| aaca-staau |
| ID: | 1433429891 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 237 (230) | ||
| Sequences: | 6919 (5126.4) | ||
| Seq/Len: | 30.083 | ||
| Nf(neff/√len): | 338.0 |
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: 30.083).
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 |
| 56_N | 72_K | 4.108 | 1.00 |
| 58_E | 72_K | 3.992 | 1.00 |
| 168_C | 197_I | 3.837 | 1.00 |
| 100_A | 225_M | 3.631 | 1.00 |
| 45_N | 56_N | 3.228 | 1.00 |
| 15_L | 19_E | 3.097 | 1.00 |
| 15_L | 73_E | 3.041 | 1.00 |
| 22_F | 70_G | 3.021 | 1.00 |
| 178_L | 189_I | 3.008 | 1.00 |
| 97_R | 225_M | 2.628 | 1.00 |
| 74_I | 187_G | 2.575 | 1.00 |
| 20_Y | 58_E | 2.446 | 1.00 |
| 98_D | 101_S | 2.421 | 1.00 |
| 21_I | 73_E | 2.407 | 1.00 |
| 38_K | 57_I | 2.351 | 1.00 |
| 102_F | 188_I | 2.228 | 1.00 |
| 172_F | 188_I | 2.211 | 1.00 |
| 107_H | 226_Y | 2.206 | 1.00 |
| 19_E | 73_E | 2.152 | 1.00 |
| 3_E | 15_L | 2.075 | 1.00 |
| 99_I | 177_L | 2.001 | 1.00 |
| 103_L | 172_F | 1.959 | 1.00 |
| 41_Y | 57_I | 1.940 | 1.00 |
| 99_I | 172_F | 1.926 | 1.00 |
| 166_C | 199_E | 1.883 | 1.00 |
| 49_E | 105_Q | 1.882 | 1.00 |
| 19_E | 75_K | 1.770 | 1.00 |
| 97_R | 221_D | 1.756 | 1.00 |
| 101_S | 228_N | 1.746 | 1.00 |
| 180_D | 184_R | 1.739 | 1.00 |
| 171_D | 176_H | 1.705 | 1.00 |
| 3_E | 17_N | 1.628 | 1.00 |
| 101_S | 225_M | 1.618 | 1.00 |
| 88_S | 91_E | 1.562 | 1.00 |
| 37_E | 41_Y | 1.515 | 1.00 |
| 100_A | 104_R | 1.513 | 1.00 |
| 171_D | 190_D | 1.509 | 1.00 |
| 16_V | 70_G | 1.501 | 1.00 |
| 98_D | 184_R | 1.500 | 1.00 |
| 35_A | 39_A | 1.473 | 1.00 |
| 13_A | 21_I | 1.465 | 1.00 |
| 74_I | 186_T | 1.433 | 1.00 |
| 42_N | 46_T | 1.428 | 1.00 |
| 100_A | 222_I | 1.422 | 1.00 |
| 221_D | 225_M | 1.402 | 0.99 |
| 53_K | 72_K | 1.394 | 0.99 |
| 98_D | 102_F | 1.385 | 0.99 |
| 11_S | 23_K | 1.375 | 0.99 |
| 104_R | 108_G | 1.363 | 0.99 |
| 168_C | 195_G | 1.361 | 0.99 |
| 108_G | 230_D | 1.358 | 0.99 |
| 61_Y | 68_I | 1.328 | 0.99 |
| 5_I | 21_I | 1.300 | 0.99 |
| 102_F | 105_Q | 1.291 | 0.99 |
| 221_D | 224_R | 1.274 | 0.99 |
| 78_F | 178_L | 1.256 | 0.99 |
| 18_N | 72_K | 1.256 | 0.99 |
| 220_E | 224_R | 1.247 | 0.99 |
| 197_I | 202_D | 1.237 | 0.98 |
| 75_K | 181_G | 1.236 | 0.98 |
| 10_D | 192_G | 1.218 | 0.98 |
| 75_K | 180_D | 1.215 | 0.98 |
| 176_H | 190_D | 1.212 | 0.98 |
| 38_K | 60_S | 1.210 | 0.98 |
| 95_L | 179_L | 1.204 | 0.98 |
| 97_R | 101_S | 1.200 | 0.98 |
| 23_K | 37_E | 1.192 | 0.98 |
| 93_N | 97_R | 1.181 | 0.98 |
| 104_R | 227_G | 1.180 | 0.98 |
| 11_S | 192_G | 1.177 | 0.98 |
| 101_S | 229_I | 1.164 | 0.97 |
| 38_K | 42_N | 1.162 | 0.97 |
| 178_L | 186_T | 1.144 | 0.97 |
| 151_F | 154_R | 1.134 | 0.97 |
| 93_N | 221_D | 1.129 | 0.97 |
| 32_K | 35_A | 1.126 | 0.97 |
| 76_G | 178_L | 1.120 | 0.96 |
| 15_L | 21_I | 1.118 | 0.96 |
| 43_F | 47_N | 1.113 | 0.96 |
| 101_S | 104_R | 1.109 | 0.96 |
| 35_A | 60_S | 1.107 | 0.96 |
| 94_L | 98_D | 1.105 | 0.96 |
| 170_N | 197_I | 1.099 | 0.96 |
| 43_F | 46_T | 1.095 | 0.96 |
| 106_M | 191_F | 1.091 | 0.96 |
| 180_D | 186_T | 1.089 | 0.96 |
| 173_S | 193_D | 1.087 | 0.96 |
| 224_R | 228_N | 1.080 | 0.95 |
| 141_T | 144_E | 1.076 | 0.95 |
| 37_E | 192_G | 1.069 | 0.95 |
| 39_A | 42_N | 1.068 | 0.95 |
| 97_R | 224_R | 1.062 | 0.95 |
| 167_L | 196_I | 1.061 | 0.95 |
| 101_S | 105_Q | 1.056 | 0.95 |
| 215_G | 218_F | 1.046 | 0.94 |
| 103_L | 107_H | 1.028 | 0.94 |
| 223_L | 227_G | 1.023 | 0.93 |
| 104_R | 107_H | 1.009 | 0.93 |
| 137_Y | 141_T | 1.009 | 0.93 |
| 41_Y | 191_F | 1.001 | 0.92 |
| 206_L | 222_I | 1.000 | 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 | |
| 4orkA | 4 | 1 | 100 | 0.204 | Contact Map |
| 4dcaA | 1 | 0.9705 | 100 | 0.248 | Contact Map |
| 3tdwA | 1 | 0.9662 | 100 | 0.27 | Contact Map |
| 3sg8A | 2 | 0.9789 | 100 | 0.274 | Contact Map |
| 2ppqA | 1 | 0.9156 | 100 | 0.307 | Contact Map |
| 3dxpA | 1 | 0.9536 | 100 | 0.319 | Contact Map |
| 4h05A | 2 | 0.9578 | 100 | 0.346 | Contact Map |
| 1nd4A | 2 | 0.9241 | 100 | 0.356 | Contact Map |
| 4gkhA | 12 | 0.9283 | 100 | 0.357 | Contact Map |
| 4ocvA | 1 | 0.9536 | 100 | 0.359 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)