| gtrb |
| ID: | 1442505859 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 318 (305) | ||
| Sequences: | 4611 (3337.6) | ||
| Seq/Len: | 15.118 | ||
| Nf(neff/√len): | 191.1 |
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: 15.118).
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 |
| 42_N | 67_N | 5.138 | 1.00 |
| 15_E | 48_K | 4.574 | 1.00 |
| 115_Y | 191_T | 3.864 | 1.00 |
| 53_L | 65_I | 3.761 | 1.00 |
| 48_K | 51_K | 3.350 | 1.00 |
| 54_I | 305_D | 3.196 | 1.00 |
| 24_R | 102_E | 2.933 | 1.00 |
| 110_K | 191_T | 2.914 | 1.00 |
| 163_R | 167_N | 2.837 | 1.00 |
| 123_R | 196_D | 2.824 | 1.00 |
| 22_F | 56_C | 2.661 | 1.00 |
| 50_L | 65_I | 2.597 | 1.00 |
| 6_S | 37_E | 2.572 | 1.00 |
| 11_M | 49_T | 2.567 | 1.00 |
| 242_S | 272_F | 2.468 | 1.00 |
| 50_L | 67_N | 2.413 | 1.00 |
| 110_K | 113_E | 2.395 | 1.00 |
| 106_E | 109_D | 2.382 | 1.00 |
| 121_T | 194_L | 2.335 | 1.00 |
| 6_S | 87_G | 2.310 | 1.00 |
| 22_F | 40_C | 2.307 | 1.00 |
| 20_H | 23_A | 2.281 | 1.00 |
| 19_E | 52_Q | 2.257 | 1.00 |
| 91_I | 104_I | 2.252 | 1.00 |
| 67_N | 304_S | 2.196 | 1.00 |
| 52_Q | 55_D | 2.122 | 1.00 |
| 89_A | 111_W | 2.119 | 1.00 |
| 99_D | 197_R | 2.091 | 1.00 |
| 235_G | 275_G | 2.090 | 1.00 |
| 116_D | 162_D | 2.075 | 1.00 |
| 90_V | 166_V | 2.059 | 1.00 |
| 40_C | 53_L | 2.055 | 1.00 |
| 4_E | 88_N | 2.042 | 1.00 |
| 9_I | 21_L | 2.032 | 1.00 |
| 288_L | 291_V | 2.019 | 1.00 |
| 168_A | 188_Y | 2.004 | 1.00 |
| 24_R | 198_E | 1.978 | 1.00 |
| 111_W | 162_D | 1.961 | 1.00 |
| 110_K | 114_G | 1.934 | 1.00 |
| 68_L | 80_A | 1.933 | 1.00 |
| 6_S | 39_I | 1.932 | 1.00 |
| 20_H | 24_R | 1.858 | 1.00 |
| 20_H | 201_F | 1.844 | 1.00 |
| 22_F | 63_I | 1.821 | 1.00 |
| 19_E | 55_D | 1.813 | 1.00 |
| 123_R | 194_L | 1.773 | 1.00 |
| 19_E | 23_A | 1.722 | 1.00 |
| 13_N | 46_K | 1.717 | 1.00 |
| 48_K | 52_Q | 1.708 | 1.00 |
| 66_V | 303_V | 1.705 | 1.00 |
| 229_K | 286_E | 1.684 | 1.00 |
| 111_W | 160_L | 1.674 | 1.00 |
| 23_A | 27_E | 1.657 | 1.00 |
| 89_A | 160_L | 1.653 | 1.00 |
| 37_E | 87_G | 1.637 | 1.00 |
| 9_I | 95_A | 1.620 | 1.00 |
| 107_L | 120_A | 1.592 | 1.00 |
| 4_E | 35_T | 1.565 | 1.00 |
| 130_W | 134_F | 1.542 | 1.00 |
| 8_V | 90_V | 1.529 | 1.00 |
| 281_L | 284_I | 1.517 | 1.00 |
| 64_K | 306_L | 1.512 | 1.00 |
| 83_D | 170_K | 1.511 | 1.00 |
| 83_D | 301_Y | 1.492 | 1.00 |
| 110_K | 115_Y | 1.468 | 1.00 |
| 141_K | 145_R | 1.458 | 1.00 |
| 103_L | 106_E | 1.448 | 1.00 |
| 28_V | 105_H | 1.440 | 1.00 |
| 250_I | 268_V | 1.438 | 1.00 |
| 18_L | 52_Q | 1.430 | 1.00 |
| 17_N | 201_F | 1.426 | 1.00 |
| 239_S | 275_G | 1.415 | 1.00 |
| 51_K | 55_D | 1.413 | 1.00 |
| 231_W | 280_S | 1.399 | 0.99 |
| 116_D | 164_K | 1.391 | 0.99 |
| 22_F | 60_N | 1.389 | 0.99 |
| 246_A | 268_V | 1.381 | 0.99 |
| 67_N | 305_D | 1.369 | 0.99 |
| 91_I | 160_L | 1.366 | 0.99 |
| 84_Y | 306_L | 1.333 | 0.99 |
| 7_I | 29_L | 1.330 | 0.99 |
