| 2K5V |
| ID: | 1424428910 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 293 (259) | ||
| Sequences: | 45095 (31349.9) | ||
| Seq/Len: | 174.112 | ||
| Nf(neff/√len): | 1948.0 |
HHblits Results: (2013_03)
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: 174.112).
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 |
| 255_Q | 260_D | 3.651 | 1.00 |
| 36_E | 45_T | 3.380 | 1.00 |
| 122_A | 207_L | 3.125 | 1.00 |
| 148_L | 158_A | 3.117 | 1.00 |
| 25_K | 33_E | 2.927 | 1.00 |
| 39_W | 42_Y | 2.643 | 1.00 |
| 24_H | 36_E | 2.611 | 1.00 |
| 130_E | 134_K | 2.578 | 1.00 |
| 130_E | 265_A | 2.542 | 1.00 |
| 252_A | 262_P | 2.346 | 1.00 |
| 37_G | 48_V | 2.293 | 1.00 |
| 102_L | 145_R | 2.291 | 1.00 |
| 126_S | 203_F | 2.288 | 1.00 |
| 37_G | 46_V | 2.265 | 1.00 |
| 252_A | 270_A | 2.226 | 1.00 |
| 25_K | 28_G | 2.216 | 1.00 |
| 253_C | 267_I | 2.209 | 1.00 |
| 36_E | 95_F | 2.151 | 1.00 |
| 204_G | 253_C | 2.148 | 1.00 |
| 124_Q | 155_V | 2.126 | 1.00 |
| 72_K | 78_Q | 2.123 | 1.00 |
| 124_Q | 154_L | 2.104 | 1.00 |
| 94_E | 156_K | 2.087 | 1.00 |
| 125_I | 147_C | 2.078 | 1.00 |
| 97_T | 151_E | 2.055 | 1.00 |
| 200_V | 253_C | 2.029 | 1.00 |
| 147_C | 155_V | 2.021 | 1.00 |
| 73_H | 131_Y | 2.014 | 1.00 |
| 38_V | 45_T | 2.010 | 1.00 |
| 150_G | 154_L | 1.997 | 1.00 |
| 129_M | 203_F | 1.983 | 1.00 |
| 257_N | 260_D | 1.865 | 1.00 |
| 142_L | 206_L | 1.784 | 1.00 |
| 185_A | 198_S | 1.775 | 1.00 |
| 114_S | 117_V | 1.731 | 1.00 |
| 78_Q | 94_E | 1.725 | 1.00 |
| 25_K | 35_Y | 1.718 | 1.00 |
| 150_G | 156_K | 1.712 | 1.00 |
| 23_K | 38_V | 1.704 | 1.00 |
| 200_V | 264_F | 1.695 | 1.00 |
| 80_L | 94_E | 1.685 | 1.00 |
| 128_A | 157_V | 1.628 | 1.00 |
| 100_N | 103_D | 1.620 | 1.00 |
| 75_N | 128_A | 1.594 | 1.00 |
| 130_E | 268_H | 1.563 | 1.00 |
| 115_A | 118_L | 1.559 | 1.00 |
| 48_V | 92_I | 1.548 | 1.00 |
| 102_L | 106_R | 1.528 | 1.00 |
| 122_A | 203_F | 1.503 | 1.00 |
| 134_K | 265_A | 1.491 | 1.00 |
| 96_M | 156_K | 1.486 | 1.00 |
| 21_T | 38_V | 1.485 | 1.00 |
| 123_T | 127_S | 1.482 | 1.00 |
| 129_M | 142_L | 1.467 | 1.00 |
| 50_T | 90_Y | 1.459 | 1.00 |
| 99_G | 107_E | 1.458 | 1.00 |
| 263_S | 266_E | 1.457 | 1.00 |
| 183_W | 209_E | 1.453 | 1.00 |
| 129_M | 264_F | 1.432 | 1.00 |
| 28_G | 33_E | 1.424 | 1.00 |
| 147_C | 206_L | 1.423 | 1.00 |
| 21_T | 40_K | 1.422 | 1.00 |
| 126_S | 267_I | 1.416 | 1.00 |
| 127_S | 268_H | 1.414 | 1.00 |
| 44_L | 80_L | 1.412 | 1.00 |
| 46_V | 92_I | 1.403 | 0.99 |
| 96_M | 150_G | 1.402 | 0.99 |
| 144_A | 206_L | 1.400 | 0.99 |
| 50_T | 88_P | 1.393 | 0.99 |
| 211_A | 246_V | 1.389 | 0.99 |
| 136_N | 196_I | 1.382 | 0.99 |
| 122_A | 210_I | 1.376 | 0.99 |
| 207_L | 249_L | 1.353 | 0.99 |
| 247_Y | 251_R | 1.350 | 0.99 |
| 75_N | 127_S | 1.346 | 0.99 |
| 143_A | 180_P | 1.330 | 0.99 |
