| s003 |
| ID: | 1481203188 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (103) | ||
| Sequences: | 17071 (13325.8) | ||
| Seq/Len: | 165.738 | ||
| Nf(neff/√len): | 1313.0 |
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: 165.738).
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 |
| 14_E | 95_R | 3.016 | 1.00 |
| 15_G | 35_I | 2.426 | 1.00 |
| 31_M | 34_D | 2.414 | 1.00 |
| 73_V | 95_R | 2.187 | 1.00 |
| 15_G | 94_V | 2.152 | 1.00 |
| 17_L | 92_V | 1.995 | 1.00 |
| 17_L | 25_I | 1.967 | 1.00 |
| 28_S | 32_A | 1.962 | 1.00 |
| 17_L | 32_A | 1.886 | 1.00 |
| 9_I | 27_L | 1.866 | 1.00 |
| 33_N | 40_D | 1.856 | 1.00 |
| 28_S | 33_N | 1.854 | 1.00 |
| 20_N | 24_Q | 1.808 | 1.00 |
| 73_V | 100_E | 1.792 | 1.00 |
| 66_E | 70_R | 1.656 | 1.00 |
| 101_H | 104_D | 1.648 | 1.00 |
| 30_K | 34_D | 1.637 | 1.00 |
| 100_E | 104_D | 1.625 | 1.00 |
| 71_F | 101_H | 1.621 | 1.00 |
| 19_I | 92_V | 1.530 | 1.00 |
| 80_D | 87_K | 1.514 | 1.00 |
| 45_A | 49_R | 1.512 | 1.00 |
| 64_D | 101_H | 1.483 | 1.00 |
| 26_I | 89_G | 1.475 | 1.00 |
| 38_N | 67_M | 1.461 | 1.00 |
| 10_N | 30_K | 1.449 | 1.00 |
| 6_D | 10_N | 1.435 | 1.00 |
| 12_M | 16_V | 1.415 | 1.00 |
| 18_G | 27_L | 1.396 | 0.99 |
| 2_A | 6_D | 1.392 | 0.99 |
| 18_G | 89_G | 1.388 | 0.99 |
| 83_E | 86_G | 1.384 | 0.99 |
| 81_K | 86_G | 1.378 | 0.99 |
| 36_M | 94_V | 1.363 | 0.99 |
| 18_G | 91_V | 1.352 | 0.99 |
| 20_N | 26_I | 1.312 | 0.99 |
| 24_Q | 46_F | 1.286 | 0.99 |
| 27_L | 40_D | 1.258 | 0.99 |
| 76_T | 92_V | 1.243 | 0.98 |
| 28_S | 43_A | 1.243 | 0.98 |
| 17_L | 94_V | 1.231 | 0.98 |
| 14_E | 93_T | 1.227 | 0.98 |
| 12_M | 93_T | 1.222 | 0.98 |
| 74_V | 94_V | 1.198 | 0.98 |
| 30_K | 33_N | 1.184 | 0.98 |
| 21_E | 88_S | 1.169 | 0.97 |
| 39_I | 42_D | 1.166 | 0.97 |
| 99_N | 102_N | 1.164 | 0.97 |
| 77_S | 91_V | 1.155 | 0.97 |
| 99_N | 103_L | 1.155 | 0.97 |
| 62_M | 73_V | 1.148 | 0.97 |
| 21_E | 87_K | 1.111 | 0.96 |
| 75_T | 95_R | 1.080 | 0.95 |
| 7_S | 11_S | 1.062 | 0.95 |
| 19_I | 25_I | 1.056 | 0.95 |
| 33_N | 39_I | 1.054 | 0.95 |
| 38_N | 42_D | 1.044 | 0.94 |
| 5_R | 9_I | 1.022 | 0.93 |
| 71_F | 98_T | 1.021 | 0.93 |
| 97_M | 101_H | 1.021 | 0.93 |
| 32_A | 36_M | 1.013 | 0.93 |
| 4_G | 27_L | 1.001 | 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 | |
| 2ykfA | 1 | 0.9048 | 98.8 | -0.052 | Contact Map |
| 2qkpA | 4 | 0.9905 | 98.7 | -0.035 | Contact Map |
| 3volA | 1 | 0.9905 | 98.7 | -0.024 | Contact Map |
| 3caxA | 1 | 0.981 | 98.7 | -0.017 | Contact Map |
| 4gw9A | 4 | 0.9714 | 98.6 | -0.003 | Contact Map |
| 2jheA | 4 | 0.9524 | 98.6 | 0.003 | Contact Map |
| 3kx0X | 1 | 0.9619 | 98.6 | 0.011 | Contact Map |
| 3lyxA | 2 | 0.9333 | 98.6 | 0.015 | Contact Map |
| 3k3cA | 4 | 0.981 | 98.5 | 0.026 | Contact Map |
| 3a0rA | 1 | 0.9619 | 98.5 | 0.032 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)