| amanuelkibrom |
| ID: | 1455912937 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 271 (271) | ||
| Sequences: | 2685 (1690.2) | ||
| Seq/Len: | 9.908 | ||
| Nf(neff/√len): | 102.7 |
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: 9.908).
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 |
| 36_L | 68_F | 3.626 | 1.00 |
| 43_I | 61_K | 3.199 | 1.00 |
| 69_L | 97_F | 2.441 | 1.00 |
| 160_W | 171_F | 2.441 | 1.00 |
| 143_G | 147_A | 2.272 | 1.00 |
| 66_N | 135_Y | 2.173 | 1.00 |
| 255_V | 259_V | 2.172 | 1.00 |
| 144_I | 148_I | 2.110 | 1.00 |
| 113_Y | 118_E | 2.103 | 1.00 |
| 95_H | 99_L | 2.077 | 1.00 |
| 43_I | 68_F | 2.065 | 1.00 |
| 31_G | 251_A | 2.007 | 1.00 |
| 1_H | 5_F | 1.970 | 1.00 |
| 96_Y | 100_A | 1.953 | 1.00 |
| 262_C | 268_V | 1.924 | 1.00 |
| 169_W | 173_G | 1.902 | 1.00 |
| 106_C | 110_V | 1.891 | 1.00 |
| 85_V | 89_I | 1.890 | 1.00 |
| 38_C | 255_V | 1.827 | 1.00 |
| 184_V | 188_V | 1.788 | 1.00 |
| 107_L | 134_G | 1.716 | 1.00 |
| 87_C | 159_C | 1.716 | 1.00 |
| 5_F | 8_L | 1.660 | 1.00 |
| 34_I | 38_C | 1.643 | 1.00 |
| 134_G | 138_P | 1.632 | 1.00 |
| 2_L | 5_F | 1.628 | 1.00 |
| 231_G | 246_F | 1.597 | 1.00 |
| 113_Y | 188_V | 1.550 | 1.00 |
| 60_H | 108_E | 1.549 | 1.00 |
| 106_C | 133_G | 1.548 | 1.00 |
| 92_G | 142_V | 1.548 | 1.00 |
| 43_I | 64_C | 1.531 | 1.00 |
| 254_G | 257_I | 1.521 | 1.00 |
| 104_W | 134_G | 1.521 | 1.00 |
| 54_T | 57_N | 1.518 | 1.00 |
| 245_L | 249_F | 1.517 | 1.00 |
| 189_T | 193_M | 1.514 | 1.00 |
| 103_S | 134_G | 1.507 | 1.00 |
| 38_C | 258_F | 1.492 | 1.00 |
| 3_T | 6_A | 1.479 | 1.00 |
| 1_H | 6_A | 1.477 | 1.00 |
| 66_N | 100_A | 1.475 | 1.00 |
| 6_A | 9_M | 1.472 | 1.00 |
| 106_C | 181_V | 1.463 | 1.00 |
| 70_A | 98_F | 1.457 | 1.00 |
| 189_T | 192_K | 1.428 | 1.00 |
| 254_G | 258_F | 1.424 | 1.00 |
| 10_A | 13_E | 1.422 | 1.00 |
| 171_F | 175_V | 1.418 | 1.00 |
| 74_F | 78_I | 1.391 | 0.99 |
| 104_W | 135_Y | 1.378 | 0.99 |
| 92_G | 146_A | 1.367 | 0.99 |
| 31_G | 35_S | 1.364 | 0.99 |
| 188_V | 191_H | 1.363 | 0.99 |
| 250_N | 253_Q | 1.338 | 0.99 |
| 99_L | 141_V | 1.337 | 0.99 |
| 29_W | 33_V | 1.334 | 0.99 |
| 228_W | 250_N | 1.332 | 0.99 |
| 39_L | 67_L | 1.310 | 0.99 |
| 110_V | 185_F | 1.297 | 0.99 |
| 26_V | 30_V | 1.289 | 0.99 |
| 231_G | 247_T | 1.286 | 0.99 |
| 95_H | 142_V | 1.282 | 0.99 |
| 100_A | 104_W | 1.281 | 0.99 |
| 56_R | 60_H | 1.278 | 0.99 |
| 138_P | 142_V | 1.269 | 0.99 |
| 74_F | 77_G | 1.260 | 0.99 |
| 131_Y | 135_Y | 1.249 | 0.98 |
| 95_H | 153_Y | 1.247 | 0.98 |
| 109_G | 224_L | 1.246 | 0.98 |
| 258_F | 263_A | 1.240 | 0.98 |
| 182_N | 225_G | 1.239 | 0.98 |
| 220_L | 225_G | 1.226 | 0.98 |
