| TasA_test |
| ID: | 1481041183 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 233 (181) | ||
| Sequences: | 423 (345) | ||
| Seq/Len: | 2.337 | ||
| Nf(neff/√len): | 25.6 |
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: 2.337).
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 |
| 53_I | 203_A | 2.515 | 1.00 |
| 4_D | 18_D | 2.481 | 1.00 |
| 188_N | 191_Q | 2.219 | 1.00 |
| 15_G | 205_Q | 2.109 | 1.00 |
| 80_S | 109_K | 2.043 | 0.99 |
| 16_T | 50_S | 2.005 | 0.99 |
| 16_T | 49_G | 1.936 | 0.99 |
| 34_K | 37_D | 1.925 | 0.99 |
| 28_V | 39_L | 1.855 | 0.99 |
| 28_V | 33_L | 1.682 | 0.97 |
| 56_V | 203_A | 1.664 | 0.97 |
| 34_K | 51_L | 1.652 | 0.97 |
| 82_F | 171_I | 1.650 | 0.96 |
| 19_L | 53_I | 1.647 | 0.96 |
| 2_F | 188_N | 1.616 | 0.96 |
| 77_D | 190_Y | 1.603 | 0.96 |
| 83_E | 174_K | 1.600 | 0.96 |
| 61_N | 198_Q | 1.598 | 0.96 |
| 173_F | 190_Y | 1.575 | 0.95 |
| 16_T | 51_L | 1.568 | 0.95 |
| 32_N | 188_N | 1.555 | 0.95 |
| 157_V | 162_T | 1.542 | 0.94 |
| 3_N | 174_K | 1.462 | 0.92 |
| 58_M | 169_M | 1.426 | 0.91 |
| 82_F | 173_F | 1.409 | 0.90 |
| 1_A | 8_K | 1.362 | 0.88 |
| 64_D | 79_L | 1.343 | 0.87 |
| 82_F | 174_K | 1.286 | 0.83 |
| 15_G | 51_L | 1.276 | 0.83 |
| 157_V | 161_P | 1.269 | 0.82 |
| 17_L | 205_Q | 1.254 | 0.81 |
| 195_I | 201_F | 1.242 | 0.80 |
| 62_Y | 201_F | 1.234 | 0.80 |
| 66_K | 72_N | 1.232 | 0.80 |
| 25_S | 169_M | 1.227 | 0.79 |
| 169_M | 199_F | 1.225 | 0.79 |
| 123_A | 126_I | 1.213 | 0.78 |
| 85_T | 105_D | 1.190 | 0.76 |
| 3_N | 7_S | 1.183 | 0.76 |
| 76_E | 192_G | 1.183 | 0.76 |
| 81_Q | 174_K | 1.175 | 0.75 |
| 14_S | 205_Q | 1.172 | 0.75 |
| 75_P | 189_K | 1.171 | 0.75 |
| 30_L | 169_M | 1.171 | 0.75 |
| 17_L | 172_Q | 1.169 | 0.74 |
| 48_N | 110_D | 1.159 | 0.74 |
| 98_P | 101_I | 1.157 | 0.73 |
| 13_A | 43_F | 1.150 | 0.73 |
| 2_F | 190_Y | 1.147 | 0.72 |
| 41_K | 45_F | 1.147 | 0.72 |
| 51_L | 169_M | 1.144 | 0.72 |
| 81_Q | 176_D | 1.143 | 0.72 |
| 37_D | 173_F | 1.141 | 0.72 |
| 14_S | 51_L | 1.131 | 0.71 |
| 81_Q | 187_Q | 1.124 | 0.70 |
| 4_D | 205_Q | 1.121 | 0.70 |
| 39_L | 208_G | 1.117 | 0.70 |
| 125_K | 152_P | 1.112 | 0.69 |
| 84_V | 111_L | 1.110 | 0.69 |
| 40_T | 168_Q | 1.102 | 0.68 |
| 32_N | 51_L | 1.101 | 0.68 |
| 28_V | 201_F | 1.101 | 0.68 |
| 6_K | 10_A | 1.097 | 0.68 |
| 3_N | 81_Q | 1.096 | 0.67 |
| 81_Q | 190_Y | 1.093 | 0.67 |
| 79_L | 195_I | 1.090 | 0.67 |
| 39_L | 171_I | 1.088 | 0.67 |
| 106_A | 110_D | 1.081 | 0.66 |
| 188_N | 205_Q | 1.079 | 0.66 |
| 93_G | 128_K | 1.077 | 0.65 |
| 66_K | 70_G | 1.077 | 0.65 |
| 175_D | 187_Q | 1.073 | 0.65 |
| 17_L | 188_N | 1.073 | 0.65 |
| 47_N | 84_V | 1.067 | 0.64 |
| 2_F | 77_D | 1.058 | 0.63 |
| 57_L | 207_N | 1.058 | 0.63 |
| 9_D | 203_A | 1.048 | 0.62 |
| 108_L | 111_L | 1.043 | 0.62 |
| 176_D | 187_Q | 1.043 | 0.62 |
| 124_E | 127_K | 1.036 | 0.61 |
| 113_L | 131_D | 1.026 | 0.60 |
| 90_G | 93_G | 1.021 | 0.59 |
| 177_K | 190_Y | 1.020 | 0.59 |
| 44_Q | 166_Q | 1.020 | 0.59 |
| 187_Q | 190_Y | 1.019 | 0.59 |
| 15_G | 19_L | 1.018 | 0.59 |
| 191_Q | 195_I | 1.017 | 0.59 |
| 57_L | 204_T | 1.017 | 0.59 |
| 92_E | 165_D | 1.015 | 0.59 |
| 83_E | 105_D | 1.008 | 0.58 |
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 | |
| 2kutA | 1 | 0.5021 | 10.5 | 0.95 | Contact Map |
| 2qsvA | 1 | 0.5579 | 6.4 | 0.955 | Contact Map |
| 4e9lA | 1 | 0 | 5.7 | 0.956 | Contact Map |
| 2e6jA | 1 | 0.4635 | 5.7 | 0.956 | Contact Map |
| 3isyA | 1 | 0.5021 | 5 | 0.957 | Contact Map |
| 1u9kA | 2 | 0.2618 | 4.7 | 0.958 | Contact Map |
| 3wuzA | 1 | 0.2876 | 4.4 | 0.958 | Contact Map |
| 1gyuA | 1 | 0.3391 | 4.3 | 0.958 | Contact Map |
| 2l0dA | 1 | 0.485 | 3.9 | 0.959 | Contact Map |
| 4cayC | 1 | 0.0987 | 3.9 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)