| ACT SYNTH low coverage |
| ID: | 1425291194 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 208 (205) | ||
| Sequences: | 1402 (882.5) | ||
| Seq/Len: | 6.839 | ||
| Nf(neff/√len): | 61.6 |
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: 6.839).
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 |
| 133_D | 190_E | 3.730 | 1.00 |
| 131_I | 190_E | 3.105 | 1.00 |
| 85_I | 145_V | 3.027 | 1.00 |
| 134_S | 137_D | 3.023 | 1.00 |
| 88_R | 91_S | 2.737 | 1.00 |
| 12_A | 18_Q | 2.678 | 1.00 |
| 99_F | 193_D | 2.638 | 1.00 |
| 95_P | 133_D | 2.518 | 1.00 |
| 97_R | 190_E | 2.398 | 1.00 |
| 61_S | 73_V | 2.296 | 1.00 |
| 78_V | 100_G | 2.175 | 1.00 |
| 117_I | 122_M | 2.155 | 1.00 |
| 80_L | 179_R | 2.085 | 1.00 |
| 130_V | 141_A | 1.976 | 1.00 |
| 145_V | 175_V | 1.950 | 1.00 |
| 132_V | 141_A | 1.898 | 1.00 |
| 86_A | 90_E | 1.821 | 1.00 |
| 28_G | 56_H | 1.809 | 1.00 |
| 81_V | 183_I | 1.756 | 1.00 |
| 12_A | 15_V | 1.717 | 1.00 |
| 5_L | 61_S | 1.675 | 1.00 |
| 7_A | 64_L | 1.672 | 1.00 |
| 88_R | 148_A | 1.660 | 1.00 |
| 4_R | 48_D | 1.612 | 1.00 |
| 141_A | 144_V | 1.610 | 1.00 |
| 87_A | 91_S | 1.591 | 1.00 |
| 23_I | 49_V | 1.574 | 1.00 |
| 125_I | 161_S | 1.562 | 1.00 |
| 136_E | 140_R | 1.550 | 0.99 |
| 146_H | 173_T | 1.531 | 0.99 |
| 137_D | 140_R | 1.475 | 0.99 |
| 132_V | 137_D | 1.475 | 0.99 |
| 190_E | 194_R | 1.471 | 0.99 |
| 169_R | 195_V | 1.449 | 0.99 |
| 9_I | 15_V | 1.413 | 0.99 |
| 155_R | 174_T | 1.402 | 0.99 |
| 6_H | 74_D | 1.394 | 0.99 |
| 21_T | 25_E | 1.385 | 0.99 |
| 16_L | 29_N | 1.383 | 0.99 |
| 81_V | 128_F | 1.373 | 0.98 |
| 33_L | 47_I | 1.370 | 0.98 |
| 110_R | 114_R | 1.365 | 0.98 |
| 20_C | 69_T | 1.355 | 0.98 |
| 82_S | 86_A | 1.352 | 0.98 |
| 79_A | 83_Q | 1.337 | 0.98 |
| 112_L | 159_F | 1.333 | 0.98 |
| 151_S | 161_S | 1.321 | 0.98 |
| 35_M | 45_V | 1.319 | 0.98 |
| 139_Y | 146_H | 1.316 | 0.98 |
| 133_D | 137_D | 1.316 | 0.98 |
| 82_S | 98_V | 1.302 | 0.98 |
| 4_R | 46_D | 1.282 | 0.97 |
| 157_K | 174_T | 1.274 | 0.97 |
| 135_E | 147_R | 1.264 | 0.97 |
| 18_Q | 67_C | 1.249 | 0.97 |
| 20_C | 30_I | 1.246 | 0.97 |
| 92_S | 144_V | 1.244 | 0.97 |
| 146_H | 156_F | 1.243 | 0.97 |
| 23_I | 47_I | 1.243 | 0.97 |
| 82_S | 128_F | 1.237 | 0.96 |
| 84_E | 149_W | 1.214 | 0.96 |
| 142_L | 146_H | 1.208 | 0.96 |
| 13_P | 29_N | 1.203 | 0.96 |
| 79_A | 82_S | 1.202 | 0.96 |
| 17_G | 24_G | 1.198 | 0.96 |
| 194_R | 198_E | 1.197 | 0.95 |
| 22_I | 60_I | 1.184 | 0.95 |
| 97_R | 112_L | 1.164 | 0.95 |
| 49_V | 60_I | 1.162 | 0.94 |
| 14_G | 29_N | 1.149 | 0.94 |
| 32_N | 122_M | 1.131 | 0.93 |
| 89_L | 141_A | 1.127 | 0.93 |
| 92_S | 141_A | 1.120 | 0.93 |
| 176_V | 180_G | 1.113 | 0.93 |
| 157_K | 170_S | 1.111 | 0.93 |
| 14_G | 20_C | 1.108 | 0.92 |
| 2_L | 31_V | 1.106 | 0.92 |
| 81_V | 149_W | 1.101 | 0.92 |
| 53_D | 56_H | 1.081 | 0.91 |
| 162_T | 167_N | 1.075 | 0.91 |
| 53_D | 59_N | 1.070 | 0.91 |
| 127_A | 183_I | 1.068 | 0.90 |
| 139_Y | 143_G | 1.065 | 0.90 |
| 12_A | 69_T | 1.061 | 0.90 |
| 96_A | 141_A | 1.056 | 0.90 |
| 23_I | 30_I | 1.054 | 0.90 |
| 117_I | 155_R | 1.053 | 0.90 |
| 26_A | 63_A | 1.044 | 0.89 |
| 11_N | 29_N | 1.041 | 0.89 |
| 193_D | 197_E | 1.039 | 0.89 |
| 70_V | 73_V | 1.033 | 0.88 |
| 139_Y | 142_L | 1.029 | 0.88 |
| 143_G | 146_H | 1.028 | 0.88 |
| 126_Y | 183_I | 1.011 | 0.87 |
| 90_E | 96_A | 1.010 | 0.87 |
| 85_I | 185_M | 1.004 | 0.86 |
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 | |
| 1vj7A | 2 | 0.9183 | 100 | 0.424 | Contact Map |
| 3l9dA | 2 | 0.7163 | 100 | 0.522 | Contact Map |
| 2be3A | 2 | 0.7212 | 100 | 0.542 | Contact Map |
| 2ko1A | 2 | 0.4087 | 99 | 0.864 | Contact Map |
| 2lvwA | 2 | 0.4279 | 98.8 | 0.871 | Contact Map |
| 1zpvA | 3 | 0.4135 | 98.6 | 0.882 | Contact Map |
| 2fgcA | 1 | 0.6298 | 98.4 | 0.888 | Contact Map |
| 2pc6A | 4 | 0.7788 | 98.2 | 0.893 | Contact Map |
| 2f1fA | 2 | 0.7692 | 98.1 | 0.896 | Contact Map |
| 1y7pA | 3 | 0.7163 | 98.1 | 0.896 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)