| YJDL 2 |
| ID: | 1432814745 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (448) | ||
| Sequences: | 1129 (545.8) | ||
| Seq/Len: | 2.520 | ||
| Nf(neff/√len): | 25.8 |
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: 2.520).
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 |
| 87_L | 108_I | 5.381 | 1.00 |
| 43_D | 294_R | 3.561 | 1.00 |
| 91_V | 108_I | 3.366 | 1.00 |
| 160_A | 172_L | 3.211 | 1.00 |
| 162_Q | 307_T | 3.117 | 1.00 |
| 139_F | 400_T | 3.019 | 1.00 |
| 158_G | 308_A | 2.961 | 1.00 |
| 263_A | 468_A | 2.929 | 1.00 |
| 90_V | 174_G | 2.925 | 1.00 |
| 67_L | 71_L | 2.855 | 1.00 |
| 292_I | 377_M | 2.754 | 1.00 |
| 24_F | 54_A | 2.610 | 1.00 |
| 50_F | 285_G | 2.604 | 1.00 |
| 150_S | 315_A | 2.534 | 1.00 |
| 37_H | 166_W | 2.458 | 1.00 |
| 161_A | 308_A | 2.408 | 1.00 |
| 313_V | 378_I | 2.316 | 1.00 |
| 354_C | 383_L | 2.289 | 1.00 |
| 28_R | 50_F | 2.180 | 1.00 |
| 456_L | 460_A | 2.115 | 1.00 |
| 162_Q | 308_A | 2.076 | 1.00 |
| 286_S | 428_A | 2.071 | 1.00 |
| 155_I | 309_L | 2.020 | 0.99 |
| 351_L | 386_F | 2.011 | 0.99 |
| 316_I | 320_L | 2.001 | 0.99 |
| 317_A | 378_I | 1.987 | 0.99 |
| 317_A | 382_A | 1.980 | 0.99 |
| 353_A | 459_V | 1.940 | 0.99 |
| 151_I | 316_I | 1.934 | 0.99 |
| 165_G | 168_V | 1.932 | 0.99 |
| 151_I | 319_M | 1.912 | 0.99 |
| 161_A | 168_V | 1.846 | 0.99 |
| 85_M | 113_Y | 1.838 | 0.99 |
| 281_A | 385_G | 1.832 | 0.99 |
| 324_V | 328_L | 1.803 | 0.99 |
| 87_L | 91_V | 1.796 | 0.98 |
| 146_G | 413_M | 1.775 | 0.98 |
| 89_H | 167_H | 1.772 | 0.98 |
| 192_Q | 196_S | 1.743 | 0.98 |
| 281_A | 284_G | 1.738 | 0.98 |
| 358_L | 379_S | 1.729 | 0.98 |
| 397_A | 401_R | 1.729 | 0.98 |
| 113_Y | 116_F | 1.728 | 0.98 |
| 90_V | 178_F | 1.683 | 0.97 |
| 33_L | 289_S | 1.678 | 0.97 |
| 355_G | 384_M | 1.676 | 0.97 |
| 274_G | 415_A | 1.671 | 0.97 |
| 32_I | 46_A | 1.638 | 0.97 |
| 23_S | 89_H | 1.629 | 0.97 |
| 86_T | 178_F | 1.624 | 0.97 |
| 359_L | 362_D | 1.614 | 0.96 |
| 158_G | 309_L | 1.611 | 0.96 |
| 262_R | 468_A | 1.596 | 0.96 |
| 60_T | 110_I | 1.577 | 0.96 |
| 313_V | 317_A | 1.576 | 0.96 |
| 395_A | 412_Y | 1.576 | 0.96 |
| 401_R | 469_T | 1.570 | 0.96 |
| 54_A | 421_N | 1.551 | 0.95 |
| 30_L | 157_C | 1.551 | 0.95 |
