| O27564_cytodomain |
| ID: | 1426230856 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 220 (217) | ||
| Sequences: | 4507 (3413.8) | ||
| Seq/Len: | 20.770 | ||
| Nf(neff/√len): | 231.7 |
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: 20.770).
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 |
| 153_I | 196_F | 4.032 | 1.00 |
| 182_R | 200_D | 3.652 | 1.00 |
| 46_G | 53_D | 3.280 | 1.00 |
| 65_V | 82_I | 3.143 | 1.00 |
| 48_P | 78_C | 3.136 | 1.00 |
| 3_V | 62_A | 3.124 | 1.00 |
| 79_I | 109_A | 2.796 | 1.00 |
| 182_R | 197_R | 2.673 | 1.00 |
| 5_C | 48_P | 2.535 | 1.00 |
| 180_V | 194_Y | 2.478 | 1.00 |
| 30_E | 45_H | 2.409 | 1.00 |
| 163_S | 166_D | 2.319 | 1.00 |
| 30_E | 34_K | 2.160 | 1.00 |
| 83_R | 91_I | 2.155 | 1.00 |
| 33_R | 43_F | 2.100 | 1.00 |
| 67_V | 75_T | 2.082 | 1.00 |
| 79_I | 93_A | 2.080 | 1.00 |
| 4_I | 12_L | 2.080 | 1.00 |
| 163_S | 195_S | 2.021 | 1.00 |
| 207_K | 210_E | 1.999 | 1.00 |
| 83_R | 110_D | 1.997 | 1.00 |
| 165_L | 193_D | 1.989 | 1.00 |
| 162_V | 166_D | 1.949 | 1.00 |
| 164_V | 177_I | 1.915 | 1.00 |
| 182_R | 194_Y | 1.902 | 1.00 |
| 3_V | 65_V | 1.873 | 1.00 |
| 161_G | 197_R | 1.872 | 1.00 |
| 55_E | 60_R | 1.865 | 1.00 |
| 58_N | 61_G | 1.853 | 1.00 |
| 182_R | 187_I | 1.801 | 1.00 |
| 155_E | 198_A | 1.798 | 1.00 |
| 65_V | 78_C | 1.779 | 1.00 |
| 27_A | 33_R | 1.778 | 1.00 |
| 3_V | 59_V | 1.774 | 1.00 |
| 174_G | 210_E | 1.755 | 1.00 |
| 32_V | 35_K | 1.691 | 1.00 |
| 27_A | 43_F | 1.653 | 1.00 |
| 67_V | 82_I | 1.653 | 1.00 |
| 90_R | 110_D | 1.629 | 1.00 |
| 150_E | 201_I | 1.596 | 1.00 |
| 101_I | 114_S | 1.581 | 1.00 |
| 57_A | 62_A | 1.566 | 1.00 |
| 5_C | 65_V | 1.564 | 1.00 |
| 165_L | 192_R | 1.542 | 1.00 |
| 159_L | 167_A | 1.536 | 1.00 |
| 160_E | 198_A | 1.525 | 1.00 |
| 16_R | 41_A | 1.505 | 1.00 |
| 44_V | 57_A | 1.494 | 1.00 |
| 65_V | 89_V | 1.456 | 1.00 |
| 8_S | 68_D | 1.436 | 1.00 |
| 86_D | 89_V | 1.434 | 1.00 |
| 161_G | 198_A | 1.405 | 0.99 |
| 8_S | 94_E | 1.389 | 0.99 |
| 29_D | 32_V | 1.389 | 0.99 |
| 150_E | 203_L | 1.381 | 0.99 |
| 9_E | 36_V | 1.365 | 0.99 |
| 67_V | 79_I | 1.361 | 0.99 |
| 52_S | 55_E | 1.361 | 0.99 |
| 51_V | 55_E | 1.353 | 0.99 |
| 197_R | 200_D | 1.351 | 0.99 |
| 177_I | 204_G | 1.340 | 0.99 |
| 168_D | 171_D | 1.330 | 0.99 |
| 7_W | 25_V | 1.324 | 0.99 |
| 24_F | 62_A | 1.285 | 0.99 |
| 210_E | 213_R | 1.276 | 0.99 |
| 79_I | 91_I | 1.268 | 0.99 |
| 69_L | 74_E | 1.244 | 0.98 |
| 151_V | 204_G | 1.236 | 0.98 |
| 93_A | 109_A | 1.203 | 0.98 |
| 95_A | 104_L | 1.200 | 0.98 |
| 180_V | 200_D | 1.199 | 0.98 |
| 148_M | 178_I | 1.193 | 0.98 |
| 84_K | 106_M | 1.179 | 0.98 |
| 4_I | 11_T | 1.172 | 0.98 |
| 182_R | 185_E | 1.143 | 0.97 |
| 36_V | 43_F | 1.139 | 0.97 |
| 175_V | 206_G | 1.135 | 0.97 |
| 4_I | 23_V | 1.127 | 0.97 |
| 46_G | 57_A | 1.127 | 0.97 |
| 11_T | 66_I | 1.126 | 0.97 |
| 170_H | 176_I | 1.124 | 0.97 |
| 5_C | 26_L | 1.123 | 0.97 |
| 51_V | 81_G | 1.112 | 0.96 |
| 8_S | 12_L | 1.109 | 0.96 |
| 153_I | 160_E | 1.107 | 0.96 |
| 52_S | 56_K | 1.105 | 0.96 |
| 181_G | 201_I | 1.101 | 0.96 |
| 179_G | 186_L | 1.100 | 0.96 |
| 206_G | 211_I | 1.096 | 0.96 |
| 75_T | 93_A | 1.076 | 0.95 |
| 187_I | 194_Y | 1.074 | 0.95 |
| 26_L | 46_G | 1.063 | 0.95 |
| 12_L | 25_V | 1.063 | 0.95 |
| 2_V | 21_S | 1.056 | 0.95 |
| 76_I | 104_L | 1.051 | 0.94 |
| 8_S | 27_A | 1.050 | 0.94 |
| 5_C | 78_C | 1.048 | 0.94 |
| 54_L | 59_V | 1.038 | 0.94 |
| 26_L | 57_A | 1.038 | 0.94 |
| 40_G | 43_F | 1.034 | 0.94 |
| 2_V | 64_A | 1.032 | 0.94 |
| 55_E | 85_I | 1.030 | 0.94 |
| 101_I | 105_R | 1.024 | 0.93 |
| 1_H | 61_G | 1.004 | 0.93 |
| 7_W | 33_R | 1.002 | 0.92 |
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 | |
| 2aefA | 2 | 0.9955 | 100 | 0.149 | Contact Map |
| 1lnqA | 8 | 0.9955 | 100 | 0.151 | Contact Map |
| 4g65A | 2 | 0.9591 | 100 | 0.219 | Contact Map |
| 4gx0A | 4 | 0.9591 | 100 | 0.224 | Contact Map |
| 3mt5A | 1 | 0.9636 | 100 | 0.229 | Contact Map |
| 3nafA | 1 | 0.9864 | 100 | 0.232 | Contact Map |
| 4hpfA | 2 | 0.9273 | 100 | 0.246 | Contact Map |
| 3l4bC | 4 | 0.9591 | 100 | 0.321 | Contact Map |
| 4j91A | 4 | 0.9591 | 100 | 0.362 | Contact Map |
| 3c85A | 4 | 0.6273 | 99.9 | 0.499 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)