| rand1244 |
| ID: | 1478452626 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (92) | ||
| Sequences: | 500 (500) | ||
| Seq/Len: | 5.435 | ||
| Nf(neff/√len): | 52.1 |
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: 5.435).
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 |
| 57_D | 76_E | 1.694 | 1.00 |
| 18_L | 25_E | 1.604 | 0.99 |
| 17_L | 69_H | 1.559 | 0.99 |
| 19_L | 75_H | 1.543 | 0.99 |
| 25_E | 46_K | 1.463 | 0.98 |
| 36_V | 40_I | 1.447 | 0.98 |
| 14_D | 75_H | 1.410 | 0.98 |
| 21_V | 50_W | 1.367 | 0.97 |
| 47_L | 55_Q | 1.361 | 0.97 |
| 32_R | 49_C | 1.343 | 0.97 |
| 33_M | 46_K | 1.338 | 0.97 |
| 24_C | 89_Y | 1.337 | 0.97 |
| 20_R | 35_T | 1.307 | 0.96 |
| 1_G | 37_C | 1.304 | 0.96 |
| 46_K | 79_V | 1.289 | 0.96 |
| 12_N | 68_K | 1.267 | 0.95 |
| 14_D | 53_L | 1.261 | 0.95 |
| 31_V | 39_Y | 1.253 | 0.95 |
| 2_Y | 92_F | 1.245 | 0.95 |
| 37_C | 85_D | 1.228 | 0.94 |
| 23_S | 48_A | 1.177 | 0.92 |
| 23_S | 41_S | 1.175 | 0.92 |
| 72_G | 82_E | 1.174 | 0.92 |
| 3_S | 55_Q | 1.172 | 0.92 |
| 17_L | 92_F | 1.150 | 0.91 |
| 26_F | 81_Q | 1.148 | 0.91 |
| 81_Q | 85_D | 1.141 | 0.91 |
| 71_S | 80_V | 1.132 | 0.90 |
| 43_A | 70_P | 1.123 | 0.90 |
| 26_F | 68_K | 1.120 | 0.90 |
| 9_H | 24_C | 1.114 | 0.89 |
| 17_L | 61_A | 1.114 | 0.89 |
| 1_G | 14_D | 1.107 | 0.89 |
| 40_I | 44_K | 1.107 | 0.89 |
| 1_G | 34_I | 1.102 | 0.89 |
| 80_V | 88_E | 1.101 | 0.89 |
| 12_N | 54_A | 1.086 | 0.88 |
| 61_A | 68_K | 1.077 | 0.87 |
| 12_N | 27_P | 1.074 | 0.87 |
| 74_T | 81_Q | 1.070 | 0.87 |
| 19_L | 29_P | 1.064 | 0.86 |
| 48_A | 87_W | 1.061 | 0.86 |
| 30_T | 74_T | 1.043 | 0.85 |
| 70_P | 84_M | 1.038 | 0.84 |
| 4_C | 7_T | 1.029 | 0.84 |
| 2_Y | 65_P | 1.029 | 0.84 |
| 55_Q | 64_C | 1.026 | 0.83 |
| 19_L | 39_Y | 1.017 | 0.83 |
| 43_A | 51_D | 1.005 | 0.82 |
| 66_C | 71_S | 1.005 | 0.82 |
| 34_I | 71_S | 1.004 | 0.82 |
| 16_K | 76_E | 1.004 | 0.82 |
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 | |
| 3nf5A | 2 | 0.2609 | 0.6 | 0.88 | Contact Map |
| 3ejvA | 1 | 0.337 | 0.2 | 0.922 | Contact Map |
| 2cs7A | 3 | 0.413 | 0.2 | 0.922 | Contact Map |
| 2ofcA | 2 | 0.5 | 0.2 | 0.923 | Contact Map |
| 2ldfA | 1 | 0.2609 | 0.2 | 0.925 | Contact Map |
| 3dmqA | 2 | 0.3587 | 0.2 | 0.928 | Contact Map |
| 3p06A | 1 | 0.337 | 0.2 | 0.928 | Contact Map |
| 4xglA | 1 | 0 | 0.2 | 0.929 | Contact Map |
| 2uxtA | 2 | 0.2717 | 0.2 | 0.929 | Contact Map |
| 2rngA | 1 | 0.413 | 0.2 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)