| kdpC |
| ID: | 1416984825 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (189) | ||
| Sequences: | 772 (604.8) | ||
| Seq/Len: | 4.085 | ||
| Nf(neff/√len): | 44.0 |
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: 4.085).
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 |
| 31_Q | 39_N | 4.472 | 1.00 |
| 120_L | 136_A | 3.670 | 1.00 |
| 97_L | 101_R | 3.636 | 1.00 |
| 65_F | 181_L | 3.461 | 1.00 |
| 141_I | 159_I | 3.274 | 1.00 |
| 138_A | 156_T | 2.780 | 1.00 |
| 131_N | 164_Q | 2.709 | 1.00 |
| 148_R | 186_D | 2.539 | 1.00 |
| 5_R | 9_S | 2.433 | 1.00 |
| 141_I | 152_V | 2.394 | 1.00 |
| 56_G | 67_G | 2.392 | 1.00 |
| 72_T | 76_P | 2.389 | 1.00 |
| 66_H | 108_A | 2.371 | 1.00 |
| 42_L | 49_V | 2.313 | 1.00 |
| 64_Y | 186_D | 2.305 | 1.00 |
| 158_L | 181_L | 2.135 | 1.00 |
| 142_P | 152_V | 2.133 | 1.00 |
| 53_A | 180_E | 2.068 | 1.00 |
| 82_S | 128_L | 2.035 | 1.00 |
| 65_F | 144_V | 1.921 | 1.00 |
| 72_T | 78_N | 1.892 | 1.00 |
| 29_L | 33_W | 1.870 | 1.00 |
| 167_L | 175_V | 1.863 | 1.00 |
| 120_L | 139_W | 1.841 | 1.00 |
| 150_L | 155_L | 1.777 | 0.99 |
| 166_P | 174_P | 1.772 | 0.99 |
| 11_F | 15_L | 1.718 | 0.99 |
| 93_E | 96_K | 1.714 | 0.99 |
| 138_A | 163_S | 1.665 | 0.99 |
| 96_K | 100_A | 1.663 | 0.99 |
| 166_P | 173_Q | 1.658 | 0.99 |
| 141_I | 155_L | 1.622 | 0.99 |
| 119_E | 132_I | 1.610 | 0.99 |
| 132_I | 137_A | 1.593 | 0.99 |
| 106_R | 109_N | 1.559 | 0.98 |
| 64_Y | 148_R | 1.554 | 0.98 |
| 36_W | 53_A | 1.539 | 0.98 |
| 144_V | 159_I | 1.537 | 0.98 |
| 102_V | 121_V | 1.528 | 0.98 |
| 73_A | 76_P | 1.518 | 0.98 |
| 134_P | 163_S | 1.512 | 0.98 |
| 51_G | 179_V | 1.500 | 0.98 |
| 132_I | 178_I | 1.437 | 0.97 |
| 152_V | 156_T | 1.437 | 0.97 |
| 156_T | 160_A | 1.426 | 0.97 |
| 169_K | 175_V | 1.422 | 0.96 |
| 138_A | 160_A | 1.406 | 0.96 |
| 162_Y | 180_E | 1.396 | 0.96 |
| 105_L | 139_W | 1.351 | 0.95 |
| 65_F | 158_L | 1.345 | 0.95 |
| 148_R | 185_L | 1.298 | 0.93 |
| 144_V | 181_L | 1.259 | 0.92 |
| 105_L | 110_P | 1.231 | 0.91 |
| 66_H | 109_N | 1.215 | 0.90 |
| 119_E | 133_T | 1.175 | 0.88 |
| 72_T | 83_G | 1.172 | 0.88 |
| 14_L | 18_T | 1.169 | 0.87 |
| 65_F | 159_I | 1.157 | 0.87 |
| 20_G | 26_T | 1.140 | 0.86 |
| 109_N | 139_W | 1.137 | 0.85 |
| 104_A | 108_A | 1.136 | 0.85 |
| 55_I | 82_S | 1.127 | 0.85 |
| 34_F | 37_Q | 1.121 | 0.84 |
| 131_N | 175_V | 1.117 | 0.84 |
| 137_A | 178_I | 1.107 | 0.83 |
| 15_L | 19_G | 1.107 | 0.83 |
| 138_A | 142_P | 1.095 | 0.82 |
| 154_Q | 157_Q | 1.090 | 0.82 |
| 167_L | 171_I | 1.085 | 0.82 |
| 117_P | 139_W | 1.076 | 0.81 |
| 164_Q | 180_E | 1.076 | 0.81 |
| 62_N | 108_A | 1.075 | 0.81 |
| 67_G | 147_A | 1.075 | 0.81 |
| 92_P | 96_K | 1.065 | 0.80 |
| 9_S | 12_I | 1.065 | 0.80 |
| 41_S | 52_S | 1.062 | 0.80 |
| 73_A | 83_G | 1.056 | 0.79 |
| 136_A | 139_W | 1.050 | 0.79 |
| 66_H | 143_R | 1.049 | 0.79 |
| 16_L | 21_V | 1.048 | 0.78 |
| 38_A | 52_S | 1.048 | 0.78 |
| 23_P | 82_S | 1.037 | 0.77 |
| 134_P | 159_I | 1.033 | 0.77 |
| 59_F | 148_R | 1.028 | 0.77 |
| 106_R | 111_D | 1.027 | 0.76 |
| 44_R | 48_T | 1.013 | 0.75 |
| 44_R | 47_D | 1.009 | 0.75 |
| 19_G | 27_T | 1.008 | 0.75 |
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 | |
| 4dx5A | 3 | 0.9632 | 38.6 | 0.956 | Contact Map |
| 4utpA | 2 | 0.7421 | 37.1 | 0.956 | Contact Map |
| 4k3vA | 2 | 0.7474 | 28.3 | 0.959 | Contact Map |
| 1s3aA | 1 | 0.4474 | 16.9 | 0.963 | Contact Map |
| 3thgA | 1 | 0.3105 | 16.9 | 0.963 | Contact Map |
| 1ufmA | 1 | 0.3632 | 16.3 | 0.963 | Contact Map |
| 2otmA | 3 | 0.4842 | 12.1 | 0.965 | Contact Map |
| 4h63V | 1 | 0.5316 | 11.3 | 0.966 | Contact Map |
| 1toaA | 2 | 0.7474 | 10.2 | 0.966 | Contact Map |
| 1xrsA | 1 | 0.3211 | 10.1 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)