| 1LM7_A |
| ID: | 1400293700 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 248 (244) | ||
| Sequences: | 854 (421.5) | ||
| Seq/Len: | 3.500 | ||
| Nf(neff/√len): | 27.0 |
Jackhmmer Results: (2014_04_16)
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: 3.500).
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 |
| 62_Q | 72_I | 2.616 | 1.00 |
| 108_Y | 113_V | 1.966 | 1.00 |
| 100_L | 110_R | 1.959 | 1.00 |
| 67_Y | 114_G | 1.875 | 1.00 |
| 214_E | 224_R | 1.824 | 0.99 |
| 2_F | 11_V | 1.821 | 0.99 |
| 21_R | 24_T | 1.776 | 0.99 |
| 70_M | 80_A | 1.758 | 0.99 |
| 17_S | 21_R | 1.716 | 0.99 |
| 88_A | 124_A | 1.710 | 0.99 |
| 36_D | 40_E | 1.703 | 0.99 |
| 78_G | 208_F | 1.701 | 0.99 |
| 22_P | 26_N | 1.663 | 0.99 |
| 13_E | 17_S | 1.627 | 0.98 |
| 190_N | 197_L | 1.612 | 0.98 |
| 227_K | 234_C | 1.593 | 0.98 |
| 105_E | 118_K | 1.562 | 0.98 |
| 15_V | 25_V | 1.550 | 0.98 |
| 133_D | 148_K | 1.527 | 0.97 |
| 2_F | 38_V | 1.492 | 0.97 |
| 10_T | 16_D | 1.481 | 0.96 |
| 199_D | 205_K | 1.460 | 0.96 |
| 225_C | 237_P | 1.458 | 0.96 |
| 19_I | 42_I | 1.443 | 0.96 |
| 130_G | 168_G | 1.409 | 0.95 |
| 10_T | 13_E | 1.380 | 0.94 |
| 15_V | 26_N | 1.375 | 0.94 |
| 166_T | 177_R | 1.370 | 0.94 |
| 15_V | 19_I | 1.369 | 0.94 |
| 2_F | 35_Y | 1.367 | 0.94 |
| 7_Q | 10_T | 1.339 | 0.93 |
| 184_Y | 194_S | 1.336 | 0.93 |
| 189_F | 194_S | 1.332 | 0.93 |
| 5_I | 10_T | 1.329 | 0.93 |
| 13_E | 16_D | 1.320 | 0.92 |
| 33_I | 37_E | 1.306 | 0.92 |
| 12_T | 16_D | 1.291 | 0.91 |
| 189_F | 215_N | 1.290 | 0.91 |
| 222_K | 226_I | 1.283 | 0.91 |
| 157_I | 196_I | 1.282 | 0.91 |
| 2_F | 28_L | 1.272 | 0.90 |
| 60_T | 79_T | 1.266 | 0.90 |
| 115_I | 118_K | 1.259 | 0.90 |
| 203_D | 206_G | 1.256 | 0.89 |
| 171_D | 218_Y | 1.253 | 0.89 |
| 109_K | 115_I | 1.249 | 0.89 |
| 93_I | 138_N | 1.237 | 0.89 |
| 86_A | 168_G | 1.234 | 0.88 |
| 4_G | 9_V | 1.205 | 0.87 |
| 152_E | 155_H | 1.198 | 0.86 |
| 26_N | 29_E | 1.197 | 0.86 |
| 3_Q | 47_Q | 1.186 | 0.86 |
| 66_I | 217_T | 1.183 | 0.85 |
| 25_V | 39_G | 1.182 | 0.85 |
| 125_E | 150_L | 1.181 | 0.85 |
| 52_I | 225_C | 1.179 | 0.85 |
| 11_V | 25_V | 1.178 | 0.85 |
| 147_N | 190_N | 1.177 | 0.85 |
| 17_S | 20_L | 1.177 | 0.85 |
| 11_V | 33_I | 1.175 | 0.85 |
| 146_M | 156_G | 1.174 | 0.85 |
| 25_V | 115_I | 1.173 | 0.85 |
| 95_D | 130_G | 1.170 | 0.84 |
| 38_V | 106_E | 1.169 | 0.84 |
| 5_I | 18_G | 1.167 | 0.84 |
| 20_L | 42_I | 1.167 | 0.84 |
| 141_S | 188_Y | 1.154 | 0.83 |
| 153_K | 157_I | 1.153 | 0.83 |
| 105_E | 151_I | 1.152 | 0.83 |
| 108_Y | 118_K | 1.152 | 0.83 |
| 41_R | 44_D | 1.137 | 0.82 |
