| Random500 |
| ID: | 1478434893 |
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 |
| 11_A | 55_G | 1.587 | 0.99 |
| 2_M | 57_Y | 1.499 | 0.99 |
| 71_N | 85_R | 1.408 | 0.98 |
| 51_C | 75_S | 1.404 | 0.98 |
| 63_Y | 83_P | 1.386 | 0.98 |
| 27_D | 49_A | 1.373 | 0.97 |
| 14_A | 91_S | 1.359 | 0.97 |
| 57_Y | 92_V | 1.335 | 0.97 |
| 68_R | 92_V | 1.289 | 0.96 |
| 28_N | 73_K | 1.275 | 0.96 |
| 51_C | 70_N | 1.267 | 0.95 |
| 70_N | 89_C | 1.263 | 0.95 |
| 32_L | 62_N | 1.247 | 0.95 |
| 50_Y | 74_K | 1.241 | 0.95 |
| 22_V | 59_A | 1.225 | 0.94 |
| 6_I | 25_T | 1.222 | 0.94 |
| 17_S | 57_Y | 1.216 | 0.94 |
| 1_C | 7_G | 1.183 | 0.93 |
| 1_C | 50_Y | 1.180 | 0.92 |
| 22_V | 83_P | 1.153 | 0.91 |
| 66_W | 69_A | 1.150 | 0.91 |
| 4_T | 21_L | 1.145 | 0.91 |
| 20_V | 34_C | 1.139 | 0.91 |
| 12_H | 43_W | 1.128 | 0.90 |
| 10_M | 37_T | 1.128 | 0.90 |
| 28_N | 71_N | 1.122 | 0.90 |
| 30_M | 46_D | 1.121 | 0.90 |
| 47_P | 75_S | 1.115 | 0.89 |
| 46_D | 81_T | 1.103 | 0.89 |
| 69_A | 90_K | 1.099 | 0.88 |
| 8_C | 19_N | 1.097 | 0.88 |
| 3_W | 78_Q | 1.097 | 0.88 |
| 52_N | 71_N | 1.090 | 0.88 |
| 1_C | 44_N | 1.087 | 0.88 |
| 45_P | 72_M | 1.084 | 0.88 |
| 38_S | 75_S | 1.082 | 0.87 |
| 57_Y | 84_P | 1.073 | 0.87 |
| 60_M | 76_N | 1.065 | 0.86 |
| 2_M | 56_P | 1.061 | 0.86 |
| 30_M | 73_K | 1.056 | 0.86 |
| 40_R | 59_A | 1.049 | 0.85 |
| 4_T | 85_R | 1.047 | 0.85 |
| 28_N | 80_G | 1.044 | 0.85 |
| 32_L | 67_I | 1.036 | 0.84 |
| 26_Q | 87_G | 1.033 | 0.84 |
| 70_N | 75_S | 1.031 | 0.84 |
| 9_S | 42_Q | 1.030 | 0.84 |
| 63_Y | 68_R | 1.026 | 0.83 |
| 85_R | 89_C | 1.023 | 0.83 |
| 28_N | 39_F | 1.023 | 0.83 |
| 13_R | 32_L | 1.018 | 0.83 |
| 5_N | 51_C | 1.011 | 0.82 |
| 17_S | 24_H | 1.009 | 0.82 |
| 32_L | 85_R | 1.007 | 0.82 |
| 15_D | 40_R | 1.001 | 0.81 |
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 | |
| 2yq2A | 2 | 0.2935 | 0.1 | 0.693 | Contact Map |
| 2yp5A | 1 | 0.3804 | 0 | 0.733 | Contact Map |
| 1i7fA | 1 | 0 | 0 | 0.746 | Contact Map |
| 3ku3B | 1 | 0.3587 | 0 | 0.773 | Contact Map |
| 3llqA | 2 | 0.4565 | 0 | 0.773 | Contact Map |
| 1vk9A | 1 | 0.3261 | 0 | 0.799 | Contact Map |
| 2y3aA | 1 | 0.1848 | 0 | 0.799 | Contact Map |
| 4dv8A | 1 | 0.2609 | 0 | 0.813 | Contact Map |
| 4artA | 2 | 0.3261 | 0 | 0.813 | Contact Map |
| 4o6bA | 2 | 0.4565 | 0 | 0.826 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)