| 3zja |
| ID: | 1500381994 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 114 (113) | ||
| Sequences: | 1937 (1503.1) | ||
| Seq/Len: | 17.142 | ||
| Nf(neff/√len): | 141.4 |
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: 17.142).
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 |
| 34_E | 100_A | 2.432 | 1.00 |
| 8_A | 109_L | 2.257 | 1.00 |
| 32_A | 62_E | 2.246 | 1.00 |
| 43_G | 82_K | 2.194 | 1.00 |
| 39_T | 98_H | 2.188 | 1.00 |
| 64_P | 67_G | 2.050 | 1.00 |
| 92_S | 108_K | 1.987 | 1.00 |
| 37_S | 98_H | 1.896 | 1.00 |
| 38_V | 45_V | 1.886 | 1.00 |
| 88_K | 91_Q | 1.873 | 1.00 |
| 34_E | 60_R | 1.860 | 1.00 |
| 55_M | 79_M | 1.841 | 1.00 |
| 26_T | 68_Q | 1.830 | 1.00 |
| 32_A | 65_A | 1.820 | 1.00 |
| 46_T | 57_E | 1.819 | 1.00 |
| 4_S | 26_T | 1.819 | 1.00 |
| 35_L | 99_F | 1.809 | 1.00 |
| 21_G | 109_L | 1.787 | 1.00 |
| 41_E | 94_A | 1.773 | 1.00 |
| 61_I | 71_F | 1.748 | 1.00 |
| 98_H | 104_P | 1.696 | 1.00 |
| 95_V | 109_L | 1.673 | 1.00 |
| 47_V | 61_I | 1.662 | 1.00 |
| 5_V | 23_L | 1.638 | 1.00 |
| 43_G | 84_K | 1.631 | 1.00 |
| 69_L | 76_N | 1.581 | 1.00 |
| 46_T | 81_E | 1.580 | 1.00 |
| 6_D | 26_T | 1.544 | 1.00 |
| 61_I | 69_L | 1.516 | 1.00 |
| 94_A | 108_K | 1.515 | 1.00 |
| 4_S | 28_E | 1.495 | 1.00 |
| 23_L | 71_F | 1.463 | 1.00 |
| 21_G | 95_V | 1.455 | 1.00 |
| 49_E | 56_K | 1.448 | 1.00 |
| 50_T | 53_G | 1.420 | 1.00 |
| 33_D | 102_S | 1.406 | 0.99 |
| 10_I | 19_A | 1.402 | 0.99 |
| 87_P | 111_V | 1.362 | 0.99 |
| 23_L | 78_L | 1.361 | 0.99 |
| 33_D | 101_H | 1.357 | 0.99 |
| 94_A | 106_A | 1.357 | 0.99 |
| 21_G | 80_F | 1.335 | 0.99 |
| 24_T | 70_V | 1.303 | 0.99 |
| 44_E | 81_E | 1.295 | 0.99 |
| 10_I | 21_G | 1.236 | 0.98 |
| 33_D | 103_D | 1.227 | 0.98 |
| 9_Y | 73_S | 1.222 | 0.98 |
| 85_Q | 91_Q | 1.218 | 0.98 |
| 35_L | 97_L | 1.205 | 0.98 |
| 40_S | 45_V | 1.185 | 0.98 |
| 93_V | 109_L | 1.178 | 0.98 |
| 10_I | 93_V | 1.153 | 0.97 |
| 7_A | 24_T | 1.141 | 0.97 |
| 24_T | 68_Q | 1.131 | 0.97 |
| 51_I | 56_K | 1.117 | 0.96 |
| 89_Q | 113_A | 1.107 | 0.96 |
| 58_V | 76_N | 1.107 | 0.96 |
| 13_P | 16_D | 1.099 | 0.96 |
| 33_D | 100_A | 1.082 | 0.96 |
| 21_G | 78_L | 1.066 | 0.95 |
| 39_T | 104_P | 1.065 | 0.95 |
| 44_E | 82_K | 1.063 | 0.95 |
| 72_K | 75_G | 1.055 | 0.95 |
| 34_E | 62_E | 1.051 | 0.94 |
| 6_D | 24_T | 1.035 | 0.94 |
| 40_S | 80_F | 1.030 | 0.94 |
| 5_V | 8_A | 1.030 | 0.94 |
| 61_I | 76_N | 1.014 | 0.93 |
| 92_S | 110_P | 1.008 | 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
- 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 | |
| 3zjaA | 1 | 1 | 100 | 0.06 | Contact Map |
| 1x9lA | 1 | 1 | 100 | 0.105 | Contact Map |
| 2k6wA | 1 | 0.9737 | 100 | 0.119 | Contact Map |
| 1ufgA | 1 | 0.8947 | 71.1 | 0.876 | Contact Map |
| 3umnA | 3 | 0.886 | 65.3 | 0.881 | Contact Map |
| 1ifrA | 1 | 0.8684 | 63.3 | 0.882 | Contact Map |
| 2lllA | 1 | 0.8947 | 60 | 0.885 | Contact Map |
| 2x3cA | 1 | 0.9035 | 59 | 0.886 | Contact Map |
| 3isyA | 1 | 0.8772 | 46.5 | 0.894 | Contact Map |
| 3jt0A | 2 | 0.8684 | 34 | 0.902 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)