| Aishwarya Mudgal |
| ID: | 1475172768 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (99) | ||
| Sequences: | 5233 (3509.6) | ||
| Seq/Len: | 52.859 | ||
| Nf(neff/√len): | 352.7 |
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: 52.859).
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 |
| 46_W | 49_L | 2.980 | 1.00 |
| 36_D | 79_Y | 2.966 | 1.00 |
| 31_P | 38_R | 2.906 | 1.00 |
| 53_R | 58_E | 2.884 | 1.00 |
| 77_Y | 91_R | 2.793 | 1.00 |
| 59_Y | 68_D | 2.632 | 1.00 |
| 77_Y | 94_E | 2.383 | 1.00 |
| 70_R | 98_E | 2.309 | 1.00 |
| 19_M | 51_K | 2.235 | 1.00 |
| 69_M | 97_M | 2.230 | 1.00 |
| 81_R | 87_S | 2.002 | 1.00 |
| 19_M | 28_A | 2.000 | 1.00 |
| 50_I | 69_M | 1.968 | 1.00 |
| 70_R | 94_E | 1.874 | 1.00 |
| 43_H | 71_L | 1.766 | 1.00 |
| 66_I | 70_R | 1.726 | 1.00 |
| 60_T | 64_A | 1.665 | 1.00 |
| 45_M | 72_V | 1.499 | 1.00 |
| 43_H | 67_N | 1.494 | 1.00 |
| 77_Y | 87_S | 1.445 | 1.00 |
| 76_C | 90_A | 1.430 | 1.00 |
| 41_I | 78_D | 1.409 | 1.00 |
| 66_I | 101_F | 1.385 | 0.99 |
| 17_V | 100_L | 1.370 | 0.99 |
| 84_S | 87_S | 1.359 | 0.99 |
| 30_D | 33_K | 1.316 | 0.99 |
| 61_S | 64_A | 1.287 | 0.99 |
| 15_L | 65_F | 1.287 | 0.99 |
| 94_E | 98_E | 1.282 | 0.99 |
| 77_Y | 90_A | 1.281 | 0.99 |
| 37_Y | 41_I | 1.255 | 0.99 |
| 74_Q | 78_D | 1.244 | 0.98 |
| 26_I | 89_L | 1.221 | 0.98 |
| 21_L | 96_A | 1.214 | 0.98 |
| 83_E | 88_T | 1.201 | 0.98 |
| 50_I | 72_V | 1.196 | 0.98 |
| 45_M | 68_D | 1.193 | 0.98 |
| 87_S | 91_R | 1.188 | 0.98 |
| 81_R | 84_S | 1.177 | 0.98 |
| 63_S | 67_N | 1.175 | 0.98 |
| 12_R | 55_T | 1.167 | 0.97 |
| 96_A | 100_L | 1.166 | 0.97 |
| 53_R | 68_D | 1.158 | 0.97 |
| 47_W | 72_V | 1.151 | 0.97 |
| 8_Y | 57_Y | 1.102 | 0.96 |
| 76_C | 80_N | 1.079 | 0.95 |
| 29_R | 48_D | 1.077 | 0.95 |
| 73_V | 93_I | 1.070 | 0.95 |
| 30_D | 34_L | 1.068 | 0.95 |
| 89_L | 92_R | 1.062 | 0.95 |
| 23_R | 92_R | 1.041 | 0.94 |
| 75_N | 80_N | 1.031 | 0.94 |
| 26_I | 86_F | 1.008 | 0.93 |
| 66_I | 97_M | 1.008 | 0.93 |
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 | |
| 4qc3A | 2 | 0.9813 | 99.9 | 0.093 | Contact Map |
| 4ir5A | 1 | 1 | 99.9 | 0.099 | Contact Map |
| 4algA | 1 | 1 | 99.9 | 0.104 | Contact Map |
| 3fkmX | 1 | 0.972 | 99.9 | 0.109 | Contact Map |
| 4qnsA | 4 | 0.972 | 99.9 | 0.111 | Contact Map |
| 3q2eA | 1 | 0.9533 | 99.9 | 0.111 | Contact Map |
| 4uydA | 1 | 1 | 99.9 | 0.113 | Contact Map |
| 4uygA | 6 | 0.9813 | 99.9 | 0.116 | Contact Map |
| 4ptbA | 2 | 0.9907 | 99.9 | 0.116 | Contact Map |
| 4bhwA | 2 | 1 | 99.9 | 0.12 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)