1.128 | 0.97 |
| 198_G | 203_Y | 1.122 | 0.97 |
| 22_C | 88_Y | 1.115 | 0.96 |
| 67_Y | 70_S | 1.114 | 0.96 |
| 198_G | 204_T | 1.114 | 0.96 |
| 82_Y | 85_T | 1.114 | 0.96 |
| 193_T | 199_V | 1.110 | 0.96 |
| 141_F | 187_I | 1.094 | 0.96 |
| 125_I | 163_A | 1.088 | 0.96 |
| 68_P | 131_S | 1.087 | 0.96 |
| 15_P | 47_E | 1.085 | 0.96 |
| 118_E | 122_L | 1.072 | 0.95 |
| 7_W | 13_V | 1.068 | 0.95 |
| 28_F | 88_Y | 1.066 | 0.95 |
| 125_I | 130_V | 1.065 | 0.95 |
| 30_A | 131_S | 1.060 | 0.95 |
| 159_H | 175_N | 1.056 | 0.95 |
| 28_F | 32_V | 1.053 | 0.95 |
| 70_S | 73_Q | 1.046 | 0.94 |
| 14_T | 17_K | 1.040 | 0.94 |
| 37_I | 41_R | 1.036 | 0.94 |
| 144_Y | 147_G | 1.028 | 0.94 |
| 159_H | 176_S | 1.023 | 0.93 |
| 38_I | 42_T | 1.022 | 0.93 |
| 169_N | 191_R | 1.018 | 0.93 |
| 37_I | 40_I | 1.015 | 0.93 |
| 19_Q | 159_H | 1.014 | 0.93 |
| 24_S | 28_F | 1.012 | 0.93 |
| 53_L | 71_A | 1.007 | 0.93 |
| 2_P | 126_A | 1.001 | 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 | |
| 4qrgA | 2 | 0 | 100 | -0.036 | Contact Map |
| 1pciA | 3 | 0.9953 | 100 | -0.024 | Contact Map |
| 2cioA | 1 | 0.9906 | 100 | -0.014 | Contact Map |
| 2bdzA | 4 | 0.9953 | 100 | -0.013 | Contact Map |
| 3ioqA | 1 | 0.9953 | 100 | -0.005 | Contact Map |
| 1yalA | 1 | 0.9858 | 100 | -0.004 | Contact Map |
| 1ppoA | 1 | 0.9953 | 100 | -0.001 | Contact Map |
| 2fo5A | 4 | 1 | 100 | 0 | Contact Map |
| 2o6xA | 1 | 0.9764 | 100 | 0 | Contact Map |
| 2c0yA | 1 | 0.9764 | 100 | 0.002 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)