| 1bkr |
| ID: | 1408344302 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (106) | ||
| Sequences: | 795 (501.6) | ||
| Seq/Len: | 7.500 | ||
| Nf(neff/√len): | 48.7 |
HHblits Results: (2013_03)
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: 7.500).
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 |
| 37_N | 64_N | 2.981 | 1.00 |
| 57_N | 60_Y | 2.612 | 1.00 |
| 23_I | 35_A | 2.095 | 1.00 |
| 67_N | 71_Q | 2.009 | 1.00 |
| 25_N | 28_T | 2.002 | 1.00 |
| 63_Q | 67_N | 1.990 | 1.00 |
| 75_L | 101_Y | 1.924 | 1.00 |
| 91_E | 99_V | 1.878 | 1.00 |
| 44_R | 47_L | 1.752 | 1.00 |
| 14_K | 42_K | 1.645 | 1.00 |
| 38_A | 50_F | 1.515 | 0.99 |
| 14_K | 39_L | 1.504 | 0.99 |
| 36_F | 62_L | 1.478 | 0.99 |
| 14_K | 43_H | 1.448 | 0.99 |
| 36_F | 66_F | 1.435 | 0.99 |
| 11_C | 23_I | 1.428 | 0.99 |
| 69_A | 101_Y | 1.419 | 0.99 |
| 48_I | 64_N | 1.402 | 0.99 |
| 61_N | 65_A | 1.402 | 0.99 |
| 89_P | 98_V | 1.402 | 0.99 |
| 15_T | 34_M | 1.397 | 0.99 |
| 63_Q | 77_K | 1.373 | 0.99 |
| 18_Y | 41_H | 1.369 | 0.99 |
| 84_I | 94_I | 1.351 | 0.99 |
| 36_F | 80_D | 1.309 | 0.98 |
| 21_V | 29_S | 1.303 | 0.98 |
| 58_A | 85_S | 1.296 | 0.98 |
| 30_W | 33_G | 1.287 | 0.98 |
| 49_D | 52_K | 1.215 | 0.97 |
| 30_W | 35_A | 1.199 | 0.96 |
| 69_A | 79_L | 1.197 | 0.96 |
| 84_I | 97_Y | 1.189 | 0.96 |
| 15_T | 30_W | 1.164 | 0.95 |
| 34_M | 38_A | 1.159 | 0.95 |
| 68_L | 72_H | 1.158 | 0.95 |
| 90_D | 97_Y | 1.157 | 0.95 |
| 93_S | 99_V | 1.151 | 0.95 |
| 8_L | 12_Q | 1.146 | 0.95 |
| 67_N | 77_K | 1.142 | 0.95 |
| 59_H | 81_P | 1.137 | 0.95 |
| 59_H | 63_Q | 1.118 | 0.94 |
| 37_N | 53_L | 1.118 | 0.94 |
| 41_H | 46_D | 1.106 | 0.93 |
| 41_H | 66_F | 1.099 | 0.93 |
| 50_F | 53_L | 1.097 | 0.93 |
| 94_I | 98_V | 1.086 | 0.93 |
| 56_S | 60_Y | 1.081 | 0.92 |
| 63_Q | 81_P | 1.071 | 0.92 |
| 53_L | 61_N | 1.060 | 0.91 |
| 89_P | 94_I | 1.041 | 0.90 |
| 40_I | 44_R | 1.037 | 0.90 |
| 84_I | 89_P | 1.035 | 0.90 |
| 80_D | 83_D | 1.035 | 0.90 |
| 61_N | 64_N | 1.031 | 0.90 |
| 8_L | 26_F | 1.027 | 0.90 |
| 47_L | 93_S | 1.021 | 0.89 |
| 43_H | 101_Y | 1.016 | 0.89 |
| 56_S | 61_N | 1.011 | 0.89 |
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 | |
| 1bkrA | 1 | 1 | 100 | 0.092 | Contact Map |
| 1wyqA | 1 | 1 | 100 | 0.111 | Contact Map |
| 1bhdA | 2 | 1 | 100 | 0.114 | Contact Map |
| 2d87A | 1 | 1 | 100 | 0.122 | Contact Map |
| 1wylA | 1 | 0.9907 | 100 | 0.139 | Contact Map |
| 3f7pA | 2 | 0.9815 | 100 | 0.157 | Contact Map |
| 1sjjA | 2 | 1 | 100 | 0.159 | Contact Map |
| 2d88A | 1 | 1 | 100 | 0.161 | Contact Map |
| 2d89A | 1 | 0.9907 | 100 | 0.176 | Contact Map |
| 1sh5A | 2 | 0.9815 | 100 | 0.176 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)