| T0806 |
| ID: | 1401991170 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 258 (256) | ||
| Sequences: | 1208 (876.1) | ||
| Seq/Len: | 4.719 | ||
| Nf(neff/√len): | 54.8 |
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: 4.719).
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 |
| 30_N | 150_I | 4.183 | 1.00 |
| 52_I | 56_L | 3.537 | 1.00 |
| 142_D | 145_Q | 2.851 | 1.00 |
| 60_N | 63_R | 2.762 | 1.00 |
| 100_D | 223_R | 2.757 | 1.00 |
| 241_D | 244_S | 2.631 | 1.00 |
| 47_S | 54_D | 2.584 | 1.00 |
| 17_L | 77_R | 2.484 | 1.00 |
| 81_L | 101_F | 2.448 | 1.00 |
| 92_Q | 95_T | 2.445 | 1.00 |
| 168_I | 219_I | 2.413 | 1.00 |
| 100_D | 221_E | 2.377 | 1.00 |
| 4_L | 167_V | 2.373 | 1.00 |
| 149_D | 153_N | 2.355 | 1.00 |
| 104_A | 220_I | 2.225 | 1.00 |
| 241_D | 253_K | 2.146 | 1.00 |
| 187_E | 248_G | 2.126 | 1.00 |
| 10_T | 84_K | 2.113 | 1.00 |
| 3_I | 219_I | 2.099 | 1.00 |
| 228_E | 231_T | 2.095 | 1.00 |
| 217_R | 221_E | 2.007 | 1.00 |
| 151_I | 178_S | 1.970 | 1.00 |
| 96_F | 217_R | 1.965 | 1.00 |
| 244_S | 253_K | 1.928 | 1.00 |
| 226_K | 229_Q | 1.921 | 1.00 |
| 137_N | 140_G | 1.852 | 1.00 |
| 13_Y | 82_A | 1.845 | 1.00 |
| 61_A | 65_H | 1.815 | 1.00 |
| 194_L | 253_K | 1.808 | 1.00 |
| 59_I | 63_R | 1.755 | 1.00 |
| 246_S | 249_E | 1.755 | 1.00 |
| 15_S | 77_R | 1.753 | 1.00 |
| 196_E | 255_Y | 1.717 | 0.99 |
| 38_A | 64_F | 1.710 | 0.99 |
| 96_F | 101_F | 1.679 | 0.99 |
| 5_I | 216_S | 1.642 | 0.99 |
| 26_E | 158_A | 1.632 | 0.99 |
| 31_S | 67_W | 1.620 | 0.99 |
| 219_I | 224_L | 1.599 | 0.99 |
| 231_T | 250_L | 1.598 | 0.99 |
| 5_I | 87_V | 1.598 | 0.99 |
| 219_I | 230_L | 1.596 | 0.99 |
| 5_I | 108_L | 1.589 | 0.99 |
| 192_V | 249_E | 1.587 | 0.99 |
| 96_F | 104_A | 1.585 | 0.99 |
| 46_I | 52_I | 1.573 | 0.99 |
| 103_F | 107_H | 1.571 | 0.99 |
| 58_G | 62_A | 1.559 | 0.99 |
| 8_A | 11_L | 1.556 | 0.99 |
| 26_E | 154_K | 1.541 | 0.99 |
| 227_P | 250_L | 1.533 | 0.99 |
| 105_Q | 121_L | 1.530 | 0.99 |
| 97_S | 100_D | 1.513 | 0.98 |
| 52_I | 57_A | 1.510 | 0.98 |
| 109_R | 158_A | 1.501 | 0.98 |
| 168_I | 230_L | 1.496 | 0.98 |
| 141_K | 145_Q | 1.491 | 0.98 |
| 100_D | 220_I | 1.471 | 0.98 |
| 37_E | 135_L | 1.463 | 0.98 |
| 103_F | 220_I | 1.457 | 0.98 |
| 214_L | 236_E | 1.455 | 0.98 |
| 151_I | 179_V | 1.455 | 0.98 |
| 168_I | 191_P | 1.447 | 0.98 |
| 96_F | 100_D | 1.438 | 0.98 |
| 224_L | 229_Q | 1.419 | 0.97 |
