| RAB33B |
| ID: | 1667555759 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 229 (194) | ||
| Sequences: | 1580 (1051.4) | ||
| Seq/Len: | 8.144 | ||
| Nf(neff/√len): | 75.5 |
HHblits Results: (2016_02)
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 |
| 41_D | 124_S | 4.028 | 1.00 |
| 114_Y | 174_L | 3.655 | 1.00 |
| 49_L | 188_V | 3.650 | 1.00 |
| 118_N | 121_S | 3.213 | 1.00 |
| 119_M | 162_L | 3.204 | 1.00 |
| 164_Q | 168_D | 2.921 | 1.00 |
| 49_L | 113_V | 2.873 | 1.00 |
| 113_V | 148_N | 2.715 | 1.00 |
| 148_N | 179_A | 2.641 | 1.00 |
| 112_F | 125_L | 2.565 | 1.00 |
| 78_D | 197_H | 2.537 | 1.00 |
| 160_T | 164_Q | 2.447 | 1.00 |
| 163_A | 167_A | 2.429 | 1.00 |
| 181_N | 186_D | 2.418 | 1.00 |
| 156_I | 176_E | 2.172 | 1.00 |
| 114_Y | 163_A | 2.066 | 1.00 |
| 145_L | 172_M | 2.009 | 1.00 |
| 163_A | 174_L | 1.989 | 1.00 |
| 52_R | 56_G | 1.968 | 1.00 |
| 90_A | 93_E | 1.967 | 1.00 |
| 166_F | 170_H | 1.925 | 1.00 |
| 116_M | 150_C | 1.913 | 1.00 |
| 38_V | 50_T | 1.840 | 1.00 |
| 150_C | 186_D | 1.759 | 1.00 |
| 88_D | 91_G | 1.752 | 1.00 |
| 187_H | 190_A | 1.738 | 1.00 |
| 119_M | 123_H | 1.722 | 1.00 |
| 165_K | 169_T | 1.630 | 1.00 |
| 146_V | 191_I | 1.565 | 1.00 |
| 159_P | 162_L | 1.564 | 1.00 |
| 163_A | 166_F | 1.547 | 1.00 |
| 84_I | 196_A | 1.472 | 0.99 |
| 40_G | 45_G | 1.466 | 0.99 |
| 144_I | 175_F | 1.425 | 0.99 |
| 145_L | 167_A | 1.403 | 0.99 |
| 126_P | 166_F | 1.366 | 0.99 |
| 35_K | 40_G | 1.359 | 0.99 |
| 144_I | 191_I | 1.352 | 0.99 |
| 91_G | 95_F | 1.348 | 0.99 |
| 52_R | 58_F | 1.344 | 0.99 |
| 76_E | 79_G | 1.334 | 0.99 |
| 126_P | 169_T | 1.324 | 0.99 |
| 110_V | 132_C | 1.299 | 0.98 |
| 147_G | 176_E | 1.293 | 0.98 |
| 53_F | 73_R | 1.279 | 0.98 |
| 198_K | 201_S | 1.279 | 0.98 |
| 40_G | 46_K | 1.252 | 0.98 |
| 129_I | 172_M | 1.229 | 0.97 |
| 129_I | 133_K | 1.217 | 0.97 |
| 109_A | 199_L | 1.217 | 0.97 |
| 165_K | 168_D | 1.178 | 0.96 |
| 175_F | 194_T | 1.177 | 0.96 |
| 213_N | 220_E | 1.157 | 0.96 |
| 110_V | 141_I | 1.157 | 0.96 |
| 133_K | 143_R | 1.151 | 0.96 |
| 190_A | 194_T | 1.125 | 0.95 |
| 58_F | 180_K | 1.115 | 0.95 |
| 125_L | 145_L | 1.112 | 0.95 |
| 107_V | 110_V | 1.111 | 0.95 |
| 104_Y | 107_V | 1.104 | 0.94 |
| 41_D | 128_W | 1.096 | 0.94 |
| 188_V | 192_F | 1.087 | 0.94 |
| 93_E | 103_Y | 1.083 | 0.93 |
| 67_G | 70_F | 1.074 | 0.93 |
| 182_P | 185_N | 1.070 | 0.93 |
| 88_D | 92_Q | 1.063 | 0.93 |
| 215_I | 218_K | 1.061 | 0.93 |
| 44_V | 148_N | 1.061 | 0.93 |
| 34_F | 199_L | 1.060 | 0.93 |
| 48_C | 58_F | 1.054 | 0.92 |
| 92_Q | 105_R | 1.050 | 0.92 |
| 52_R | 67_G | 1.043 | 0.92 |
| 109_A | 195_L | 1.041 | 0.92 |
| 69_D | 110_V | 1.040 | 0.92 |
| 191_I | 196_A | 1.032 | 0.91 |
| 214_G | 218_K | 1.028 | 0.91 |
| 116_M | 156_I | 1.025 | 0.91 |
| 156_I | 159_P | 1.011 | 0.90 |
| 30_R | 33_I | 1.004 | 0.90 |
| 68_V | 102_H | 1.002 | 0.89 |
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 | |
| 4cymA | 3 | 0.7511 | 100 | 0.388 | Contact Map |
| 2f7sA | 2 | 0.7686 | 100 | 0.395 | Contact Map |
| 2yc2C | 2 | 0.6376 | 100 | 0.395 | Contact Map |
| 2bcgY | 1 | 0.8166 | 100 | 0.396 | Contact Map |
| 1z06A | 1 | 0.7205 | 100 | 0.398 | Contact Map |
| 2a5jA | 1 | 0.7729 | 100 | 0.399 | Contact Map |
| 4dkxA | 2 | 0.6812 | 100 | 0.401 | Contact Map |
| 4lhwA | 5 | 0.7598 | 100 | 0.404 | Contact Map |
| 3cpjB | 1 | 0.7162 | 100 | 0.404 | Contact Map |
| 2g3yA | 1 | 0.7293 | 100 | 0.408 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)