| shortest |
| ID: | 1488502592 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (110) | ||
| Sequences: | 2424 (182.7) | ||
| Seq/Len: | 22.036 | ||
| Nf(neff/√len): | 17.4 |
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: 22.036).
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 |
| 103_Q | 106_E | 2.134 | 1.00 |
| 79_G | 83_V | 2.031 | 1.00 |
| 106_E | 109_L | 1.864 | 1.00 |
| 91_C | 95_R | 1.845 | 1.00 |
| 15_R | 19_L | 1.782 | 1.00 |
| 59_Q | 63_N | 1.749 | 1.00 |
| 78_E | 83_V | 1.700 | 1.00 |
| 37_E | 40_G | 1.697 | 1.00 |
| 17_L | 26_R | 1.615 | 1.00 |
| 84_I | 87_V | 1.549 | 1.00 |
| 71_A | 75_A | 1.492 | 1.00 |
| 4_N | 10_I | 1.414 | 1.00 |
| 92_R | 95_R | 1.397 | 0.99 |
| 62_K | 66_V | 1.387 | 0.99 |
| 12_D | 18_C | 1.379 | 0.99 |
| 99_R | 103_Q | 1.366 | 0.99 |
| 103_Q | 109_L | 1.346 | 0.99 |
| 67_S | 71_A | 1.341 | 0.99 |
| 100_R | 106_E | 1.332 | 0.99 |
| 24_R | 27_D | 1.324 | 0.99 |
| 102_R | 106_E | 1.321 | 0.99 |
| 96_H | 107_R | 1.315 | 0.99 |
| 42_R | 51_W | 1.313 | 0.99 |
| 7_L | 15_R | 1.298 | 0.99 |
| 100_R | 103_Q | 1.292 | 0.99 |
| 29_L | 50_W | 1.290 | 0.99 |
| 95_R | 100_R | 1.250 | 0.99 |
| 88_Q | 92_R | 1.244 | 0.98 |
| 47_L | 54_L | 1.235 | 0.98 |
| 98_P | 103_Q | 1.200 | 0.98 |
| 6_S | 10_I | 1.194 | 0.98 |
| 5_G | 13_D | 1.192 | 0.98 |
| 90_A | 93_A | 1.186 | 0.98 |
| 104_G | 109_L | 1.181 | 0.98 |
| 55_Q | 79_G | 1.176 | 0.98 |
| 77_A | 110_L | 1.137 | 0.97 |
| 47_L | 58_S | 1.130 | 0.97 |
| 34_R | 39_L | 1.127 | 0.97 |
| 98_P | 102_R | 1.127 | 0.97 |
| 52_N | 55_Q | 1.124 | 0.97 |
| 94_I | 98_P | 1.121 | 0.97 |
| 33_T | 37_E | 1.117 | 0.96 |
| 69_L | 72_T | 1.112 | 0.96 |
| 61_L | 65_A | 1.107 | 0.96 |
| 48_K | 52_N | 1.105 | 0.96 |
| 34_R | 37_E | 1.100 | 0.96 |
| 20_F | 24_R | 1.098 | 0.96 |
| 79_G | 87_V | 1.089 | 0.96 |
| 86_V | 90_A | 1.087 | 0.96 |
| 36_V | 40_G | 1.085 | 0.96 |
| 1_R | 12_D | 1.078 | 0.95 |
| 65_A | 68_L | 1.074 | 0.95 |
| 102_R | 109_L | 1.061 | 0.95 |
| 73_A | 76_V | 1.049 | 0.94 |
| 105_L | 108_I | 1.049 | 0.94 |
| 9_L | 12_D | 1.048 | 0.94 |
| 51_W | 63_N | 1.047 | 0.94 |
| 38_L | 41_R | 1.045 | 0.94 |
| 56_Y | 60_E | 1.044 | 0.94 |
| 53_L | 68_L | 1.042 | 0.94 |
| 58_S | 61_L | 1.031 | 0.94 |
| 61_L | 68_L | 1.030 | 0.94 |
| 57_W | 64_S | 1.029 | 0.94 |
| 57_W | 60_E | 1.014 | 0.93 |
| 52_N | 63_N | 1.008 | 0.93 |
| 60_E | 65_A | 1.001 | 0.92 |
| 23_H | 27_D | 1.001 | 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 | |
| 4oavB | 2 | 0.3364 | 3.9 | 0.943 | Contact Map |
| 2qfaC | 1 | 0.4091 | 2.8 | 0.947 | Contact Map |
| 1tbfA | 1 | 0.4 | 2.4 | 0.949 | Contact Map |
| 2a01A | 3 | 0.7182 | 2.3 | 0.95 | Contact Map |
| 3ibjA | 2 | 0.4364 | 1.8 | 0.952 | Contact Map |
| 2rioA | 2 | 0.3727 | 1.4 | 0.955 | Contact Map |
| 1y2kA | 2 | 0.4091 | 1.3 | 0.957 | Contact Map |
| 2ourA | 2 | 0.4818 | 1.2 | 0.957 | Contact Map |
| 3hr1A | 1 | 0.4 | 1.1 | 0.958 | Contact Map |
| 4nkgB | 2 | 0.2364 | 1.1 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)