| 1DS1A |
| ID: | 1411760660 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 323 (294) | ||
| Sequences: | 1239 (912.3) | ||
| Seq/Len: | 4.214 | ||
| Nf(neff/√len): | 53.2 |
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: 4.214).
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 |
| 248_A | 252_K | 2.768 | 1.00 |
| 118_V | 121_D | 2.656 | 1.00 |
| 189_A | 193_D | 2.604 | 1.00 |
| 117_T | 121_D | 2.411 | 1.00 |
| 118_V | 122_V | 2.343 | 1.00 |
| 244_K | 248_A | 2.235 | 1.00 |
| 101_G | 297_V | 2.187 | 1.00 |
| 184_D | 245_E | 2.036 | 1.00 |
| 117_T | 120_H | 2.022 | 1.00 |
| 170_A | 260_A | 1.975 | 1.00 |
| 42_P | 46_A | 1.922 | 1.00 |
| 178_K | 182_L | 1.922 | 1.00 |
| 87_D | 90_L | 1.901 | 1.00 |
| 231_Y | 247_V | 1.871 | 1.00 |
| 231_Y | 236_L | 1.818 | 1.00 |
| 154_N | 301_T | 1.795 | 1.00 |
| 85_P | 88_R | 1.737 | 0.99 |
| 196_M | 236_L | 1.731 | 0.99 |
| 280_R | 283_F | 1.720 | 0.99 |
| 173_V | 269_L | 1.710 | 0.99 |
| 240_D | 244_K | 1.619 | 0.99 |
| 41_L | 45_L | 1.617 | 0.99 |
| 64_L | 67_L | 1.602 | 0.99 |
| 261_V | 269_L | 1.591 | 0.99 |
| 187_T | 249_A | 1.589 | 0.99 |
| 237_A | 240_D | 1.579 | 0.99 |
| 182_L | 256_E | 1.571 | 0.99 |
| 184_D | 187_T | 1.568 | 0.98 |
| 85_P | 90_L | 1.541 | 0.98 |
| 123_Y | 126_P | 1.533 | 0.98 |
| 76_P | 80_S | 1.527 | 0.98 |
| 45_L | 48_A | 1.524 | 0.98 |
| 48_A | 52_F | 1.499 | 0.98 |
| 147_A | 230_G | 1.497 | 0.98 |
| 157_M | 270_I | 1.469 | 0.97 |
| 182_L | 257_V | 1.465 | 0.97 |
| 180_L | 192_L | 1.462 | 0.97 |
| 112_E | 116_G | 1.457 | 0.97 |
| 69_V | 103_R | 1.452 | 0.97 |
| 86_E | 261_V | 1.434 | 0.97 |
| 183_L | 249_A | 1.433 | 0.97 |
| 86_E | 89_S | 1.432 | 0.97 |
| 124_P | 127_G | 1.412 | 0.97 |
| 233_R | 248_A | 1.411 | 0.97 |
| 196_M | 219_P | 1.397 | 0.96 |
| 86_E | 269_L | 1.384 | 0.96 |
| 236_L | 251_S | 1.378 | 0.96 |
| 160_C | 263_L | 1.367 | 0.96 |
| 98_G | 102_R | 1.365 | 0.96 |
| 170_A | 281_T | 1.356 | 0.95 |
| 146_M | 153_P | 1.354 | 0.95 |
| 133_S | 140_L | 1.345 | 0.95 |
| 222_G | 227_P | 1.337 | 0.95 |
| 125_S | 128_A | 1.335 | 0.95 |
| 305_G | 308_S | 1.331 | 0.95 |
| 46_A | 88_R | 1.331 | 0.95 |
| 310_G | 313_A | 1.320 | 0.94 |
| 45_L | 49_L | 1.312 | 0.94 |
| 306_Q | 309_G | 1.295 | 0.94 |
| 158_L | 294_L | 1.291 | 0.93 |
| 118_V | 124_P | 1.291 | 0.93 |
| 161_S | 293_W | 1.290 | 0.93 |
| 120_H | 123_Y | 1.285 | 0.93 |
| 115_S | 120_H | 1.278 | 0.93 |
| 180_L | 188_R | 1.278 | 0.93 |
| 81_S | 84_A | 1.260 | 0.92 |
| 52_F | 55_E | 1.259 | 0.92 |
| 115_S | 121_D | 1.254 | 0.92 |
| 47_T | 51_T | 1.253 | 0.92 |
| 103_R | 107_H | 1.248 | 0.92 |
| 307_L | 310_G | 1.239 | 0.92 |
| 40_S | 47_T | 1.236 | 0.91 |
| 48_A | 51_T | 1.223 | 0.91 |
| 304_N | 307_L | 1.220 | 0.91 |
| 179_A | 253_A | 1.216 | 0.90 |
| 86_E | 90_L | 1.212 | 0.90 |
| 147_A | 198_C | 1.209 | 0.90 |
| 49_L | 52_F | 1.205 | 0.90 |