| 120_Y | 124_Q | 1.322 | 0.99 |
| 205_V | 254_W | 1.296 | 0.99 |
| 38_V | 43_S | 1.291 | 0.99 |
| 250_M | 254_W | 1.291 | 0.99 |
| 48_V | 90_Y | 1.277 | 0.99 |
| 77_V | 158_A | 1.267 | 0.99 |
| 131_Y | 135_K | 1.263 | 0.99 |
| 137_F | 163_S | 1.255 | 0.99 |
| 34_V | 47_A | 1.253 | 0.99 |
| 249_L | 267_I | 1.247 | 0.99 |
| 126_S | 264_F | 1.243 | 0.98 |
| 129_M | 133_E | 1.232 | 0.98 |
| 144_A | 183_W | 1.228 | 0.98 |
| 35_Y | 50_T | 1.221 | 0.98 |
| 121_M | 155_V | 1.217 | 0.98 |
| 39_W | 44_L | 1.208 | 0.98 |
| 23_K | 36_E | 1.204 | 0.98 |
| 115_A | 243_P | 1.196 | 0.98 |
| 197_K | 263_S | 1.191 | 0.98 |
| 96_M | 148_L | 1.184 | 0.98 |
| 123_T | 272_E | 1.182 | 0.98 |
| 77_V | 96_M | 1.174 | 0.98 |
| 203_F | 207_L | 1.168 | 0.97 |
| 252_A | 255_Q | 1.165 | 0.97 |
| 105_L | 209_E | 1.158 | 0.97 |
| 249_L | 253_C | 1.157 | 0.97 |
| 19_D | 39_W | 1.156 | 0.97 |
| 77_V | 93_T | 1.150 | 0.97 |
| 102_L | 209_E | 1.142 | 0.97 |
| 141_D | 146_N | 1.139 | 0.97 |
| 127_S | 130_E | 1.137 | 0.97 |
| 45_T | 95_F | 1.135 | 0.97 |
| 139_H | 142_L | 1.130 | 0.97 |
| 264_F | 267_I | 1.127 | 0.97 |
| 144_A | 209_E | 1.126 | 0.97 |
| 133_E | 264_F | 1.124 | 0.97 |
| 248_E | 252_A | 1.102 | 0.96 |
| 125_I | 155_V | 1.100 | 0.96 |
| 118_L | 211_A | 1.095 | 0.96 |
| 67_V | 163_S | 1.091 | 0.96 |
| 185_A | 188_S | 1.090 | 0.96 |
| 45_T | 97_T | 1.088 | 0.96 |
| 209_E | 216_S | 1.084 | 0.96 |
| 203_F | 253_C | 1.082 | 0.96 |
| 70_E | 135_K | 1.081 | 0.95 |
| 46_V | 80_L | 1.080 | 0.95 |
| 125_I | 206_L | 1.075 | 0.95 |
| 188_S | 198_S | 1.069 | 0.95 |
| 98_Y | 153_H | 1.062 | 0.95 |
| 140_R | 194_F | 1.049 | 0.94 |
| 126_S | 268_H | 1.044 | 0.94 |
| 26_L | 95_F | 1.043 | 0.94 |
| 29_G | 32_G | 1.037 | 0.94 |
| 70_E | 165_L | 1.027 | 0.94 |
| 149_V | 155_V | 1.024 | 0.93 |
| 194_F | 198_S | 1.019 | 0.93 |
| 204_G | 254_W | 1.017 | 0.93 |
| 130_E | 264_F | 1.014 | 0.93 |
| 142_L | 157_V | 1.012 | 0.93 |
| 83_C | 90_Y | 1.009 | 0.93 |
| 76_L | 132_L | 1.009 | 0.93 |
| 125_I | 142_L | 1.008 | 0.93 |
| 231_E | 234_Y | 1.007 | 0.93 |
| 197_K | 259_S | 1.006 | 0.93 |
| 99_G | 103_D | 1.005 | 0.93 |
| 79_L | 82_V | 1.004 | 0.93 |
| 262_P | 267_I | 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
- 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 | |
| 4c0tA | 1 | 0.9113 | 100 | 0.117 | Contact Map |
| 1opkA | 1 | 0.9898 | 100 | 0.136 | Contact Map |
| 2vwiA | 4 | 0.9113 | 100 | 0.158 | Contact Map |
| 3a7iA | 1 | 0.9522 | 100 | 0.165 | Contact Map |
| 3cokA | 2 | 0.7986 | 100 | 0.17 | Contact Map |
| 2rkuA | 1 | 0.9522 | 100 | 0.173 | Contact Map |
| 2wqmA | 1 | 0.8259 | 100 | 0.174 | Contact Map |
| 3comA | 2 | 0.9249 | 100 | 0.175 | Contact Map |
| 3cblA | 1 | 0.942 | 100 | 0.178 | Contact Map |
| 2x4fA | 2 | 0.9352 | 100 | 0.183 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)