| ATPB 90-250 |
| ID: | 1381128420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 161 (161) | ||
| Sequences: | 161 (99.6) | ||
| Seq/Len: | 1.000 | ||
| Nf(neff/√len): | 7.8 |
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: 1.000).
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 |
| 11_F | 14_I | 2.345 | 0.99 |
| 82_R | 147_I | 2.149 | 0.97 |
| 127_I | 131_E | 1.967 | 0.95 |
| 10_T | 14_I | 1.750 | 0.89 |
| 47_E | 51_Q | 1.730 | 0.89 |
| 32_G | 36_D | 1.717 | 0.88 |
| 34_F | 79_D | 1.626 | 0.84 |
| 4_Y | 7_T | 1.625 | 0.84 |
| 32_G | 100_V | 1.601 | 0.83 |
| 5_V | 17_I | 1.586 | 0.82 |
| 67_Q | 70_L | 1.567 | 0.81 |
| 55_K | 58_Q | 1.479 | 0.75 |
| 64_E | 68_Q | 1.454 | 0.74 |
| 52_A | 152_A | 1.440 | 0.73 |
| 3_I | 20_L | 1.422 | 0.71 |
| 100_V | 148_A | 1.393 | 0.69 |
| 43_I | 47_E | 1.382 | 0.68 |
| 32_G | 37_K | 1.374 | 0.67 |
| 62_D | 65_K | 1.339 | 0.64 |
| 118_M | 151_I | 1.336 | 0.64 |
| 9_E | 54_I | 1.329 | 0.64 |
| 79_D | 136_Q | 1.324 | 0.63 |
| 6_I | 40_E | 1.320 | 0.63 |
| 79_D | 86_A | 1.317 | 0.63 |
| 3_I | 24_V | 1.317 | 0.63 |
| 37_K | 79_D | 1.289 | 0.60 |
| 13_A | 16_T | 1.285 | 0.60 |
| 132_K | 135_V | 1.282 | 0.59 |
| 20_L | 24_V | 1.280 | 0.59 |
| 107_R | 110_Y | 1.274 | 0.59 |
| 93_Y | 97_L | 1.268 | 0.58 |
| 125_H | 142_Q | 1.257 | 0.57 |
| 104_V | 120_Q | 1.233 | 0.55 |
| 61_I | 144_K | 1.232 | 0.55 |
| 10_T | 36_D | 1.218 | 0.54 |
| 34_F | 61_I | 1.195 | 0.52 |
| 66_S | 69_A | 1.193 | 0.51 |
| 153_D | 156_L | 1.177 | 0.50 |
| 6_I | 11_F | 1.168 | 0.49 |
| 37_K | 76_Y | 1.167 | 0.49 |
| 55_K | 59_D | 1.162 | 0.48 |
| 36_D | 40_E | 1.160 | 0.48 |
| 119_R | 143_E | 1.159 | 0.48 |
| 2_E | 90_E | 1.159 | 0.48 |
| 25_K | 146_T | 1.156 | 0.48 |
| 34_F | 37_K | 1.154 | 0.48 |
| 86_A | 90_E | 1.149 | 0.47 |
| 66_S | 72_Q | 1.143 | 0.47 |
| 5_V | 62_D | 1.117 | 0.44 |
| 19_F | 140_A | 1.115 | 0.44 |
| 4_Y | 103_E | 1.112 | 0.44 |
| 61_I | 76_Y | 1.110 | 0.44 |
| 129_W | 154_L | 1.107 | 0.43 |
| 124_E | 130_V | 1.104 | 0.43 |
| 82_R | 155_K | 1.098 | 0.43 |
| 26_K | 61_I | 1.098 | 0.43 |
| 26_K | 90_E | 1.097 | 0.42 |
| 53_S | 90_E | 1.089 | 0.42 |
| 23_I | 86_A | 1.080 | 0.41 |
| 1_K | 36_D | 1.080 | 0.41 |
| 60_A | 138_I | 1.078 | 0.41 |
| 7_T | 13_A | 1.078 | 0.41 |
| 28_G | 143_E | 1.077 | 0.41 |
| 81_Q | 88_A | 1.073 | 0.40 |
| 69_A | 73_K | 1.072 | 0.40 |
| 48_E | 138_I | 1.067 | 0.40 |
| 28_G | 142_Q | 1.065 | 0.40 |
| 57_I | 134_V | 1.057 | 0.39 |
| 59_D | 157_L | 1.053 | 0.39 |
| 33_E | 37_K | 1.046 | 0.38 |
| 85_I | 99_R | 1.043 | 0.38 |
| 132_K | 136_Q | 1.040 | 0.37 |
| 40_E | 76_Y | 1.040 | 0.37 |
| 17_I | 132_K | 1.038 | 0.37 |
| 85_I | 117_M | 1.038 | 0.37 |
| 153_D | 157_L | 1.035 | 0.37 |
| 5_V | 24_V | 1.028 | 0.36 |
| 60_A | 155_K | 1.027 | 0.36 |
| 120_Q | 150_C | 1.025 | 0.36 |
| 4_Y | 10_T | 1.023 | 0.36 |
| 41_Q | 67_Q | 1.019 | 0.36 |
| 19_F | 59_D | 1.017 | 0.35 |
| 38_L | 98_H | 1.016 | 0.35 |
| 144_K | 148_A | 1.015 | 0.35 |
| 5_V | 145_E | 1.012 | 0.35 |
| 69_A | 133_R | 1.010 | 0.35 |
| 4_Y | 9_E | 1.009 | 0.35 |
| 15_S | 30_S | 1.001 | 0.34 |
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 | |
| 2clyA | 2 | 0.6522 | 100 | 0.107 | Contact Map |
| 4l23B | 1 | 0.9565 | 13 | 0.952 | Contact Map |
| 3d5pA | 2 | 0.2298 | 10.5 | 0.954 | Contact Map |
| 3k3pA | 2 | 0.3043 | 7.5 | 0.957 | Contact Map |
| 2ww9B | 1 | 0.2236 | 6.4 | 0.958 | Contact Map |
| 3i12A | 4 | 0.3478 | 5.7 | 0.959 | Contact Map |
| 1b9uA | 1 | 0.1863 | 5.3 | 0.96 | Contact Map |
| 2p22C | 1 | 0.8447 | 4.9 | 0.96 | Contact Map |
| 2wwbC | 1 | 0.205 | 4.7 | 0.961 | Contact Map |
| 3kdqA | 4 | 0.3913 | 4.6 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)