| 185_F | 189_T | 1.224 | 0.98 |
| 70_A | 171_F | 1.223 | 0.98 |
| 16_Q | 19_I | 1.221 | 0.98 |
| 215_L | 219_A | 1.216 | 0.98 |
| 3_T | 8_L | 1.210 | 0.98 |
| 227_T | 231_G | 1.209 | 0.98 |
| 62_N | 131_Y | 1.206 | 0.98 |
| 259_V | 264_L | 1.202 | 0.98 |
| 91_A | 154_G | 1.191 | 0.98 |
| 44_S | 48_F | 1.187 | 0.98 |
| 86_A | 89_I | 1.186 | 0.98 |
| 182_N | 253_Q | 1.184 | 0.98 |
| 252_F | 255_V | 1.176 | 0.98 |
| 67_L | 70_A | 1.168 | 0.97 |
| 42_C | 258_F | 1.162 | 0.97 |
| 225_G | 253_Q | 1.160 | 0.97 |
| 182_N | 186_L | 1.159 | 0.97 |
| 105_L | 182_N | 1.149 | 0.97 |
| 46_F | 61_K | 1.140 | 0.97 |
| 104_W | 136_C | 1.137 | 0.97 |
| 188_V | 192_K | 1.135 | 0.97 |
| 175_V | 179_I | 1.126 | 0.97 |
| 85_V | 88_P | 1.118 | 0.96 |
| 12_R | 15_Y | 1.113 | 0.96 |
| 176_S | 232_L | 1.111 | 0.96 |
| 228_W | 231_G | 1.109 | 0.96 |
| 191_H | 195_R | 1.092 | 0.96 |
| 105_L | 108_E | 1.091 | 0.96 |
| 33_V | 37_V | 1.091 | 0.96 |
| 171_F | 174_P | 1.085 | 0.96 |
| 109_G | 182_N | 1.082 | 0.95 |
| 100_A | 135_Y | 1.075 | 0.95 |
| 159_C | 174_P | 1.070 | 0.95 |
| 192_K | 199_V | 1.066 | 0.95 |
| 60_H | 220_L | 1.065 | 0.95 |
| 103_S | 107_L | 1.065 | 0.95 |
| 17_G | 20_N | 1.060 | 0.95 |
| 31_G | 39_L | 1.057 | 0.95 |
| 266_K | 270_K | 1.057 | 0.95 |
| 106_C | 178_V | 1.056 | 0.95 |
| 225_G | 230_F | 1.055 | 0.95 |
| 40_A | 68_F | 1.054 | 0.95 |
| 73_L | 140_L | 1.050 | 0.94 |
| 259_V | 263_A | 1.050 | 0.94 |
| 216_G | 219_A | 1.050 | 0.94 |
| 27_I | 247_T | 1.049 | 0.94 |
| 215_L | 220_L | 1.044 | 0.94 |
| 53_Q | 58_T | 1.044 | 0.94 |
| 241_V | 245_L | 1.038 | 0.94 |
| 105_L | 109_G | 1.038 | 0.94 |
| 49_L | 52_L | 1.035 | 0.94 |
| 42_C | 46_F | 1.032 | 0.94 |
| 186_L | 213_W | 1.025 | 0.93 |
| 96_Y | 142_V | 1.024 | 0.93 |
| 16_Q | 20_N | 1.023 | 0.93 |
| 42_C | 64_C | 1.020 | 0.93 |
| 257_I | 267_K | 1.019 | 0.93 |
| 103_S | 106_C | 1.012 | 0.93 |
| 109_G | 112_L | 1.011 | 0.93 |
| 30_V | 34_I | 1.010 | 0.93 |
| 1_H | 8_L | 1.010 | 0.93 |
| 96_Y | 135_Y | 1.007 | 0.93 |
| 225_G | 257_I | 1.001 | 0.92 |
| 230_F | 242_M | 1.000 | 0.92 |
| 93_L | 97_F | 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 | |
| 4k5yA | 3 | 0.8967 | 100 | 0.228 | Contact Map |
| 4l6rA | 1 | 0.952 | 100 | 0.345 | Contact Map |
| 4jkvA | 2 | 0.9336 | 99.9 | 0.489 | Contact Map |
| 4qinA | 1 | 0.941 | 99.9 | 0.503 | Contact Map |
| 4zwjA | 4 | 0 | 99.6 | 0.674 | Contact Map |
| 4ldeA | 1 | 0.9742 | 99.5 | 0.695 | Contact Map |
| 2z73A | 2 | 1 | 99.5 | 0.701 | Contact Map |
| 4xnvA | 1 | 0.952 | 99.4 | 0.705 | Contact Map |
| 4n6hA | 1 | 0.9963 | 99.4 | 0.713 | Contact Map |
| 3pblA | 2 | 0.9114 | 99.4 | 0.713 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)