| Adam Frost LEM2 CTD |
| ID: | 1492735188 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (101) | ||
| Sequences: | 316 (206.9) | ||
| Seq/Len: | 3.129 | ||
| Nf(neff/√len): | 20.6 |
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: 3.129).
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 |
| 25_V | 78_I | 2.201 | 1.00 |
| 72_A | 91_L | 1.821 | 0.99 |
| 21_I | 67_A | 1.787 | 0.99 |
| 60_M | 91_L | 1.606 | 0.98 |
| 10_E | 66_R | 1.576 | 0.97 |
| 81_E | 94_R | 1.573 | 0.97 |
| 89_D | 94_R | 1.474 | 0.95 |
| 67_A | 71_L | 1.446 | 0.95 |
| 43_G | 46_H | 1.433 | 0.94 |
| 79_Q | 91_L | 1.414 | 0.94 |
| 32_W | 36_M | 1.408 | 0.94 |
| 14_M | 18_V | 1.381 | 0.93 |
| 48_R | 64_W | 1.369 | 0.93 |
| 24_V | 94_R | 1.359 | 0.92 |
| 83_H | 89_D | 1.344 | 0.92 |
| 83_H | 94_R | 1.308 | 0.90 |
| 2_Y | 5_R | 1.307 | 0.90 |
| 18_V | 70_F | 1.305 | 0.90 |
| 70_F | 76_S | 1.291 | 0.89 |
| 47_V | 91_L | 1.270 | 0.88 |
| 47_V | 76_S | 1.257 | 0.88 |
| 60_M | 67_A | 1.233 | 0.86 |
| 78_I | 93_W | 1.210 | 0.85 |
| 28_H | 67_A | 1.210 | 0.85 |
| 76_S | 95_W | 1.196 | 0.84 |
| 16_E | 20_K | 1.186 | 0.83 |
| 11_E | 66_R | 1.184 | 0.83 |
| 77_R | 84_R | 1.180 | 0.83 |
| 79_Q | 93_W | 1.173 | 0.82 |
| 60_M | 76_S | 1.163 | 0.81 |
| 52_I | 84_R | 1.157 | 0.81 |
| 37_E | 69_E | 1.134 | 0.79 |
| 16_E | 34_Q | 1.120 | 0.78 |
| 49_D | 52_I | 1.108 | 0.77 |
| 75_E | 90_M | 1.091 | 0.75 |
| 21_I | 54_P | 1.076 | 0.74 |
| 23_D | 27_D | 1.073 | 0.74 |
| 14_M | 66_R | 1.066 | 0.73 |
| 3_R | 101_F | 1.066 | 0.73 |
| 52_I | 74_N | 1.065 | 0.73 |
| 42_V | 46_H | 1.064 | 0.73 |
| 28_H | 71_L | 1.063 | 0.73 |
| 21_I | 45_L | 1.052 | 0.72 |
| 67_A | 77_R | 1.048 | 0.71 |
| 47_V | 74_N | 1.038 | 0.70 |
| 82_S | 89_D | 1.037 | 0.70 |
| 10_E | 16_E | 1.035 | 0.70 |
| 7_L | 27_D | 1.032 | 0.69 |
| 60_M | 63_V | 1.025 | 0.69 |
| 49_D | 74_N | 1.025 | 0.69 |
| 1_K | 22_I | 1.022 | 0.68 |
| 42_V | 58_R | 1.018 | 0.68 |
| 16_E | 27_D | 1.009 | 0.67 |
| 68_V | 93_W | 1.009 | 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 | |
| 2ch0A | 1 | 1 | 100 | 0.069 | Contact Map |
| 4gl6A | 2 | 0.3398 | 5.8 | 0.924 | Contact Map |
| 1hskA | 1 | 0.4175 | 4.7 | 0.927 | Contact Map |
| 1jjrA | 1 | 0.2621 | 4 | 0.929 | Contact Map |
| 4l5gA | 2 | 0.6796 | 3.1 | 0.933 | Contact Map |
| 3pg5A | 4 | 0.2039 | 2.8 | 0.934 | Contact Map |
| 4waiA | 4 | 0.3495 | 2.6 | 0.936 | Contact Map |
| 4h9nC | 1 | 0.9029 | 2.1 | 0.939 | Contact Map |
| 3cmqA | 1 | 0.3398 | 2.1 | 0.939 | Contact Map |
| 1wjwA | 1 | 0.4078 | 2.1 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)