| d3qd8x1 |
| ID: | 1447473761 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 154 (151) | ||
| Sequences: | 3578 (2038.4) | ||
| Seq/Len: | 23.695 | ||
| Nf(neff/√len): | 165.9 |
HHblits Results: (2015_06)
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: 23.695).
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 |
| 52_M | 118_W | 2.689 | 1.00 |
| 80_R | 84_A | 2.639 | 1.00 |
| 12_N | 96_Q | 2.638 | 1.00 |
| 57_L | 62_L | 2.529 | 1.00 |
| 27_F | 82_A | 2.273 | 1.00 |
| 84_A | 138_D | 2.253 | 1.00 |
| 80_R | 138_D | 2.176 | 1.00 |
| 80_R | 134_V | 2.155 | 1.00 |
| 105_R | 113_E | 2.134 | 1.00 |
| 5_L | 103_V | 2.108 | 1.00 |
| 10_I | 57_L | 2.053 | 1.00 |
| 35_L | 79_P | 2.002 | 1.00 |
| 103_V | 107_E | 1.982 | 1.00 |
| 95_D | 99_R | 1.924 | 1.00 |
| 102_A | 108_G | 1.899 | 1.00 |
| 102_A | 106_D | 1.887 | 1.00 |
| 78_R | 81_E | 1.826 | 1.00 |
| 128_A | 132_T | 1.785 | 1.00 |
| 114_Q | 121_Q | 1.763 | 1.00 |
| 84_A | 88_D | 1.721 | 1.00 |
| 92_T | 96_Q | 1.604 | 1.00 |
| 59_D | 128_A | 1.580 | 1.00 |
| 85_L | 88_D | 1.576 | 1.00 |
| 86_A | 130_M | 1.538 | 1.00 |
| 20_Y | 90_E | 1.526 | 1.00 |
| 13_E | 49_H | 1.524 | 1.00 |
| 28_D | 36_A | 1.507 | 1.00 |
| 61_D | 131_A | 1.496 | 1.00 |
| 3_H | 62_L | 1.491 | 1.00 |
| 77_D | 81_E | 1.460 | 1.00 |
| 87_L | 91_R | 1.426 | 1.00 |
| 27_F | 39_F | 1.424 | 1.00 |
| 39_F | 86_A | 1.424 | 1.00 |
| 44_V | 47_R | 1.423 | 1.00 |
| 6_M | 57_L | 1.422 | 1.00 |
| 25_V | 54_V | 1.416 | 1.00 |
| 6_M | 112_G | 1.412 | 1.00 |
| 26_Y | 30_E | 1.353 | 0.99 |
| 46_E | 49_H | 1.351 | 0.99 |
| 123_Q | 126_E | 1.337 | 0.99 |
| 4_A | 8_E | 1.334 | 0.99 |
| 37_K | 41_S | 1.324 | 0.99 |
| 6_M | 53_L | 1.321 | 0.99 |
| 92_T | 95_D | 1.290 | 0.99 |
| 28_D | 33_P | 1.267 | 0.99 |
| 7_Q | 62_L | 1.258 | 0.99 |
| 101_T | 117_Q | 1.248 | 0.99 |
| 101_T | 116_M | 1.238 | 0.98 |
| 17_A | 43_A | 1.235 | 0.98 |
| 94_T | 127_V | 1.230 | 0.98 |
| 40_Y | 55_Q | 1.189 | 0.98 |
| 102_A | 110_F | 1.171 | 0.98 |
| 87_L | 131_A | 1.169 | 0.97 |
| 88_D | 91_R | 1.138 | 0.97 |
| 18_Q | 66_I | 1.133 | 0.97 |
| 15_T | 19_Q | 1.118 | 0.96 |
| 83_L | 133_L | 1.107 | 0.96 |
| 16_A | 46_E | 1.099 | 0.96 |
| 31_D | 135_R | 1.098 | 0.96 |
| 14_F | 50_A | 1.085 | 0.96 |
| 94_T | 123_Q | 1.081 | 0.95 |
| 100_L | 116_M | 1.081 | 0.95 |
| 53_L | 115_F | 1.079 | 0.95 |
| 94_T | 98_G | 1.077 | 0.95 |
| 46_E | 126_E | 1.068 | 0.95 |
| 68_G | 71_T | 1.064 | 0.95 |
| 49_H | 90_E | 1.064 | 0.95 |
| 45_E | 49_H | 1.062 | 0.95 |
| 5_L | 100_L | 1.059 | 0.95 |
| 56_H | 112_G | 1.057 | 0.95 |
| 28_D | 55_Q | 1.044 | 0.94 |
| 39_F | 82_A | 1.038 | 0.94 |
| 83_L | 137_A | 1.035 | 0.94 |
| 81_E | 84_A | 1.025 | 0.93 |
| 27_F | 79_P | 1.022 | 0.93 |
| 9_Q | 97_V | 1.020 | 0.93 |
| 67_P | 71_T | 1.014 | 0.93 |
| 42_Q | 129_L | 1.010 | 0.93 |
| 52_M | 119_F | 1.010 | 0.93 |
| 42_Q | 126_E | 1.009 | 0.93 |
| 11_H | 15_T | 1.006 | 0.93 |
| 114_Q | 117_Q | 1.000 | 0.92 |
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 | |
| 1z6oA | 12 | 0.9935 | 100 | 0.066 | Contact Map |
| 1vlgA | 8 | 1 | 100 | 0.085 | Contact Map |
| 3a68A | 24 | 1 | 100 | 0.092 | Contact Map |
| 3vnxA | 1 | 1 | 100 | 0.102 | Contact Map |
| 3wnwA | 12 | 1 | 100 | 0.104 | Contact Map |
| 1s3qA | 12 | 1 | 100 | 0.109 | Contact Map |
| 3kxuA | 1 | 0.9221 | 100 | 0.11 | Contact Map |
| 1z6oM | 12 | 1 | 100 | 0.111 | Contact Map |
| 3bvfA | 6 | 1 | 100 | 0.112 | Contact Map |
| 1eumA | 6 | 1 | 100 | 0.117 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)