| 1BKR |
| ID: | 1446031304 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (106) | ||
| Sequences: | 1183 (742.5) | ||
| Seq/Len: | 11.160 | ||
| Nf(neff/√len): | 72.1 |
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: 11.160).
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_N | 60_Y | 3.151 | 1.00 |
| 37_N | 64_N | 3.041 | 1.00 |
| 67_N | 71_Q | 2.354 | 1.00 |
| 63_Q | 67_N | 2.330 | 1.00 |
| 23_I | 35_A | 2.313 | 1.00 |
| 75_L | 101_Y | 2.070 | 1.00 |
| 44_R | 47_L | 1.911 | 1.00 |
| 25_N | 28_T | 1.834 | 1.00 |
| 63_Q | 77_K | 1.751 | 1.00 |
| 69_A | 101_Y | 1.598 | 1.00 |
| 14_K | 42_K | 1.597 | 1.00 |
| 36_F | 62_L | 1.562 | 1.00 |
| 68_L | 72_H | 1.555 | 1.00 |
| 91_E | 99_V | 1.514 | 1.00 |
| 54_K | 57_N | 1.473 | 1.00 |
| 38_A | 50_F | 1.465 | 1.00 |
| 25_N | 29_S | 1.444 | 1.00 |
| 14_K | 39_L | 1.416 | 1.00 |
| 84_I | 94_I | 1.383 | 0.99 |
| 18_Y | 41_H | 1.295 | 0.99 |
| 37_N | 53_L | 1.265 | 0.99 |
| 67_N | 77_K | 1.264 | 0.99 |
| 14_K | 43_H | 1.261 | 0.99 |
| 4_K | 91_E | 1.258 | 0.99 |
| 89_P | 98_V | 1.244 | 0.98 |
| 61_N | 65_A | 1.239 | 0.98 |
| 30_W | 33_G | 1.235 | 0.98 |
| 26_F | 98_V | 1.234 | 0.98 |
| 94_I | 98_V | 1.193 | 0.98 |
| 43_H | 105_F | 1.167 | 0.97 |
| 11_C | 23_I | 1.161 | 0.97 |
| 36_F | 66_F | 1.144 | 0.97 |
| 58_A | 85_S | 1.126 | 0.97 |
| 49_D | 52_K | 1.119 | 0.96 |
| 89_P | 94_I | 1.114 | 0.96 |
| 8_L | 12_Q | 1.108 | 0.96 |
| 48_I | 64_N | 1.098 | 0.96 |
| 75_L | 105_F | 1.097 | 0.96 |
| 31_R | 58_A | 1.094 | 0.96 |
| 78_L | 92_K | 1.079 | 0.95 |
| 50_F | 53_L | 1.071 | 0.95 |
| 59_H | 81_P | 1.065 | 0.95 |
| 44_R | 72_H | 1.063 | 0.95 |
| 78_L | 100_T | 1.047 | 0.94 |
| 40_I | 68_L | 1.044 | 0.94 |
| 27_T | 88_H | 1.039 | 0.94 |
| 33_G | 38_A | 1.039 | 0.94 |
| 7_L | 10_W | 1.038 | 0.94 |
| 53_L | 61_N | 1.033 | 0.94 |
| 13_M | 16_A | 1.027 | 0.94 |
| 27_T | 91_E | 1.006 | 0.93 |
| 21_V | 35_A | 1.002 | 0.92 |
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 | |
| 1bhdA | 2 | 1 | 100 | 0.018 | Contact Map |
| 1bkrA | 1 | 1 | 100 | 0.019 | Contact Map |
| 1wyqA | 1 | 1 | 100 | 0.024 | Contact Map |
| 2d87A | 1 | 1 | 100 | 0.045 | Contact Map |
| 2d88A | 1 | 1 | 100 | 0.054 | Contact Map |
| 1wylA | 1 | 0.9907 | 100 | 0.064 | Contact Map |
| 2d89A | 1 | 0.9907 | 100 | 0.067 | Contact Map |
| 4q57B | 1 | 0.9722 | 100 | 0.087 | Contact Map |
| 3f7pA | 2 | 0.9815 | 100 | 0.087 | Contact Map |
| 4d1eA | 1 | 0.9722 | 100 | 0.087 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)