| 156_A | 172_L | 1.538 | 0.95 |
| 121_S | 413_M | 1.522 | 0.95 |
| 273_V | 463_V | 1.518 | 0.94 |
| 72_L | 77_A | 1.517 | 0.94 |
| 84_L | 111_C | 1.486 | 0.94 |
| 296_V | 377_M | 1.472 | 0.93 |
| 298_R | 307_T | 1.466 | 0.93 |
| 299_Q | 304_E | 1.457 | 0.93 |
| 92_L | 105_A | 1.453 | 0.93 |
| 321_A | 386_F | 1.453 | 0.93 |
| 347_F | 351_L | 1.446 | 0.92 |
| 51_S | 55_S | 1.432 | 0.92 |
| 360_A | 449_S | 1.432 | 0.92 |
| 314_N | 318_V | 1.423 | 0.92 |
| 144_A | 322_G | 1.421 | 0.92 |
| 171_A | 175_G | 1.415 | 0.91 |
| 161_A | 164_Y | 1.397 | 0.91 |
| 321_A | 382_A | 1.395 | 0.90 |
| 56_L | 110_I | 1.394 | 0.90 |
| 55_S | 422_W | 1.378 | 0.90 |
| 37_H | 293_D | 1.378 | 0.90 |
| 36_T | 290_L | 1.377 | 0.90 |
| 85_M | 116_F | 1.367 | 0.89 |
| 28_R | 282_Q | 1.360 | 0.89 |
| 284_G | 381_L | 1.340 | 0.88 |
| 84_L | 108_I | 1.339 | 0.88 |
| 267_I | 399_I | 1.331 | 0.88 |
| 120_I | 142_L | 1.317 | 0.87 |
| 6_Q | 322_G | 1.304 | 0.86 |
| 385_G | 389_L | 1.302 | 0.86 |
| 284_G | 384_M | 1.289 | 0.85 |
| 292_I | 296_V | 1.274 | 0.84 |
| 53_Y | 89_H | 1.271 | 0.84 |
| 382_A | 386_F | 1.266 | 0.84 |
| 60_T | 63_L | 1.261 | 0.83 |
| 298_R | 304_E | 1.259 | 0.83 |
| 274_G | 345_F | 1.250 | 0.83 |
| 49_L | 103_Y | 1.246 | 0.82 |
| 47_I | 286_S | 1.246 | 0.82 |
| 266_Q | 465_L | 1.240 | 0.82 |
| 86_T | 90_V | 1.237 | 0.82 |
| 135_R | 400_T | 1.232 | 0.81 |
| 288_I | 380_G | 1.225 | 0.81 |
| 91_V | 105_A | 1.222 | 0.81 |
| 332_E | 335_G | 1.220 | 0.81 |
| 178_F | 182_L | 1.219 | 0.80 |
| 295_F | 443_A | 1.219 | 0.80 |
| 140_S | 326_A | 1.218 | 0.80 |
| 151_I | 315_A | 1.216 | 0.80 |
| 67_L | 72_L | 1.212 | 0.80 |
| 275_T | 420_A | 1.210 | 0.80 |
| 121_S | 409_T | 1.203 | 0.79 |
| 50_F | 286_S | 1.201 | 0.79 |
| 18_I | 148_I | 1.201 | 0.79 |
| 83_L | 87_L | 1.195 | 0.79 |
| 131_N | 469_T | 1.194 | 0.79 |
| 179_I | 182_L | 1.190 | 0.78 |
| 320_L | 324_V | 1.185 | 0.78 |
| 109_I | 153_A | 1.176 | 0.77 |
| 168_V | 308_A | 1.173 | 0.77 |
| 121_S | 142_L | 1.162 | 0.76 |
| 291_F | 372_A | 1.149 | 0.75 |
| 325_L | 386_F | 1.149 | 0.75 |
| 279_V | 420_A | 1.148 | 0.75 |
| 136_D | 397_A | 1.147 | 0.75 |
| 89_H | 171_A | 1.143 | 0.74 |
| 210_P | 213_S | 1.137 | 0.74 |
| 43_D | 290_L | 1.129 | 0.73 |
| 142_L | 413_M | 1.123 | 0.72 |
