| 1DC7 |
| ID: | 1487352110 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (120) | ||
| Sequences: | 97977 (70250.4) | ||
| Seq/Len: | 816.475 | ||
| Nf(neff/√len): | 6413.0 |
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: 816.475).
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 |
| 16_R | 32_T | 3.023 | 1.00 |
| 20_E | 32_T | 2.797 | 1.00 |
| 16_R | 34_E | 2.712 | 1.00 |
| 9_V | 39_V | 2.362 | 1.00 |
| 40_L | 68_Q | 2.164 | 1.00 |
| 56_R | 84_H | 2.147 | 1.00 |
| 31_T | 48_P | 2.063 | 1.00 |
| 53_S | 65_L | 2.025 | 1.00 |
| 37_N | 59_G | 1.967 | 1.00 |
| 100_D | 114_L | 1.954 | 1.00 |
| 26_A | 112_V | 1.889 | 1.00 |
| 5_I | 31_T | 1.871 | 1.00 |
| 33_F | 42_A | 1.840 | 1.00 |
| 60_M | 68_Q | 1.828 | 1.00 |
| 66_L | 78_V | 1.725 | 1.00 |
| 36_G | 60_M | 1.662 | 1.00 |
| 31_T | 42_A | 1.651 | 1.00 |
| 80_I | 98_A | 1.640 | 1.00 |
| 34_E | 38_E | 1.631 | 1.00 |
| 22_A | 108_I | 1.626 | 1.00 |
| 31_T | 46_K | 1.615 | 1.00 |
| 67_K | 96_Q | 1.584 | 1.00 |
| 5_I | 29_T | 1.578 | 1.00 |
| 35_N | 59_G | 1.576 | 1.00 |
| 61_D | 64_A | 1.487 | 1.00 |
| 44_A | 72_R | 1.457 | 1.00 |
| 55_I | 63_L | 1.375 | 0.99 |
| 70_K | 99_F | 1.373 | 0.99 |
| 35_N | 38_E | 1.370 | 0.99 |
| 51_L | 76_L | 1.368 | 0.99 |
| 43_L | 69_I | 1.345 | 0.99 |
| 60_M | 64_A | 1.342 | 0.99 |
| 7_W | 33_F | 1.339 | 0.99 |
| 20_E | 24_A | 1.339 | 0.99 |
| 100_D | 117_R | 1.316 | 0.99 |
| 36_G | 65_L | 1.259 | 0.99 |
| 5_I | 49_D | 1.217 | 0.98 |
| 68_Q | 71_Q | 1.215 | 0.98 |
| 84_H | 89_A | 1.211 | 0.98 |
| 40_L | 65_L | 1.209 | 0.98 |
| 7_W | 48_P | 1.208 | 0.98 |
| 92_S | 96_Q | 1.207 | 0.98 |
| 42_A | 48_P | 1.201 | 0.98 |
| 114_L | 117_R | 1.196 | 0.98 |
| 68_Q | 72_R | 1.194 | 0.98 |
| 37_N | 60_M | 1.187 | 0.98 |
| 42_A | 46_K | 1.182 | 0.98 |
| 87_L | 91_V | 1.182 | 0.98 |
| 110_E | 114_L | 1.158 | 0.97 |
| 63_L | 93_A | 1.139 | 0.97 |
| 81_M | 106_F | 1.137 | 0.97 |
| 63_L | 92_S | 1.114 | 0.96 |
| 91_V | 95_Q | 1.081 | 0.95 |
| 39_V | 65_L | 1.081 | 0.95 |
| 42_A | 45_S | 1.071 | 0.95 |
| 66_L | 80_I | 1.058 | 0.95 |
| 55_I | 80_I | 1.058 | 0.95 |
| 33_F | 39_V | 1.049 | 0.94 |
| 86_D | 89_A | 1.031 | 0.94 |
| 8_V | 19_L | 1.021 | 0.93 |
| 5_I | 46_K | 1.016 | 0.93 |
| 13_S | 34_E | 1.011 | 0.93 |
| 6_V | 28_L | 1.002 | 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 | |
| 3dzdA | 2 | 0.9758 | 99.4 | -0.231 | Contact Map |
| 3rqiA | 1 | 0.9758 | 99.4 | -0.227 | Contact Map |
| 1dc7A | 1 | 1 | 99.4 | -0.225 | Contact Map |
| 3eq2A | 2 | 0.9919 | 99.4 | -0.224 | Contact Map |
| 4l4uA | 1 | 1 | 99.4 | -0.224 | Contact Map |
| 1ys7A | 2 | 0.9839 | 99.4 | -0.215 | Contact Map |
| 3r0jA | 2 | 0.9919 | 99.4 | -0.214 | Contact Map |
| 1yioA | 1 | 0.9919 | 99.4 | -0.211 | Contact Map |
| 1kgsA | 1 | 0.9839 | 99.3 | -0.206 | Contact Map |
| 3n0rA | 1 | 0.9758 | 99.3 | -0.206 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)