| 60_T | 235_L | 1.134 | 0.82 |
| 98_S | 231_T | 1.132 | 0.82 |
| 131_Y | 159_L | 1.131 | 0.82 |
| 7_Q | 12_T | 1.131 | 0.82 |
| 209_D | 224_R | 1.123 | 0.81 |
| 23_S | 27_E | 1.114 | 0.80 |
| 24_T | 38_V | 1.114 | 0.80 |
| 108_Y | 116_E | 1.114 | 0.80 |
| 189_F | 219_L | 1.110 | 0.80 |
| 4_G | 156_G | 1.107 | 0.80 |
| 184_Y | 189_F | 1.105 | 0.80 |
| 104_V | 107_A | 1.103 | 0.79 |
| 66_I | 83_L | 1.098 | 0.79 |
| 234_C | 237_P | 1.098 | 0.79 |
| 182_I | 186_R | 1.098 | 0.79 |
| 15_V | 42_I | 1.090 | 0.78 |
| 53_A | 224_R | 1.081 | 0.77 |
| 96_P | 156_G | 1.076 | 0.77 |
| 15_V | 27_E | 1.075 | 0.77 |
| 222_K | 234_C | 1.071 | 0.77 |
| 204_T | 215_N | 1.068 | 0.76 |
| 8_P | 18_G | 1.067 | 0.76 |
| 85_E | 158_R | 1.066 | 0.76 |
| 113_V | 116_E | 1.065 | 0.76 |
| 12_T | 29_E | 1.064 | 0.76 |
| 163_Q | 171_D | 1.059 | 0.75 |
| 104_V | 134_P | 1.058 | 0.75 |
| 208_F | 217_T | 1.057 | 0.75 |
| 7_Q | 18_G | 1.055 | 0.75 |
| 94_V | 97_V | 1.051 | 0.75 |
| 65_G | 112_L | 1.051 | 0.75 |
| 13_E | 26_N | 1.051 | 0.75 |
| 18_G | 185_K | 1.047 | 0.74 |
| 86_A | 89_A | 1.041 | 0.74 |
| 124_A | 218_Y | 1.038 | 0.73 |
| 67_Y | 214_E | 1.036 | 0.73 |
| 56_Y | 61_K | 1.035 | 0.73 |
| 156_G | 197_L | 1.035 | 0.73 |
| 19_I | 45_F | 1.035 | 0.73 |
| 85_E | 127_A | 1.034 | 0.73 |
| 145_A | 167_G | 1.033 | 0.73 |
| 35_Y | 39_G | 1.032 | 0.73 |
| 21_R | 29_E | 1.030 | 0.72 |
| 7_Q | 35_Y | 1.029 | 0.72 |
| 8_P | 25_V | 1.027 | 0.72 |
| 8_P | 15_V | 1.026 | 0.72 |
| 204_T | 216_L | 1.025 | 0.72 |
| 222_K | 235_L | 1.024 | 0.72 |
| 133_D | 136_T | 1.023 | 0.72 |
| 87_Q | 91_G | 1.022 | 0.72 |
| 68_E | 71_K | 1.022 | 0.72 |
| 11_V | 35_Y | 1.018 | 0.71 |
| 100_L | 113_V | 1.018 | 0.71 |
| 16_D | 24_T | 1.017 | 0.71 |
| 3_Q | 8_P | 1.012 | 0.71 |
| 30_S | 37_E | 1.010 | 0.70 |
| 76_R | 79_T | 1.007 | 0.70 |
| 60_T | 177_R | 1.007 | 0.70 |
| 4_G | 14_L | 1.006 | 0.70 |
| 91_G | 163_Q | 1.005 | 0.70 |
| 165_A | 221_L | 1.005 | 0.70 |
| 28_L | 38_V | 1.003 | 0.70 |
| 89_A | 171_D | 1.001 | 0.69 |
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 | |
| 1lm7A | 2 | 0.9597 | 100 | 0.136 | Contact Map |
| 1lm5A | 2 | 0.7903 | 100 | 0.286 | Contact Map |
| 3ne8A | 1 | 0.2419 | 11 | 0.968 | Contact Map |
| 4binA | 1 | 0.2056 | 10.8 | 0.968 | Contact Map |
| 3vz6A | 1 | 0.2661 | 8.8 | 0.969 | Contact Map |
| 4je3B | 1 | 0.1895 | 8.5 | 0.969 | Contact Map |
| 3f3fC | 4 | 0.0726 | 6.3 | 0.971 | Contact Map |
| 3p8cE | 1 | 0.2581 | 6.2 | 0.971 | Contact Map |
| 1srvA | 1 | 0.2621 | 6.1 | 0.971 | Contact Map |
| 3bbzA | 2 | 0.1452 | 6.1 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)