| 1sbp from pdb |
| ID: | 1513748048 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 309 (261) | ||
| Sequences: | 14944 (8772.8) | ||
| Seq/Len: | 57.257 | ||
| Nf(neff/√len): | 543.0 |
HHblits Results: (2016_02)
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: 57.257).
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 |
| 103_K | 209_E | 4.196 | 1.00 |
| 23_A | 245_Y | 3.528 | 1.00 |
| 79_D | 236_K | 3.501 | 1.00 |
| 4_Q | 39_D | 3.212 | 1.00 |
| 104_G | 207_K | 3.068 | 1.00 |
| 157_D | 161_A | 2.939 | 1.00 |
| 34_D | 238_V | 2.905 | 1.00 |
| 18_E | 22_K | 2.899 | 1.00 |
| 6_L | 39_D | 2.733 | 1.00 |
| 241_A | 244_K | 2.597 | 1.00 |
| 4_Q | 35_N | 2.596 | 1.00 |
| 248_S | 251_G | 2.496 | 1.00 |
| 23_A | 26_A | 2.476 | 1.00 |
| 236_K | 240_E | 2.437 | 1.00 |
| 25_S | 35_N | 2.388 | 1.00 |
| 249_P | 253_E | 2.346 | 1.00 |
| 23_A | 254_I | 2.342 | 1.00 |
| 101_V | 209_E | 2.339 | 1.00 |
| 28_W | 241_A | 2.307 | 1.00 |
| 24_F | 241_A | 2.300 | 1.00 |
| 21_N | 242_Y | 2.231 | 1.00 |
| 28_W | 32_T | 2.224 | 1.00 |
| 235_T | 238_V | 2.189 | 1.00 |
| 105_N | 187_D | 2.165 | 1.00 |
| 19_Q | 22_K | 2.130 | 1.00 |
| 154_K | 157_D | 2.106 | 1.00 |
| 110_H | 214_S | 2.095 | 1.00 |
| 102_R | 105_N | 2.090 | 1.00 |
| 123_I | 186_G | 2.056 | 1.00 |
| 22_K | 26_A | 2.035 | 1.00 |
| 253_E | 257_K | 1.999 | 1.00 |
| 24_F | 242_Y | 1.976 | 1.00 |
| 101_V | 211_V | 1.962 | 1.00 |
| 27_H | 248_S | 1.960 | 1.00 |
| 114_D | 117_K | 1.935 | 1.00 |
| 21_N | 25_S | 1.933 | 1.00 |
| 78_I | 224_S | 1.921 | 1.00 |
| 223_V | 243_L | 1.886 | 1.00 |
| 237_A | 240_E | 1.876 | 1.00 |
| 23_A | 27_H | 1.867 | 1.00 |
| 22_K | 25_S | 1.847 | 1.00 |
| 225_V | 239_A | 1.825 | 1.00 |
| 24_F | 34_D | 1.820 | 1.00 |
| 79_D | 227_D | 1.799 | 1.00 |
| 160_K | 164_K | 1.759 | 1.00 |
| 3_I | 238_V | 1.754 | 1.00 |
| 103_K | 207_K | 1.740 | 1.00 |
| 158_F | 161_A | 1.721 | 1.00 |
| 240_E | 244_K | 1.695 | 1.00 |
| 32_T | 241_A | 1.684 | 1.00 |
| 254_I | 257_K | 1.681 | 1.00 |
| 59_D | 235_T | 1.663 | 1.00 |
| 110_H | 114_D | 1.650 | 1.00 |
| 237_A | 241_A | 1.648 | 1.00 |
| 111_D | 114_D | 1.636 | 1.00 |
| 249_P | 264_D | 1.629 | 1.00 |
| 53_I | 75_R | 1.602 | 1.00 |
| 249_P | 266_D | 1.588 | 1.00 |
| 5_L | 238_V | 1.582 | 1.00 |
| 116_I | 162_L | 1.577 | 1.00 |
| 98_V | 210_I | 1.568 | 1.00 |
| 27_H | 32_T | 1.565 | 1.00 |
| 225_V | 243_L | 1.549 | 1.00 |
| 180_F | 185_I | 1.541 | 1.00 |
| 157_D | 160_K | 1.536 | 1.00 |
| 229_V | 235_T | 1.534 | 1.00 |
| 153_A | 157_D | 1.524 | 1.00 |
| 121_S | 187_D | 1.515 | 1.00 |
| 89_D | 222_T | 1.499 | 1.00 |
| 25_S | 32_T | 1.498 | 1.00 |
| 76_G | 227_D | 1.494 | 1.00 |
