| 1rqm |
| ID: | 1408343193 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (102) | ||
| Sequences: | 14766 (10880.4) | ||
| Seq/Len: | 144.765 | ||
| Nf(neff/√len): | 1077.3 |
HHblits Results: (2013_03)
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: 144.765).
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 |
| 83_P | 86_Q | 2.841 | 1.00 |
| 45_A | 97_E | 2.420 | 1.00 |
| 97_E | 101_A | 2.294 | 1.00 |
| 41_E | 93_K | 2.271 | 1.00 |
| 11_Q | 66_Q | 2.242 | 1.00 |
| 57_V | 64_T | 2.125 | 1.00 |
| 29_C | 32_C | 2.070 | 1.00 |
| 7_D | 63_T | 1.956 | 1.00 |
| 18_G | 51_T | 1.926 | 1.00 |
| 20_V | 51_T | 1.864 | 1.00 |
| 19_P | 79_K | 1.852 | 1.00 |
| 92_P | 95_Q | 1.847 | 1.00 |
| 76_I | 86_Q | 1.825 | 1.00 |
| 67_F | 78_F | 1.798 | 1.00 |
| 35_M | 75_L | 1.781 | 1.00 |
| 57_V | 72_I | 1.764 | 1.00 |
| 78_F | 83_P | 1.672 | 1.00 |
| 85_K | 99_Q | 1.656 | 1.00 |
| 76_I | 83_P | 1.651 | 1.00 |
| 7_D | 62_E | 1.635 | 1.00 |
| 5_L | 53_A | 1.629 | 1.00 |
| 36_A | 54_K | 1.539 | 1.00 |
| 56_N | 59_E | 1.498 | 1.00 |
| 46_H | 101_A | 1.486 | 1.00 |
| 23_D | 35_M | 1.447 | 1.00 |
| 9_N | 13_A | 1.362 | 0.99 |
| 93_K | 97_E | 1.346 | 0.99 |
| 95_Q | 98_A | 1.307 | 0.99 |
| 27_A | 56_N | 1.306 | 0.99 |
| 25_W | 54_K | 1.290 | 0.99 |
| 23_D | 31_P | 1.273 | 0.99 |
| 23_D | 54_K | 1.269 | 0.99 |
| 34_M | 90_Y | 1.263 | 0.99 |
| 77_L | 103_V | 1.245 | 0.98 |
| 21_L | 39_L | 1.229 | 0.98 |
| 6_T | 9_N | 1.211 | 0.98 |
| 21_L | 77_L | 1.206 | 0.98 |
| 25_W | 56_N | 1.192 | 0.98 |
| 19_P | 77_L | 1.189 | 0.98 |
| 38_V | 93_K | 1.179 | 0.98 |
| 46_H | 97_E | 1.173 | 0.98 |
| 24_F | 67_F | 1.172 | 0.98 |
| 20_V | 53_A | 1.170 | 0.97 |
| 23_D | 75_L | 1.169 | 0.97 |
| 45_A | 93_K | 1.159 | 0.97 |
| 99_Q | 102_D | 1.147 | 0.97 |
| 21_L | 75_L | 1.133 | 0.97 |
| 77_L | 99_Q | 1.131 | 0.97 |
| 38_V | 41_E | 1.128 | 0.97 |
| 39_L | 52_V | 1.127 | 0.97 |
| 40_E | 44_E | 1.113 | 0.96 |
| 7_D | 60_N | 1.091 | 0.96 |
| 99_Q | 103_V | 1.086 | 0.96 |
| 24_F | 69_I | 1.070 | 0.95 |
| 13_A | 51_T | 1.070 | 0.95 |
| 42_F | 97_E | 1.060 | 0.95 |
| 23_D | 36_A | 1.058 | 0.95 |
| 22_V | 78_F | 1.035 | 0.94 |
| 69_I | 74_T | 1.021 | 0.93 |
| 98_A | 102_D | 1.021 | 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 | |
| 3f8uA | 2 | 1 | 99.8 | 0.068 | Contact Map |
| 3apoA | 1 | 0.9238 | 99.8 | 0.071 | Contact Map |
| 2b5eA | 1 | 1 | 99.8 | 0.079 | Contact Map |
| 2r2jA | 1 | 0.981 | 99.8 | 0.082 | Contact Map |
| 3qouA | 1 | 0.9905 | 99.8 | 0.087 | Contact Map |
| 4ekzA | 1 | 1 | 99.8 | 0.093 | Contact Map |
| 4cdoA | 2 | 1 | 99.8 | 0.104 | Contact Map |
| 4kcaA | 2 | 0.9905 | 99.8 | 0.105 | Contact Map |
| 3us3A | 1 | 0.981 | 99.8 | 0.105 | Contact Map |
| 1sjiA | 2 | 0.981 | 99.8 | 0.11 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)