| 36_Y | 62_Q | 1.320 | 0.99 |
| 249_L | 264_A | 1.308 | 0.99 |
| 124_S | 196_D | 1.303 | 0.99 |
| 89_A | 108_V | 1.303 | 0.99 |
| 119_Y | 192_F | 1.299 | 0.99 |
| 74_K | 207_W | 1.294 | 0.99 |
| 29_L | 36_Y | 1.280 | 0.99 |
| 52_Q | 56_C | 1.277 | 0.99 |
| 12_Y | 46_K | 1.269 | 0.99 |
| 9_I | 93_I | 1.268 | 0.99 |
| 162_D | 165_V | 1.265 | 0.99 |
| 12_Y | 71_N | 1.265 | 0.99 |
| 175_R | 297_A | 1.257 | 0.99 |
| 144_G | 150_K | 1.254 | 0.99 |
| 5_L | 34_I | 1.252 | 0.99 |
| 134_F | 138_M | 1.252 | 0.99 |
| 117_I | 165_V | 1.251 | 0.99 |
| 169_I | 182_L | 1.248 | 0.99 |
| 291_V | 295_V | 1.248 | 0.99 |
| 168_A | 302_L | 1.240 | 0.98 |
| 24_R | 101_P | 1.240 | 0.98 |
| 93_I | 101_P | 1.240 | 0.98 |
| 3_I | 88_N | 1.237 | 0.98 |
| 200_R | 203_G | 1.231 | 0.98 |
| 66_V | 306_L | 1.221 | 0.98 |
| 11_M | 95_A | 1.219 | 0.98 |
| 161_M | 166_V | 1.217 | 0.98 |
| 247_S | 251_L | 1.205 | 0.98 |
| 66_V | 84_Y | 1.197 | 0.98 |
| 24_R | 27_E | 1.193 | 0.98 |
| 82_I | 92_P | 1.193 | 0.98 |
| 78_L | 92_P | 1.189 | 0.98 |
| 168_A | 171_Q | 1.181 | 0.98 |
| 11_M | 40_C | 1.172 | 0.98 |
| 8_V | 81_G | 1.172 | 0.98 |
| 7_I | 104_I | 1.158 | 0.97 |
| 76_I | 300_L | 1.137 | 0.97 |
| 189_R | 304_S | 1.128 | 0.97 |
| 42_N | 50_L | 1.125 | 0.97 |
| 235_G | 279_I | 1.120 | 0.96 |
| 253_T | 264_A | 1.115 | 0.96 |
| 273_L | 277_Q | 1.113 | 0.96 |
| 173_P | 297_A | 1.112 | 0.96 |
| 22_F | 26_L | 1.106 | 0.96 |
| 79_S | 300_L | 1.105 | 0.96 |
| 119_Y | 190_Q | 1.103 | 0.96 |
| 38_I | 63_I | 1.100 | 0.96 |
| 109_D | 113_E | 1.100 | 0.96 |
| 115_Y | 189_R | 1.098 | 0.96 |
| 40_C | 63_I | 1.095 | 0.96 |
| 240_L | 244_A | 1.094 | 0.96 |
| 21_L | 25_L | 1.092 | 0.96 |
| 165_V | 188_Y | 1.085 | 0.96 |
| 167_N | 170_K | 1.084 | 0.96 |
| 110_K | 193_V | 1.070 | 0.95 |
| 131_V | 135_T | 1.065 | 0.95 |
| 16_D | 202_Q | 1.062 | 0.95 |
| 100_P | 103_L | 1.043 | 0.94 |
| 270_I | 277_Q | 1.040 | 0.94 |
| 54_I | 67_N | 1.040 | 0.94 |
| 50_L | 54_I | 1.039 | 0.94 |
| 83_D | 173_P | 1.017 | 0.93 |
| 18_L | 49_T | 1.015 | 0.93 |
| 69_S | 302_L | 1.010 | 0.93 |
| 262_G | 265_S | 1.010 | 0.93 |
| 8_V | 41_V | 1.010 | 0.93 |
| 110_K | 118_V | 1.003 | 0.93 |
| 26_L | 30_T | 1.003 | 0.93 |
| 238_I | 273_L | 1.002 | 0.92 |
| 88_N | 163_R | 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
- 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 | |
| 2bo4A | 6 | 0.8711 | 100 | 0.625 | Contact Map |
| 2wvlA | 2 | 0.7704 | 100 | 0.662 | Contact Map |
| 2zu9A | 2 | 0.8082 | 99.9 | 0.665 | Contact Map |
| 3f1yA | 2 | 0.8491 | 99.9 | 0.673 | Contact Map |
| 3ckjA | 1 | 0.7736 | 99.9 | 0.676 | Contact Map |
| 2z86A | 4 | 0.7736 | 99.9 | 0.686 | Contact Map |
| 2d7iA | 1 | 0.8962 | 99.9 | 0.691 | Contact Map |
| 3bcvA | 2 | 0.5503 | 99.9 | 0.698 | Contact Map |
| 4p02A | 1 | 0.9843 | 99.9 | 0.712 | Contact Map |
| 3l7iA | 4 | 0.0157 | 99.9 | 0.714 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)