| 60_T | 239_A | 1.481 | 1.00 |
| 72_I | 78_I | 1.473 | 1.00 |
| 27_H | 250_E | 1.469 | 1.00 |
| 34_D | 241_A | 1.468 | 1.00 |
| 238_V | 241_A | 1.467 | 1.00 |
| 60_T | 242_Y | 1.465 | 1.00 |
| 180_F | 186_G | 1.457 | 1.00 |
| 3_I | 235_T | 1.443 | 1.00 |
| 116_I | 161_A | 1.434 | 1.00 |
| 229_V | 236_K | 1.427 | 1.00 |
| 242_Y | 246_L | 1.421 | 1.00 |
| 24_F | 245_Y | 1.396 | 0.99 |
| 253_E | 267_V | 1.369 | 0.99 |
| 6_L | 41_S | 1.367 | 0.99 |
| 23_A | 250_E | 1.353 | 0.99 |
| 14_R | 18_E | 1.351 | 0.99 |
| 225_V | 240_E | 1.350 | 0.99 |
| 161_A | 164_K | 1.346 | 0.99 |
| 23_A | 251_G | 1.339 | 0.99 |
| 251_G | 254_I | 1.339 | 0.99 |
| 19_Q | 23_A | 1.319 | 0.99 |
| 156_E | 160_K | 1.315 | 0.99 |
| 158_F | 162_L | 1.307 | 0.99 |
| 116_I | 165_N | 1.282 | 0.99 |
| 223_V | 246_L | 1.281 | 0.99 |
| 35_N | 39_D | 1.268 | 0.99 |
| 161_A | 165_N | 1.246 | 0.98 |
| 116_I | 158_F | 1.245 | 0.98 |
| 100_L | 191_A | 1.239 | 0.98 |
| 50_T | 54_N | 1.210 | 0.98 |
| 172_G | 176_S | 1.203 | 0.98 |
| 102_R | 207_K | 1.182 | 0.98 |
| 59_D | 229_V | 1.182 | 0.98 |
| 95_S | 219_A | 1.180 | 0.98 |
| 264_D | 267_V | 1.178 | 0.98 |
| 226_V | 229_V | 1.177 | 0.98 |
| 250_E | 254_I | 1.158 | 0.97 |
| 27_H | 245_Y | 1.151 | 0.97 |
| 28_W | 33_G | 1.151 | 0.97 |
| 106_P | 188_V | 1.149 | 0.97 |
| 44_G | 47_K | 1.147 | 0.97 |
| 177_T | 189_L | 1.143 | 0.97 |
| 60_T | 243_L | 1.142 | 0.97 |
| 2_D | 35_N | 1.137 | 0.97 |
| 229_V | 234_D | 1.135 | 0.97 |
| 245_Y | 251_G | 1.117 | 0.96 |
| 250_E | 253_E | 1.113 | 0.96 |
| 225_V | 236_K | 1.108 | 0.96 |
| 100_L | 196_A | 1.106 | 0.96 |
| 9_S | 40_Q | 1.102 | 0.96 |
| 21_N | 40_Q | 1.100 | 0.96 |
| 79_D | 229_V | 1.096 | 0.96 |
| 73_A | 88_D | 1.094 | 0.96 |
| 61_V | 224_S | 1.089 | 0.96 |
| 21_N | 38_I | 1.081 | 0.95 |
| 61_V | 226_V | 1.072 | 0.95 |
| 24_F | 32_T | 1.061 | 0.95 |
| 101_V | 108_Q | 1.051 | 0.94 |
| 113_N | 117_K | 1.044 | 0.94 |
| 179_T | 183_R | 1.043 | 0.94 |
| 20_Y | 251_G | 1.041 | 0.94 |
| 7_N | 223_V | 1.007 | 0.93 |
| 166_V | 169_L | 1.004 | 0.93 |
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 | |
| 1sbpA | 1 | 0.9838 | 100 | 0.354 | Contact Map |
| 3waeA | 2 | 0.8867 | 100 | 0.419 | Contact Map |
| 4edpA | 2 | 0.9061 | 100 | 0.425 | Contact Map |
| 1potA | 1 | 0.9223 | 100 | 0.43 | Contact Map |
| 3rpwA | 1 | 0.8997 | 100 | 0.433 | Contact Map |
| 2qryA | 4 | 0.9256 | 100 | 0.437 | Contact Map |
| 4r6yA | 1 | 0.9094 | 100 | 0.439 | Contact Map |
| 3pu5A | 1 | 0.9061 | 100 | 0.44 | Contact Map |
| 4eqbA | 2 | 0.9029 | 100 | 0.441 | Contact Map |
| 4i1dA | 4 | 0.9223 | 100 | 0.442 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)