| srg-34 |
| ID: | 1400243483 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 334 (310) | ||
| Sequences: | 1133 (938.7) | ||
| Seq/Len: | 3.655 | ||
| Nf(neff/√len): | 53.3 |
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: 3.655).
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 |
| 19_S | 23_Y | 2.823 | 1.00 |
| 78_F | 81_N | 2.615 | 1.00 |
| 48_G | 52_N | 2.559 | 1.00 |
| 192_L | 200_N | 2.541 | 1.00 |
| 188_A | 192_L | 2.301 | 1.00 |
| 42_F | 47_V | 2.271 | 1.00 |
| 23_Y | 26_I | 2.256 | 1.00 |
| 196_N | 200_N | 2.251 | 1.00 |
| 42_F | 45_F | 2.175 | 1.00 |
| 45_F | 48_G | 2.141 | 1.00 |
| 49_F | 52_N | 2.121 | 1.00 |
| 236_L | 239_L | 2.061 | 1.00 |
| 200_N | 207_L | 2.046 | 1.00 |
| 200_N | 203_A | 2.018 | 1.00 |
| 41_F | 45_F | 1.974 | 1.00 |
| 120_T | 132_W | 1.964 | 1.00 |
| 192_L | 196_N | 1.907 | 1.00 |
| 77_S | 80_S | 1.855 | 1.00 |
| 200_N | 204_G | 1.772 | 0.99 |
| 12_T | 15_Y | 1.755 | 0.99 |
| 42_F | 49_F | 1.672 | 0.99 |
| 315_N | 318_I | 1.667 | 0.99 |
| 222_L | 225_M | 1.656 | 0.99 |
| 42_F | 48_G | 1.647 | 0.99 |
| 316_S | 319_V | 1.644 | 0.99 |
| 44_L | 47_V | 1.639 | 0.99 |
| 315_N | 319_V | 1.632 | 0.99 |
| 173_D | 176_Y | 1.623 | 0.98 |
| 189_L | 192_L | 1.597 | 0.98 |
| 48_G | 51_M | 1.557 | 0.98 |
| 199_F | 203_A | 1.535 | 0.98 |
| 184_F | 187_P | 1.520 | 0.97 |
| 306_K | 309_R | 1.497 | 0.97 |
| 192_L | 195_F | 1.496 | 0.97 |
| 44_L | 48_G | 1.496 | 0.97 |
| 119_F | 124_F | 1.469 | 0.97 |
| 172_I | 176_Y | 1.465 | 0.96 |
| 203_A | 210_M | 1.442 | 0.96 |
| 15_Y | 26_I | 1.439 | 0.96 |
| 178_R | 182_Y | 1.419 | 0.96 |
| 41_F | 44_L | 1.387 | 0.95 |
| 16_G | 20_M | 1.377 | 0.95 |
| 117_N | 132_W | 1.375 | 0.94 |
| 269_T | 274_D | 1.369 | 0.94 |
| 180_N | 185_L | 1.367 | 0.94 |
| 42_F | 46_C | 1.358 | 0.94 |
| 179_S | 184_F | 1.339 | 0.93 |
| 152_T | 155_I | 1.330 | 0.93 |
| 52_N | 55_T | 1.326 | 0.93 |
| 41_F | 48_G | 1.324 | 0.93 |
| 201_V | 207_L | 1.311 | 0.92 |
| 180_N | 192_L | 1.297 | 0.92 |
| 38_K | 42_F | 1.294 | 0.92 |
| 44_L | 49_F | 1.284 | 0.91 |
| 235_F | 239_L | 1.280 | 0.91 |
| 306_K | 310_F | 1.280 | 0.91 |
| 219_E | 222_L | 1.278 | 0.91 |
| 15_Y | 18_L | 1.246 | 0.90 |
| 188_A | 191_F | 1.243 | 0.90 |
| 181_I | 184_F | 1.238 | 0.89 |
| 192_L | 203_A | 1.236 | 0.89 |
| 19_S | 282_F | 1.234 | 0.89 |
| 233_D | 236_L | 1.229 | 0.89 |
| 43_K | 48_G | 1.228 | 0.89 |
| 301_L | 308_H | 1.228 | 0.89 |
| 191_F | 199_F | 1.222 | 0.88 |
| 196_N | 202_L | 1.222 | 0.88 |
| 40_S | 47_V | 1.215 | 0.88 |
| 200_N | 210_M | 1.214 | 0.88 |
| 182_Y | 186_M | 1.197 | 0.87 |
| 222_L | 228_T | 1.193 | 0.87 |
| 229_V | 233_D | 1.193 | 0.87 |
| 167_T | 170_F | 1.189 | 0.87 |
| 272_A | 276_L | 1.188 | 0.87 |
| 239_L | 242_S | 1.186 | 0.86 |
| 172_I | 175_T | 1.186 | 0.86 |
| 177_G | 180_N | 1.185 | 0.86 |
| 164_Y | 169_N | 1.184 | 0.86 |
| 43_K | 49_F | 1.184 | 0.86 |
| 107_Q | 284_L | 1.184 | 0.86 |
| 15_Y | 23_Y | 1.182 | 0.86 |
| 204_G | 207_L | 1.175 | 0.86 |
| 15_Y | 19_S | 1.173 | 0.86 |
| 280_H | 284_L | 1.171 | 0.85 |
| 39_S | 42_F | 1.169 | 0.85 |
| 305_F | 309_R | 1.160 | 0.85 |
