| d3quhb_ |
| ID: | 1450012208 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 112 (107) | ||
| Sequences: | 182 (143.2) | ||
| Seq/Len: | 1.701 | ||
| Nf(neff/√len): | 13.8 |
HHblits Results: (2015_06)
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: 1.701).
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 |
| 93_V | 100_E | 3.317 | 1.00 |
| 91_K | 100_E | 3.073 | 1.00 |
| 22_M | 90_V | 2.197 | 0.99 |
| 42_V | 76_I | 2.138 | 0.99 |
| 45_T | 51_W | 2.033 | 0.99 |
| 38_Q | 78_P | 1.856 | 0.97 |
| 22_M | 26_V | 1.705 | 0.95 |
| 36_N | 64_V | 1.587 | 0.92 |
| 47_D | 50_Y | 1.523 | 0.89 |
| 32_T | 41_V | 1.517 | 0.89 |
| 22_M | 105_V | 1.456 | 0.86 |
| 46_K | 92_V | 1.406 | 0.84 |
| 97_I | 103_Y | 1.379 | 0.82 |
| 84_A | 105_V | 1.364 | 0.81 |
| 7_A | 32_T | 1.350 | 0.80 |
| 49_S | 71_N | 1.350 | 0.80 |
| 16_E | 106_R | 1.319 | 0.78 |
| 47_D | 71_N | 1.317 | 0.78 |
| 15_E | 106_R | 1.284 | 0.75 |
| 9_F | 22_M | 1.282 | 0.75 |
| 33_A | 42_V | 1.271 | 0.74 |
| 57_E | 87_N | 1.250 | 0.73 |
| 95_A | 100_E | 1.244 | 0.72 |
| 26_V | 88_A | 1.233 | 0.71 |
| 44_K | 56_V | 1.233 | 0.71 |
| 30_F | 82_D | 1.221 | 0.70 |
| 27_E | 72_S | 1.214 | 0.69 |
| 27_E | 54_L | 1.209 | 0.69 |
| 51_W | 92_V | 1.205 | 0.69 |
| 56_V | 77_F | 1.169 | 0.65 |
| 5_Q | 110_Q | 1.158 | 0.64 |
| 21_V | 66_K | 1.155 | 0.64 |
| 94_V | 100_E | 1.136 | 0.62 |
| 9_F | 69_K | 1.130 | 0.61 |
| 50_Y | 100_E | 1.128 | 0.61 |
| 62_T | 76_I | 1.126 | 0.61 |
| 48_D | 63_T | 1.119 | 0.60 |
| 14_S | 106_R | 1.116 | 0.60 |
| 58_G | 95_A | 1.115 | 0.60 |
| 58_G | 89_I | 1.102 | 0.58 |
| 92_V | 103_Y | 1.089 | 0.57 |
| 89_I | 105_V | 1.083 | 0.56 |
| 50_Y | 92_V | 1.077 | 0.56 |
| 54_L | 107_I | 1.063 | 0.54 |
| 80_I | 83_K | 1.061 | 0.54 |
| 11_V | 103_Y | 1.059 | 0.54 |
| 91_K | 101_G | 1.051 | 0.53 |
| 40_Y | 78_P | 1.048 | 0.53 |
| 59_K | 67_D | 1.041 | 0.52 |
| 6_E | 108_I | 1.035 | 0.51 |
| 52_K | 100_E | 1.022 | 0.50 |
| 19_E | 30_F | 1.019 | 0.50 |
| 26_V | 45_T | 1.016 | 0.49 |
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 | |
| 4xs0C | 1 | 0 | 100 | 0.08 | Contact Map |
| 3qugA | 2 | 1 | 100 | 0.107 | Contact Map |
| 3rtlA | 4 | 1 | 100 | 0.125 | Contact Map |
| 2k78A | 1 | 1 | 100 | 0.161 | Contact Map |
| 2o6pA | 2 | 1 | 100 | 0.161 | Contact Map |
| 3qzmA | 2 | 1 | 100 | 0.174 | Contact Map |
| 2o1aA | 1 | 0.9821 | 100 | 0.177 | Contact Map |
| 4h8qA | 1 | 1 | 100 | 0.193 | Contact Map |
| 3sz6A | 2 | 0.9732 | 100 | 0.202 | Contact Map |
| 4fc3E | 1 | 0.9643 | 100 | 0.203 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)