| kklkl |
| ID: | 1492063509 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (123) | ||
| Sequences: | 583 (352.3) | ||
| Seq/Len: | 4.740 | ||
| Nf(neff/√len): | 31.8 |
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: 4.740).
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 |
| 46_H | 80_T | 3.928 | 1.00 |
| 63_C | 70_C | 2.881 | 1.00 |
| 69_N | 106_A | 2.455 | 1.00 |
| 73_S | 103_F | 1.819 | 1.00 |
| 11_W | 15_Q | 1.787 | 1.00 |
| 27_A | 31_I | 1.759 | 1.00 |
| 15_Q | 39_K | 1.745 | 1.00 |
| 11_W | 14_I | 1.633 | 0.99 |
| 12_F | 16_H | 1.630 | 0.99 |
| 17_I | 52_V | 1.522 | 0.99 |
| 38_C | 92_C | 1.518 | 0.98 |
| 124_L | 127_I | 1.492 | 0.98 |
| 76_P | 102_F | 1.487 | 0.98 |
| 7_T | 11_W | 1.483 | 0.98 |
| 55_V | 103_F | 1.470 | 0.98 |
| 42_N | 123_H | 1.439 | 0.98 |
| 39_K | 123_H | 1.432 | 0.98 |
| 112_K | 115_P | 1.402 | 0.97 |
| 9_A | 13_E | 1.393 | 0.97 |
| 55_V | 68_H | 1.392 | 0.97 |
| 25_N | 80_T | 1.379 | 0.97 |
| 112_K | 117_Y | 1.305 | 0.95 |
| 72_Q | 104_I | 1.276 | 0.94 |
| 76_P | 86_S | 1.272 | 0.94 |
| 23_Q | 52_V | 1.254 | 0.94 |
| 14_I | 31_I | 1.250 | 0.93 |
| 70_C | 125_D | 1.250 | 0.93 |
| 115_P | 119_L | 1.247 | 0.93 |
| 47_D | 83_R | 1.228 | 0.93 |
| 10_H | 45_L | 1.227 | 0.93 |
| 23_Q | 33_N | 1.214 | 0.92 |
| 79_M | 101_K | 1.207 | 0.92 |
| 47_D | 51_N | 1.200 | 0.91 |
| 15_Q | 106_A | 1.193 | 0.91 |
| 28_M | 46_H | 1.192 | 0.91 |
| 112_K | 118_K | 1.190 | 0.91 |
| 113_S | 119_L | 1.188 | 0.91 |
| 113_S | 116_P | 1.184 | 0.91 |
| 16_H | 42_N | 1.178 | 0.90 |
| 15_Q | 42_N | 1.171 | 0.90 |
| 52_V | 105_V | 1.165 | 0.90 |
| 28_M | 80_T | 1.157 | 0.89 |
| 15_Q | 123_H | 1.153 | 0.89 |
| 112_K | 119_L | 1.140 | 0.88 |
| 27_A | 102_F | 1.124 | 0.88 |
| 115_P | 118_K | 1.115 | 0.87 |
| 87_G | 111_Q | 1.102 | 0.86 |
| 32_N | 125_D | 1.098 | 0.86 |
| 88_K | 111_Q | 1.085 | 0.85 |
| 39_K | 44_F | 1.078 | 0.84 |
| 7_T | 14_I | 1.076 | 0.84 |
| 23_Q | 27_A | 1.075 | 0.84 |
| 28_M | 33_N | 1.072 | 0.84 |
| 23_Q | 80_T | 1.061 | 0.83 |
| 63_C | 71_H | 1.043 | 0.82 |
| 21_P | 80_T | 1.041 | 0.81 |
| 21_P | 46_H | 1.029 | 0.80 |
| 45_L | 124_L | 1.023 | 0.80 |
| 113_S | 117_Y | 1.015 | 0.79 |
| 27_A | 46_H | 1.008 | 0.79 |
| 12_F | 42_N | 1.006 | 0.78 |
| 62_V | 89_Y | 1.001 | 0.78 |
| 11_W | 32_N | 1.000 | 0.78 |
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 | |
| 2hkyA | 1 | 1 | 100 | 0.074 | Contact Map |
| 4owzA | 2 | 1 | 100 | 0.084 | Contact Map |
| 1gqvA | 1 | 1 | 100 | 0.099 | Contact Map |
| 3mwqA | 1 | 0.9141 | 100 | 0.137 | Contact Map |
| 2apqA | 1 | 0.8984 | 100 | 0.138 | Contact Map |
| 1rraA | 1 | 0.9141 | 100 | 0.147 | Contact Map |
| 1dy5A | 2 | 0.9062 | 100 | 0.149 | Contact Map |
| 2e0jA | 2 | 0.9141 | 100 | 0.153 | Contact Map |
| 2vq9A | 1 | 0.8828 | 100 | 0.162 | Contact Map |
| 1rnfA | 2 | 0.8906 | 100 | 0.181 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)