| 187_P | 191_F | 1.155 | 0.84 |
| 98_T | 102_E | 1.155 | 0.84 |
| 42_F | 53_L | 1.147 | 0.84 |
| 51_M | 55_T | 1.135 | 0.83 |
| 196_N | 203_A | 1.134 | 0.83 |
| 198_V | 202_L | 1.133 | 0.83 |
| 37_F | 41_F | 1.132 | 0.83 |
| 45_F | 52_N | 1.128 | 0.82 |
| 39_S | 52_N | 1.126 | 0.82 |
| 111_N | 280_H | 1.121 | 0.82 |
| 225_M | 229_V | 1.118 | 0.82 |
| 207_L | 210_M | 1.116 | 0.81 |
| 182_Y | 185_L | 1.114 | 0.81 |
| 191_F | 195_F | 1.114 | 0.81 |
| 219_E | 225_M | 1.112 | 0.81 |
| 23_Y | 27_T | 1.109 | 0.81 |
| 43_K | 46_C | 1.108 | 0.81 |
| 16_G | 19_S | 1.098 | 0.80 |
| 229_V | 236_L | 1.092 | 0.80 |
| 276_L | 284_L | 1.091 | 0.79 |
| 230_F | 237_T | 1.090 | 0.79 |
| 178_R | 181_I | 1.083 | 0.79 |
| 201_V | 204_G | 1.083 | 0.79 |
| 13_T | 21_L | 1.077 | 0.78 |
| 300_R | 305_F | 1.075 | 0.78 |
| 178_R | 184_F | 1.075 | 0.78 |
| 277_T | 281_P | 1.072 | 0.78 |
| 180_N | 184_F | 1.068 | 0.77 |
| 232_I | 235_F | 1.068 | 0.77 |
| 302_L | 307_N | 1.066 | 0.77 |
| 26_I | 32_N | 1.063 | 0.77 |
| 47_V | 52_N | 1.060 | 0.77 |
| 93_L | 284_L | 1.059 | 0.77 |
| 300_R | 303_E | 1.058 | 0.76 |
| 303_E | 306_K | 1.057 | 0.76 |
| 40_S | 45_F | 1.057 | 0.76 |
| 195_F | 203_A | 1.056 | 0.76 |
| 176_Y | 181_I | 1.054 | 0.76 |
| 165_S | 170_F | 1.053 | 0.76 |
| 311_F | 314_S | 1.053 | 0.76 |
| 183_Y | 187_P | 1.053 | 0.76 |
| 303_E | 309_R | 1.051 | 0.76 |
| 225_M | 236_L | 1.049 | 0.76 |
| 314_S | 317_N | 1.047 | 0.75 |
| 18_L | 23_Y | 1.046 | 0.75 |
| 41_F | 284_L | 1.044 | 0.75 |
| 91_F | 95_I | 1.038 | 0.75 |
| 159_R | 162_F | 1.037 | 0.74 |
| 50_F | 53_L | 1.037 | 0.74 |
| 199_F | 208_Y | 1.035 | 0.74 |
| 22_I | 26_I | 1.035 | 0.74 |
| 204_G | 208_Y | 1.034 | 0.74 |
| 300_R | 307_N | 1.034 | 0.74 |
| 227_F | 231_V | 1.030 | 0.74 |
| 134_K | 138_L | 1.028 | 0.73 |
| 41_F | 47_V | 1.027 | 0.73 |
| 192_L | 199_F | 1.027 | 0.73 |
| 281_P | 284_L | 1.025 | 0.73 |
| 189_L | 200_N | 1.023 | 0.73 |
| 307_N | 311_F | 1.021 | 0.73 |
| 64_R | 120_T | 1.021 | 0.73 |
| 175_T | 181_I | 1.021 | 0.73 |
| 277_T | 280_H | 1.021 | 0.73 |
| 119_F | 123_C | 1.019 | 0.73 |
| 156_L | 159_R | 1.018 | 0.72 |
| 153_R | 157_Q | 1.017 | 0.72 |
| 185_L | 188_A | 1.014 | 0.72 |
| 314_S | 318_I | 1.012 | 0.72 |
| 52_N | 56_Y | 1.007 | 0.71 |
| 12_T | 23_Y | 1.006 | 0.71 |
| 310_F | 313_E | 1.005 | 0.71 |
| 48_G | 284_L | 1.003 | 0.71 |
| 122_I | 125_P | 1.003 | 0.71 |
| 138_L | 142_S | 1.001 | 0.71 |
| 116_A | 205_I | 1.001 | 0.71 |
| 159_R | 171_Y | 1.000 | 0.71 |
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 | |
| 3vw7A | 1 | 0.8054 | 100 | 0.478 | Contact Map |
| 4pxzA | 1 | 0.8024 | 100 | 0.479 | Contact Map |
| 4grvA | 1 | 0.8293 | 100 | 0.489 | Contact Map |
| 1u19A | 2 | 0.9102 | 100 | 0.497 | Contact Map |
| 3v2yA | 1 | 0.8084 | 100 | 0.497 | Contact Map |
| 4iarA | 1 | 0.8054 | 100 | 0.498 | Contact Map |
| 2rh1A | 1 | 0.8323 | 100 | 0.498 | Contact Map |
| 4eiyA | 1 | 0.8413 | 100 | 0.499 | Contact Map |
| 3uonA | 1 | 0.8263 | 100 | 0.5 | Contact Map |
| 4ib4A | 1 | 0.8473 | 100 | 0.5 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)