| 18_T | 81_L | 1.408 | 0.97 |
| 76_A | 123_L | 1.390 | 0.97 |
| 191_P | 250_L | 1.387 | 0.97 |
| 31_S | 146_F | 1.377 | 0.97 |
| 81_L | 96_F | 1.369 | 0.97 |
| 104_A | 216_S | 1.366 | 0.96 |
| 80_I | 91_L | 1.344 | 0.96 |
| 34_L | 137_N | 1.336 | 0.96 |
| 221_E | 235_S | 1.331 | 0.96 |
| 4_L | 155_L | 1.329 | 0.96 |
| 96_F | 221_E | 1.312 | 0.95 |
| 86_D | 206_F | 1.289 | 0.95 |
| 99_D | 223_R | 1.287 | 0.95 |
| 47_S | 57_A | 1.285 | 0.95 |
| 62_A | 66_D | 1.283 | 0.94 |
| 195_D | 205_S | 1.281 | 0.94 |
| 27_L | 154_K | 1.277 | 0.94 |
| 240_F | 250_L | 1.251 | 0.93 |
| 75_N | 125_Q | 1.251 | 0.93 |
| 207_Y | 254_R | 1.250 | 0.93 |
| 166_V | 187_E | 1.244 | 0.93 |
| 84_K | 94_E | 1.237 | 0.93 |
| 35_I | 114_L | 1.233 | 0.93 |
| 13_Y | 124_M | 1.231 | 0.93 |
| 216_S | 220_I | 1.229 | 0.93 |
| 47_S | 52_I | 1.225 | 0.92 |
| 35_I | 46_I | 1.221 | 0.92 |
| 37_E | 41_L | 1.218 | 0.92 |
| 229_Q | 232_G | 1.198 | 0.91 |
| 225_T | 229_Q | 1.179 | 0.90 |
| 30_N | 139_R | 1.164 | 0.90 |
| 166_V | 227_P | 1.160 | 0.89 |
| 201_F | 253_K | 1.158 | 0.89 |
| 192_V | 203_I | 1.157 | 0.89 |
| 148_G | 180_K | 1.146 | 0.89 |
| 93_A | 96_F | 1.144 | 0.89 |
| 103_F | 224_L | 1.129 | 0.88 |
| 71_F | 75_N | 1.126 | 0.88 |
| 31_S | 35_I | 1.119 | 0.87 |
| 144_Y | 177_K | 1.114 | 0.87 |
| 43_P | 61_A | 1.092 | 0.85 |
| 12_D | 84_K | 1.091 | 0.85 |
| 72_T | 75_N | 1.087 | 0.85 |
| 38_A | 41_L | 1.079 | 0.84 |
| 190_K | 249_E | 1.067 | 0.83 |
| 195_D | 254_R | 1.056 | 0.83 |
| 153_N | 183_K | 1.054 | 0.82 |
| 93_A | 217_R | 1.050 | 0.82 |
| 2_L | 165_N | 1.047 | 0.82 |
| 117_V | 154_K | 1.040 | 0.81 |
| 154_K | 157_E | 1.034 | 0.81 |
| 10_T | 89_T | 1.028 | 0.80 |
| 54_D | 58_G | 1.025 | 0.80 |
| 28_L | 70_D | 1.022 | 0.80 |
| 149_D | 180_K | 1.019 | 0.79 |
| 239_F | 255_Y | 1.010 | 0.79 |
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 | |
| 4a1qA | 2 | 0.2597 | 10.3 | 0.971 | Contact Map |
| 3bbnB | 1 | 0.4845 | 8.2 | 0.972 | Contact Map |
| 2vqeB | 1 | 0.4729 | 8 | 0.972 | Contact Map |
| 3eyiA | 2 | 0.2403 | 8 | 0.972 | Contact Map |
| 1r45A | 4 | 0.6008 | 6.1 | 0.974 | Contact Map |
| 1wrdA | 1 | 0.2636 | 5.5 | 0.974 | Contact Map |
| 2duyA | 1 | 0.2481 | 5.4 | 0.974 | Contact Map |
| 4ou0A | 1 | 0.2287 | 5.2 | 0.974 | Contact Map |
| 4glxA | 1 | 0.3256 | 5.1 | 0.975 | Contact Map |
| 1wy3A | 1 | 0.1318 | 4.7 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)