| 2abd |
| ID: | 1486855173 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (84) | ||
| Sequences: | 1840 (1230.3) | ||
| Seq/Len: | 21.905 | ||
| Nf(neff/√len): | 134.2 |
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: 21.905).
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 |
| 48_D | 51_G | 3.728 | 1.00 |
| 2_Q | 70_M | 3.647 | 1.00 |
| 59_N | 62_K | 3.574 | 1.00 |
| 43_R | 56_D | 2.841 | 1.00 |
| 38_D | 63_G | 2.442 | 1.00 |
| 27_I | 77_V | 2.116 | 1.00 |
| 29_S | 61_L | 2.098 | 1.00 |
| 38_D | 62_K | 2.072 | 1.00 |
| 7_K | 11_E | 2.054 | 1.00 |
| 20_A | 23_E | 2.018 | 1.00 |
| 26_F | 76_K | 1.843 | 1.00 |
| 55_W | 59_N | 1.820 | 1.00 |
| 2_Q | 6_D | 1.784 | 1.00 |
| 71_K | 75_D | 1.565 | 1.00 |
| 68_D | 72_A | 1.543 | 1.00 |
| 68_D | 71_K | 1.539 | 1.00 |
| 66_K | 70_M | 1.515 | 1.00 |
| 76_K | 79_E | 1.489 | 1.00 |
| 26_F | 30_H | 1.476 | 1.00 |
| 65_S | 68_D | 1.417 | 1.00 |
| 78_E | 81_K | 1.400 | 0.99 |
| 23_E | 76_K | 1.385 | 0.99 |
| 52_K | 56_D | 1.305 | 0.99 |
| 21_D | 24_M | 1.297 | 0.99 |
| 6_D | 10_E | 1.275 | 0.99 |
| 75_D | 79_E | 1.247 | 0.99 |
| 23_E | 84_Y | 1.237 | 0.98 |
| 11_E | 81_K | 1.228 | 0.98 |
| 33_Q | 37_G | 1.220 | 0.98 |
| 39_I | 55_W | 1.194 | 0.98 |
| 31_Y | 35_T | 1.193 | 0.98 |
| 72_A | 75_D | 1.171 | 0.98 |
| 46_M | 52_K | 1.126 | 0.97 |
| 64_T | 72_A | 1.111 | 0.96 |
| 19_P | 24_M | 1.100 | 0.96 |
| 36_V | 40_N | 1.068 | 0.95 |
| 12_V | 77_V | 1.060 | 0.95 |
| 10_E | 13_K | 1.053 | 0.95 |
| 34_A | 70_M | 1.049 | 0.94 |
| 67_E | 70_M | 1.011 | 0.93 |
| 15_L | 19_P | 1.011 | 0.93 |
| 41_T | 55_W | 1.000 | 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 | |
| 3epyA | 2 | 1 | 100 | -0.045 | Contact Map |
| 1st7A | 1 | 1 | 100 | -0.043 | Contact Map |
| 2copA | 1 | 1 | 100 | -0.041 | Contact Map |
| 2lbbA | 1 | 1 | 100 | -0.038 | Contact Map |
| 2cb8A | 2 | 1 | 99.9 | -0.035 | Contact Map |
| 1hbkA | 1 | 1 | 99.9 | -0.032 | Contact Map |
| 3flvA | 2 | 1 | 99.9 | -0.032 | Contact Map |
| 2cquA | 1 | 1 | 99.9 | -0.031 | Contact Map |
| 3fp5A | 1 | 1 | 99.9 | -0.021 | Contact Map |
| 2wh5A | 6 | 0.9884 | 99.9 | -0.012 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)