| T0778 |
| ID: | 1440612373 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (113) | ||
| Sequences: | 41478 (31642.7) | ||
| Seq/Len: | 367.062 | ||
| Nf(neff/√len): | 2976.7 |
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: 367.062).
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 |
| 29_K | 32_R | 2.506 | 1.00 |
| 88_R | 104_D | 2.436 | 1.00 |
| 72_T | 88_R | 2.431 | 1.00 |
| 54_R | 70_D | 2.424 | 1.00 |
| 63_K | 66_E | 2.397 | 1.00 |
| 97_K | 100_E | 2.382 | 1.00 |
| 51_P | 70_D | 2.292 | 1.00 |
| 85_F | 104_D | 2.279 | 1.00 |
| 55_A | 71_C | 2.219 | 1.00 |
| 17_E | 36_C | 2.101 | 1.00 |
| 38_T | 54_R | 2.069 | 1.00 |
| 20_R | 36_C | 2.052 | 1.00 |
| 89_G | 105_F | 1.921 | 1.00 |
| 58_Y | 66_E | 1.822 | 1.00 |
| 21_G | 37_Y | 1.814 | 1.00 |
| 24_F | 32_R | 1.790 | 1.00 |
| 92_R | 104_D | 1.717 | 1.00 |
| 58_Y | 70_D | 1.690 | 1.00 |
| 92_R | 100_E | 1.658 | 1.00 |
| 24_F | 36_C | 1.634 | 1.00 |
| 37_Y | 53_N | 1.598 | 1.00 |
| 71_C | 87_R | 1.583 | 1.00 |
| 108_V | 118_A | 1.577 | 1.00 |
| 68_E | 72_T | 1.465 | 1.00 |
| 34_I | 38_T | 1.410 | 1.00 |
| 105_F | 121_E | 1.377 | 0.99 |
| 40_G | 50_L | 1.371 | 0.99 |
| 102_K | 106_E | 1.345 | 0.99 |
| 81_Y | 84_A | 1.315 | 0.99 |
| 34_I | 58_Y | 1.281 | 0.99 |
| 47_N | 50_L | 1.262 | 0.99 |
| 68_E | 95_L | 1.239 | 0.98 |
| 74_A | 84_A | 1.220 | 0.98 |
| 23_G | 27_E | 1.197 | 0.98 |
| 34_I | 61_I | 1.194 | 0.98 |
| 82_S | 112_E | 1.174 | 0.98 |
| 75_I | 85_F | 1.174 | 0.98 |
| 115_N | 118_A | 1.154 | 0.97 |
| 92_R | 97_K | 1.150 | 0.97 |
| 58_Y | 63_K | 1.148 | 0.97 |
| 68_E | 92_R | 1.146 | 0.97 |
| 88_R | 92_R | 1.133 | 0.97 |
| 54_R | 58_Y | 1.126 | 0.97 |
| 56_M | 87_R | 1.105 | 0.96 |
| 41_I | 51_P | 1.098 | 0.96 |
| 65_E | 95_L | 1.090 | 0.96 |
| 41_I | 50_L | 1.090 | 0.96 |
| 48_A | 78_D | 1.083 | 0.96 |
| 75_I | 84_A | 1.077 | 0.95 |
| 64_Y | 94_F | 1.073 | 0.95 |
| 24_F | 29_K | 1.071 | 0.95 |
| 106_E | 122_L | 1.067 | 0.95 |
| 34_I | 57_A | 1.065 | 0.95 |
| 31_E | 61_I | 1.065 | 0.95 |
| 85_F | 107_T | 1.062 | 0.95 |
| 17_E | 39_R | 1.060 | 0.95 |
| 107_T | 111_L | 1.054 | 0.95 |
| 22_N | 53_N | 1.048 | 0.94 |
| 78_D | 81_Y | 1.040 | 0.94 |
| 51_P | 73_Q | 1.017 | 0.93 |
| 44_D | 47_N | 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
- 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 | |
| 2pziA | 2 | 0.9449 | 99.5 | -0.07 | Contact Map |
| 1kt0A | 1 | 0.9685 | 99.5 | -0.043 | Contact Map |
| 4l9pA | 1 | 1 | 99.5 | -0.038 | Contact Map |
| 3urzA | 2 | 0.9055 | 99.5 | -0.037 | Contact Map |
| 2fbnA | 2 | 1 | 99.4 | -0.03 | Contact Map |
| 1dceA | 2 | 1 | 99.4 | -0.03 | Contact Map |
| 3q7aA | 1 | 1 | 99.4 | -0.024 | Contact Map |
| 3dssA | 1 | 1 | 99.4 | -0.02 | Contact Map |
| 4ja7A | 1 | 0.937 | 99.4 | -0.02 | Contact Map |
| 2if4A | 1 | 0.8661 | 99.4 | -0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)