| 109_I | 174_G | 1.111 | 0.71 |
| 17_Q | 21_Y | 1.109 | 0.71 |
| 24_F | 421_N | 1.109 | 0.71 |
| 79_I | 181_L | 1.106 | 0.71 |
| 48_S | 51_S | 1.106 | 0.71 |
| 150_S | 154_P | 1.105 | 0.71 |
| 162_Q | 168_V | 1.104 | 0.70 |
| 299_Q | 302_N | 1.101 | 0.70 |
| 318_V | 389_L | 1.101 | 0.70 |
| 27_M | 92_L | 1.100 | 0.70 |
| 291_F | 363_A | 1.096 | 0.70 |
| 86_T | 174_G | 1.094 | 0.69 |
| 291_F | 360_A | 1.088 | 0.69 |
| 30_L | 153_A | 1.087 | 0.69 |
| 52_A | 422_W | 1.086 | 0.69 |
| 343_L | 466_A | 1.086 | 0.69 |
| 392_D | 396_I | 1.084 | 0.68 |
| 131_N | 427_V | 1.083 | 0.68 |
| 85_M | 109_I | 1.083 | 0.68 |
| 14_V | 18_I | 1.079 | 0.68 |
| 36_T | 40_G | 1.076 | 0.68 |
| 35_L | 102_L | 1.074 | 0.67 |
| 146_G | 396_I | 1.068 | 0.67 |
| 378_I | 382_A | 1.068 | 0.67 |
| 32_I | 290_L | 1.065 | 0.66 |
| 321_A | 346_A | 1.065 | 0.66 |
| 169_G | 173_A | 1.062 | 0.66 |
| 287_T | 406_G | 1.061 | 0.66 |
| 204_S | 240_A | 1.058 | 0.66 |
| 124_L | 127_L | 1.057 | 0.66 |
| 242_V | 246_A | 1.057 | 0.66 |
| 28_R | 285_G | 1.052 | 0.65 |
| 121_S | 146_G | 1.050 | 0.65 |
| 133_H | 137_G | 1.046 | 0.64 |
| 290_L | 294_R | 1.042 | 0.64 |
| 34_Y | 312_S | 1.030 | 0.63 |
| 142_L | 400_T | 1.025 | 0.62 |
| 50_F | 54_A | 1.024 | 0.62 |
| 275_T | 387_A | 1.018 | 0.61 |
| 345_F | 395_A | 1.016 | 0.61 |
| 168_V | 180_G | 1.016 | 0.61 |
| 280_L | 359_L | 1.015 | 0.61 |
| 120_I | 150_S | 1.015 | 0.61 |
| 72_L | 80_A | 1.010 | 0.60 |
| 120_I | 146_G | 1.009 | 0.60 |
| 24_F | 146_G | 1.009 | 0.60 |
| 42_D | 45_H | 1.007 | 0.60 |
| 32_I | 102_L | 1.006 | 0.60 |
| 200_K | 203_T | 1.004 | 0.60 |
| 75_R | 187_G | 1.003 | 0.60 |
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 | |
| 2xutA | 3 | 0.8536 | 100 | 0.548 | Contact Map |
| 4tphA | 2 | 0.8907 | 100 | 0.599 | Contact Map |
| 4d2bA | 1 | 0.8887 | 100 | 0.604 | Contact Map |
| 4q65A | 1 | 0.8804 | 100 | 0.726 | Contact Map |
| 4oh3A | 2 | 0.934 | 100 | 0.74 | Contact Map |
| 4ikvA | 1 | 0.9464 | 100 | 0.77 | Contact Map |
| 2cfqA | 1 | 0.833 | 99.9 | 0.872 | Contact Map |
| 3wdoA | 1 | 0.8227 | 99.9 | 0.876 | Contact Map |
| 1pw4A | 1 | 0.8247 | 99.8 | 0.883 | Contact Map |
| 2gfpA | 2 | 0.7608 | 99.8 | 0.886 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)