| 1FB0 |
| ID: | 1515063368 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (103) | ||
| Sequences: | 29038 (18837.2) | ||
| Seq/Len: | 281.922 | ||
| Nf(neff/√len): | 1856.1 |
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: 281.922).
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 |
| 84_R | 87_S | 2.288 | 1.00 |
| 86_E | 100_S | 2.199 | 1.00 |
| 21_V | 52_A | 2.120 | 1.00 |
| 46_E | 98_T | 1.994 | 1.00 |
| 58_T | 65_A | 1.981 | 1.00 |
| 42_E | 94_K | 1.947 | 1.00 |
| 19_V | 52_A | 1.934 | 1.00 |
| 20_P | 80_K | 1.874 | 1.00 |
| 30_C | 33_C | 1.872 | 1.00 |
| 98_T | 102_E | 1.870 | 1.00 |
| 37_A | 55_K | 1.860 | 1.00 |
| 58_T | 73_I | 1.795 | 1.00 |
| 77_L | 87_S | 1.776 | 1.00 |
| 77_L | 84_R | 1.722 | 1.00 |
| 26_W | 55_K | 1.708 | 1.00 |
| 36_I | 76_V | 1.673 | 1.00 |
| 7_D | 63_G | 1.646 | 1.00 |
| 11_K | 67_Q | 1.640 | 1.00 |
| 35_L | 91_A | 1.638 | 1.00 |
| 21_V | 54_Y | 1.583 | 1.00 |
| 47_Y | 102_E | 1.545 | 1.00 |
| 5_V | 54_Y | 1.510 | 1.00 |
| 9_S | 13_F | 1.505 | 1.00 |
| 22_M | 76_V | 1.498 | 1.00 |
| 93_P | 96_T | 1.467 | 1.00 |
| 47_Y | 98_T | 1.418 | 1.00 |
| 6_N | 9_S | 1.410 | 1.00 |
| 79_F | 84_R | 1.406 | 0.99 |
| 7_D | 64_I | 1.398 | 0.99 |
| 100_S | 104_Y | 1.376 | 0.99 |
| 7_D | 61_A | 1.364 | 0.99 |
| 68_Y | 79_F | 1.360 | 0.99 |
| 24_D | 76_V | 1.353 | 0.99 |
| 39_V | 94_K | 1.351 | 0.99 |
| 24_D | 55_K | 1.295 | 0.99 |
| 20_P | 78_F | 1.274 | 0.99 |
| 24_D | 36_I | 1.257 | 0.99 |
| 94_K | 98_T | 1.254 | 0.99 |
| 39_V | 42_E | 1.238 | 0.98 |
| 70_I | 75_T | 1.230 | 0.98 |
| 28_P | 57_N | 1.224 | 0.98 |
| 75_T | 87_S | 1.221 | 0.98 |
| 86_E | 103_K | 1.218 | 0.98 |
| 92_V | 96_T | 1.211 | 0.98 |
| 96_T | 99_D | 1.209 | 0.98 |
| 100_S | 103_K | 1.190 | 0.98 |
| 88_I | 92_V | 1.184 | 0.98 |
| 88_I | 100_S | 1.163 | 0.97 |
| 23_V | 79_F | 1.130 | 0.97 |
| 27_A | 73_I | 1.115 | 0.96 |
| 57_N | 60_E | 1.103 | 0.96 |
| 25_F | 68_Y | 1.102 | 0.96 |
| 32_P | 35_L | 1.100 | 0.96 |
| 41_D | 45_K | 1.072 | 0.95 |
| 24_D | 37_A | 1.072 | 0.95 |
| 5_V | 13_F | 1.046 | 0.94 |
| 99_D | 103_K | 1.045 | 0.94 |
| 13_F | 52_A | 1.026 | 0.94 |
| 46_E | 94_K | 1.026 | 0.94 |
| 78_F | 104_Y | 1.017 | 0.93 |
| 25_F | 58_T | 1.009 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3f8uA | 2 | 0.9905 | 99.7 | -0.015 | Contact Map |
| 3apoA | 1 | 0.9143 | 99.7 | -0.005 | Contact Map |
| 2r2jA | 1 | 0.9714 | 99.7 | 0 | Contact Map |
| 4kcaA | 2 | 0.9905 | 99.7 | 0.004 | Contact Map |
| 2b5eA | 1 | 0.9905 | 99.7 | 0.004 | Contact Map |
| 3dxbA | 8 | 1 | 99.7 | 0.031 | Contact Map |
| 1thxA | 1 | 1 | 99.7 | 0.032 | Contact Map |
| 3ed3A | 2 | 1 | 99.7 | 0.034 | Contact Map |
| 4xhmA | 2 | 0 | 99.7 | 0.034 | Contact Map |
| 3apqA | 2 | 0.9905 | 99.7 | 0.035 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)