| 5p21 |
| ID: | 1510219594 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (160) | ||
| Sequences: | 42425 (26509) | ||
| Seq/Len: | 265.156 | ||
| Nf(neff/√len): | 2095.7 |
Jackhmmer Results: (2016_04)
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: 265.156).
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 |
| 22_Q | 149_R | 2.938 | 1.00 |
| 11_A | 92_D | 2.836 | 1.00 |
| 84_I | 115_G | 2.699 | 1.00 |
| 142_I | 158_T | 2.466 | 1.00 |
| 140_P | 158_T | 2.219 | 1.00 |
| 79_L | 114_V | 2.211 | 1.00 |
| 114_V | 155_A | 2.184 | 1.00 |
| 81_V | 116_N | 2.140 | 1.00 |
| 19_L | 81_V | 2.056 | 1.00 |
| 61_Q | 64_Y | 1.896 | 1.00 |
| 158_T | 161_R | 1.867 | 1.00 |
| 114_V | 144_T | 1.837 | 1.00 |
| 7_V | 75_G | 1.816 | 1.00 |
| 8_V | 20_T | 1.778 | 1.00 |
| 82_F | 141_Y | 1.684 | 1.00 |
| 115_G | 143_E | 1.683 | 1.00 |
| 77_G | 159_L | 1.683 | 1.00 |
| 97_R | 101_K | 1.640 | 1.00 |
| 144_T | 155_A | 1.626 | 1.00 |
| 84_I | 118_C | 1.613 | 1.00 |
| 83_A | 86_N | 1.595 | 1.00 |
| 65_S | 68_R | 1.543 | 1.00 |
| 118_C | 150_Q | 1.532 | 1.00 |
| 130_A | 134_A | 1.513 | 1.00 |
| 82_F | 115_G | 1.493 | 1.00 |
| 86_N | 89_S | 1.488 | 1.00 |
| 126_E | 129_Q | 1.484 | 1.00 |
| 18_A | 146_A | 1.474 | 1.00 |
| 61_Q | 65_S | 1.449 | 1.00 |
| 133_L | 137_Y | 1.448 | 1.00 |
| 87_T | 129_Q | 1.448 | 1.00 |
| 158_T | 162_E | 1.443 | 1.00 |
| 112_V | 142_I | 1.417 | 1.00 |
| 123_R | 126_E | 1.407 | 0.99 |
| 127_S | 131_Q | 1.364 | 0.99 |
| 118_C | 143_E | 1.345 | 0.99 |
| 5_K | 54_D | 1.307 | 0.99 |
| 34_P | 38_D | 1.305 | 0.99 |
| 64_Y | 67_M | 1.292 | 0.99 |
| 85_N | 120_L | 1.288 | 0.99 |
| 131_Q | 135_R | 1.278 | 0.99 |
| 64_Y | 68_R | 1.278 | 0.99 |
| 127_S | 143_E | 1.275 | 0.99 |
| 116_N | 146_A | 1.274 | 0.99 |
| 19_L | 152_V | 1.270 | 0.99 |
| 43_Q | 52_L | 1.267 | 0.99 |
| 151_G | 154_D | 1.261 | 0.99 |
| 134_A | 137_Y | 1.261 | 0.99 |
| 99_Q | 102_R | 1.254 | 0.99 |
| 8_V | 79_L | 1.254 | 0.99 |
| 112_V | 158_T | 1.238 | 0.98 |
| 98_E | 101_K | 1.235 | 0.98 |
| 32_Y | 35_T | 1.233 | 0.98 |
| 80_C | 93_I | 1.218 | 0.98 |
| 132_D | 136_S | 1.210 | 0.98 |
| 79_L | 159_L | 1.199 | 0.98 |
| 129_Q | 132_D | 1.197 | 0.98 |
| 22_Q | 152_V | 1.184 | 0.98 |
| 69_D | 99_Q | 1.180 | 0.98 |
| 154_D | 158_T | 1.164 | 0.97 |
| 45_V | 50_T | 1.141 | 0.97 |
| 78_F | 109_V | 1.130 | 0.97 |
| 53_L | 160_V | 1.125 | 0.97 |
| 79_L | 155_A | 1.122 | 0.97 |
| 30_D | 35_T | 1.114 | 0.96 |
| 98_E | 102_R | 1.110 | 0.96 |
| 153_E | 157_Y | 1.096 | 0.96 |
| 99_Q | 103_V | 1.094 | 0.96 |
| 117_K | 120_L | 1.089 | 0.96 |
| 82_F | 113_L | 1.085 | 0.96 |
| 21_I | 25_Q | 1.080 | 0.95 |
| 128_R | 131_Q | 1.072 | 0.95 |
| 63_E | 67_M | 1.066 | 0.95 |
| 35_T | 38_D | 1.060 | 0.95 |
| 83_A | 117_K | 1.057 | 0.95 |
| 131_Q | 134_A | 1.053 | 0.95 |
| 128_R | 132_D | 1.050 | 0.94 |
| 34_P | 37_E | 1.045 | 0.94 |
| 88_K | 92_D | 1.045 | 0.94 |
| 95_Q | 99_Q | 1.035 | 0.94 |
| 32_Y | 37_E | 1.035 | 0.94 |
| 94_H | 136_S | 1.025 | 0.93 |
| 154_D | 157_Y | 1.024 | 0.93 |
| 19_L | 155_A | 1.024 | 0.93 |
| 45_V | 48_G | 1.015 | 0.93 |
| 96_Y | 99_Q | 1.014 | 0.93 |
| 130_A | 133_L | 1.014 | 0.93 |
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 | |
| 2ce2X | 1 | 1 | 100 | 0.187 | Contact Map |
| 3conA | 1 | 0.9337 | 100 | 0.195 | Contact Map |
| 1u8zA | 2 | 0.9819 | 100 | 0.201 | Contact Map |
| 4klzA | 1 | 0.9337 | 100 | 0.204 | Contact Map |
| 3kkqA | 1 | 1 | 100 | 0.205 | Contact Map |
| 1m7bA | 1 | 0.9819 | 100 | 0.205 | Contact Map |
| 3regA | 2 | 0.988 | 100 | 0.206 | Contact Map |
| 3t5gA | 1 | 0.9759 | 100 | 0.212 | Contact Map |
| 3x1xA | 1 | 0 | 100 | 0.213 | Contact Map |
| 2bovA | 1 | 1 | 100 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)