| 1aba |
| ID: | 1501248399 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (77) | ||
| Sequences: | 6645 (3471.6) | ||
| Seq/Len: | 86.299 | ||
| Nf(neff/√len): | 395.6 |
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: 86.299).
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 |
| 79_F | 83_R | 3.496 | 1.00 |
| 25_T | 31_F | 2.568 | 1.00 |
| 4_V | 68_V | 2.003 | 1.00 |
| 67_Q | 75_H | 1.952 | 1.00 |
| 1_M | 71_P | 1.919 | 1.00 |
| 20_A | 68_V | 1.893 | 1.00 |
| 22_R | 26_V | 1.868 | 1.00 |
| 62_G | 67_Q | 1.867 | 1.00 |
| 20_A | 82_L | 1.826 | 1.00 |
| 6_G | 33_F | 1.821 | 1.00 |
| 3_K | 34_I | 1.807 | 1.00 |
| 12_H | 35_N | 1.787 | 1.00 |
| 19_N | 83_R | 1.787 | 1.00 |
| 9_S | 33_F | 1.776 | 1.00 |
| 19_N | 79_F | 1.576 | 1.00 |
| 27_K | 86_F | 1.571 | 1.00 |
| 35_N | 38_P | 1.562 | 1.00 |
| 21_K | 33_F | 1.500 | 1.00 |
| 20_A | 79_F | 1.484 | 1.00 |
| 6_G | 21_K | 1.473 | 1.00 |
| 62_G | 75_H | 1.448 | 1.00 |
| 23_L | 27_K | 1.414 | 1.00 |
| 68_V | 82_L | 1.399 | 0.99 |
| 16_P | 79_F | 1.378 | 0.99 |
| 23_L | 83_R | 1.354 | 0.99 |
| 50_E | 54_K | 1.351 | 0.99 |
| 2_F | 70_A | 1.345 | 0.99 |
| 69_F | 75_H | 1.307 | 0.99 |
| 3_K | 54_K | 1.291 | 0.99 |
| 23_L | 79_F | 1.278 | 0.99 |
| 2_F | 29_Q | 1.276 | 0.99 |
| 42_V | 50_E | 1.227 | 0.98 |
| 4_V | 24_L | 1.177 | 0.98 |
| 50_E | 53_T | 1.170 | 0.97 |
| 81_Q | 84_E | 1.133 | 0.97 |
| 7_Y | 13_K | 1.131 | 0.97 |
| 18_D | 22_R | 1.117 | 0.96 |
| 78_G | 81_Q | 1.111 | 0.96 |
| 51_L | 65_M | 1.110 | 0.96 |
| 52_L | 63_L | 1.078 | 0.95 |
| 3_K | 32_E | 1.071 | 0.95 |
| 7_Y | 65_M | 1.071 | 0.95 |
| 51_L | 55_L | 1.065 | 0.95 |
| 21_K | 25_T | 1.055 | 0.95 |
| 49_A | 53_T | 1.050 | 0.94 |
| 23_L | 86_F | 1.040 | 0.94 |
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 | |
| 1u6tA | 1 | 0.8276 | 99.5 | 0.064 | Contact Map |
| 2jadA | 1 | 0.8276 | 99.5 | 0.077 | Contact Map |
| 2ct6A | 1 | 0.8276 | 99.4 | 0.136 | Contact Map |
| 2wciA | 2 | 0.8736 | 99.4 | 0.141 | Contact Map |
| 1t1vA | 2 | 0.8276 | 99.3 | 0.165 | Contact Map |
| 2wulA | 4 | 0.8736 | 99.3 | 0.191 | Contact Map |
| 3ipzA | 1 | 0.8736 | 99.2 | 0.205 | Contact Map |
| 1wikA | 1 | 0.8736 | 99.2 | 0.207 | Contact Map |
| 3gx8A | 1 | 0.8736 | 99.2 | 0.211 | Contact Map |
| 2yanA | 2 | 0.8736 | 99.2 | 0.212 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)