| mad1 |
| ID: | 1469729526 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 112 (111) | ||
| Sequences: | 347 (231.4) | ||
| Seq/Len: | 3.126 | ||
| Nf(neff/√len): | 22.0 |
Jackhmmer Results: (2016_04)
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: 3.126).
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 |
| 15_V | 19_K | 2.095 | 1.00 |
| 10_Q | 14_E | 1.916 | 0.99 |
| 96_A | 103_L | 1.847 | 0.99 |
| 25_K | 34_Q | 1.792 | 0.99 |
| 87_H | 96_A | 1.791 | 0.99 |
| 2_V | 5_A | 1.735 | 0.99 |
| 24_R | 59_F | 1.634 | 0.98 |
| 28_Y | 50_A | 1.523 | 0.96 |
| 28_Y | 48_L | 1.506 | 0.96 |
| 7_L | 11_R | 1.428 | 0.94 |
| 11_R | 15_V | 1.426 | 0.94 |
| 44_R | 56_C | 1.426 | 0.94 |
| 94_I | 102_T | 1.422 | 0.94 |
| 13_K | 49_Y | 1.397 | 0.93 |
| 19_K | 22_E | 1.375 | 0.93 |
| 57_L | 101_L | 1.337 | 0.91 |
| 85_E | 90_R | 1.335 | 0.91 |
| 41_N | 71_L | 1.324 | 0.91 |
| 30_L | 98_L | 1.315 | 0.90 |
| 28_Y | 106_F | 1.314 | 0.90 |
| 81_G | 85_E | 1.294 | 0.89 |
| 88_L | 93_S | 1.276 | 0.89 |
| 80_V | 97_F | 1.276 | 0.89 |
| 85_E | 92_D | 1.271 | 0.88 |
| 48_L | 54_G | 1.270 | 0.88 |
| 104_E | 107_S | 1.267 | 0.88 |
| 37_I | 87_H | 1.251 | 0.87 |
| 19_K | 37_I | 1.237 | 0.86 |
| 22_E | 98_L | 1.232 | 0.86 |
| 50_A | 105_L | 1.230 | 0.86 |
| 102_T | 106_F | 1.227 | 0.86 |
| 59_F | 94_I | 1.223 | 0.86 |
| 16_F | 23_F | 1.188 | 0.83 |
| 86_V | 91_Q | 1.167 | 0.82 |
| 30_L | 35_I | 1.165 | 0.82 |
| 26_A | 82_E | 1.161 | 0.81 |
| 29_T | 37_I | 1.155 | 0.81 |
| 29_T | 69_M | 1.155 | 0.81 |
| 36_D | 110_T | 1.152 | 0.81 |
| 7_L | 12_L | 1.148 | 0.80 |
| 12_L | 94_I | 1.134 | 0.79 |
| 93_S | 96_A | 1.126 | 0.78 |
| 5_A | 9_N | 1.125 | 0.78 |
| 76_F | 84_I | 1.114 | 0.77 |
| 55_D | 74_T | 1.097 | 0.76 |
| 87_H | 91_Q | 1.089 | 0.75 |
| 80_V | 105_L | 1.089 | 0.75 |
| 24_R | 35_I | 1.079 | 0.74 |
| 73_E | 78_H | 1.077 | 0.74 |
| 2_V | 33_Y | 1.069 | 0.73 |
| 86_V | 96_A | 1.063 | 0.73 |
| 6_E | 10_Q | 1.059 | 0.72 |
| 33_Y | 57_L | 1.053 | 0.72 |
| 27_C | 33_Y | 1.048 | 0.71 |
| 44_R | 82_E | 1.038 | 0.70 |
| 87_H | 100_S | 1.034 | 0.70 |
| 106_F | 110_T | 1.030 | 0.69 |
| 2_V | 110_T | 1.012 | 0.67 |
| 7_L | 19_K | 1.008 | 0.67 |
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 | |
| 4dzoA | 2 | 0.9821 | 100 | 0.019 | Contact Map |
| 2ve7A | 2 | 0.9196 | 70.1 | 0.883 | Contact Map |
| 3vz9B | 1 | 0.8661 | 18.8 | 0.918 | Contact Map |
| 1t7vA | 1 | 0.9643 | 13.1 | 0.923 | Contact Map |
| 1pgjA | 2 | 0.9375 | 12.2 | 0.924 | Contact Map |
| 4l4vA | 2 | 0.9643 | 6.3 | 0.934 | Contact Map |
| 1kcgC | 1 | 0.8304 | 5.7 | 0.935 | Contact Map |
| 4pp8C | 2 | 0.7589 | 5.6 | 0.935 | Contact Map |
| 1a6zA | 2 | 0.9732 | 5.4 | 0.935 | Contact Map |
| 2zxxA | 4 | 0.2768 | 5.2 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)