| 69_V | 72_D | 1.197 | 0.90 |
| 45_L | 53_N | 1.191 | 0.89 |
| 264_E | 267_D | 1.188 | 0.89 |
| 120_H | 124_P | 1.185 | 0.89 |
| 171_T | 269_L | 1.185 | 0.89 |
| 153_P | 156_V | 1.181 | 0.89 |
| 157_M | 268_L | 1.181 | 0.89 |
| 313_A | 317_V | 1.175 | 0.88 |
| 113_L | 116_G | 1.174 | 0.88 |
| 189_A | 192_L | 1.171 | 0.88 |
| 247_V | 251_S | 1.167 | 0.88 |
| 39_A | 42_P | 1.158 | 0.87 |
| 164_D | 169_A | 1.158 | 0.87 |
| 146_M | 235_L | 1.155 | 0.87 |
| 120_H | 125_S | 1.155 | 0.87 |
| 76_P | 79_P | 1.145 | 0.87 |
| 57_S | 82_T | 1.143 | 0.86 |
| 121_D | 125_S | 1.139 | 0.86 |
| 99_L | 102_R | 1.137 | 0.86 |
| 45_L | 52_F | 1.132 | 0.86 |
| 233_R | 251_S | 1.129 | 0.86 |
| 311_E | 314_G | 1.121 | 0.85 |
| 46_A | 49_L | 1.116 | 0.85 |
| 30_F | 34_A | 1.108 | 0.84 |
| 190_R | 193_D | 1.108 | 0.84 |
| 282_P | 285_P | 1.107 | 0.84 |
| 118_V | 123_Y | 1.106 | 0.84 |
| 309_G | 312_R | 1.105 | 0.84 |
| 193_D | 242_A | 1.101 | 0.84 |
| 113_L | 117_T | 1.098 | 0.83 |
| 53_N | 92_T | 1.086 | 0.82 |
| 100_V | 175_S | 1.077 | 0.82 |
| 98_G | 107_H | 1.076 | 0.82 |
| 68_P | 71_A | 1.072 | 0.81 |
| 88_R | 96_M | 1.072 | 0.81 |
| 131_L | 136_S | 1.069 | 0.81 |
| 32_D | 36_T | 1.065 | 0.81 |
| 283_F | 286_R | 1.063 | 0.81 |
| 237_A | 243_D | 1.062 | 0.80 |
| 160_C | 163_A | 1.061 | 0.80 |
| 117_T | 124_P | 1.060 | 0.80 |
| 46_A | 50_D | 1.055 | 0.80 |
| 161_S | 297_V | 1.054 | 0.80 |
| 41_L | 78_T | 1.051 | 0.79 |
| 85_P | 89_S | 1.044 | 0.79 |
| 282_P | 286_R | 1.042 | 0.79 |
| 238_P | 241_P | 1.040 | 0.78 |
| 232_D | 236_L | 1.035 | 0.78 |
| 174_A | 179_A | 1.032 | 0.78 |
| 278_H | 292_R | 1.031 | 0.78 |
| 181_P | 188_R | 1.028 | 0.77 |
| 110_Y | 116_G | 1.028 | 0.77 |
| 183_L | 250_L | 1.027 | 0.77 |
| 93_M | 96_M | 1.025 | 0.77 |
| 143_H | 292_R | 1.021 | 0.77 |
| 165_H | 291_D | 1.021 | 0.77 |
| 121_D | 124_P | 1.020 | 0.77 |
| 50_D | 55_E | 1.018 | 0.76 |
| 308_S | 312_R | 1.016 | 0.76 |
| 43_G | 46_A | 1.014 | 0.76 |
| 76_P | 82_T | 1.009 | 0.76 |
| 115_S | 118_V | 1.007 | 0.75 |
| 172_L | 281_T | 1.007 | 0.75 |
| 306_Q | 310_G | 1.006 | 0.75 |
| 186_R | 190_R | 1.005 | 0.75 |
| 311_E | 315_D | 1.004 | 0.75 |
| 229_L | 253_A | 1.003 | 0.75 |
| 34_A | 41_L | 1.000 | 0.75 |
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 | |
| 1ds1A | 1 | 0.9969 | 100 | 0.297 | Contact Map |
| 2og5A | 1 | 0.9567 | 100 | 0.342 | Contact Map |
| 2wbqA | 1 | 0.9628 | 100 | 0.372 | Contact Map |
| 4m23A | 4 | 0.9567 | 100 | 0.373 | Contact Map |
| 4c5wA | 1 | 0.9381 | 100 | 0.482 | Contact Map |
| 1otjA | 4 | 0.7895 | 100 | 0.492 | Contact Map |
| 3eatX | 1 | 0.808 | 100 | 0.504 | Contact Map |
| 3pvjA | 4 | 0.774 | 100 | 0.505 | Contact Map |
| 1oihA | 4 | 0.7492 | 100 | 0.507 | Contact Map |
| 4j5iA | 8 | 0.808 | 100 | 0.514 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)