| T0812 |
| ID: | 1403918320 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (200) | ||
| Sequences: | 363 (188.6) | ||
| Seq/Len: | 1.815 | ||
| Nf(neff/√len): | 13.3 |
Jackhmmer Results: (2014_04_16)
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: 1.815).
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 |
| 20_L | 62_L | 2.582 | 1.00 |
| 199_A | 202_I | 2.549 | 1.00 |
| 4_K | 62_L | 2.212 | 0.99 |
| 179_I | 182_I | 2.118 | 0.99 |
| 73_A | 186_V | 2.083 | 0.99 |
| 4_K | 20_L | 1.827 | 0.97 |
| 4_K | 7_I | 1.805 | 0.97 |
| 79_K | 128_E | 1.755 | 0.96 |
| 66_F | 161_I | 1.713 | 0.96 |
| 20_L | 66_F | 1.645 | 0.94 |
| 70_K | 187_A | 1.613 | 0.93 |
| 101_I | 161_I | 1.587 | 0.93 |
| 23_V | 165_L | 1.579 | 0.92 |
| 27_L | 150_T | 1.564 | 0.92 |
| 62_L | 66_F | 1.541 | 0.91 |
| 56_E | 165_L | 1.523 | 0.91 |
| 104_G | 154_F | 1.520 | 0.90 |
| 82_I | 170_Y | 1.450 | 0.87 |
| 67_E | 179_I | 1.441 | 0.87 |
| 17_Q | 62_L | 1.423 | 0.86 |
| 157_I | 185_E | 1.422 | 0.86 |
| 4_K | 11_V | 1.420 | 0.86 |
| 62_L | 136_W | 1.405 | 0.85 |
| 150_T | 153_D | 1.394 | 0.84 |
| 71_L | 159_Y | 1.389 | 0.84 |
| 138_Y | 149_V | 1.386 | 0.84 |
| 103_G | 108_H | 1.376 | 0.83 |
| 76_G | 185_E | 1.360 | 0.82 |
| 22_L | 140_G | 1.344 | 0.81 |
| 32_T | 184_M | 1.325 | 0.80 |
| 4_K | 17_Q | 1.322 | 0.80 |
| 22_L | 139_Y | 1.307 | 0.79 |
| 17_Q | 66_F | 1.302 | 0.78 |
| 17_Q | 20_L | 1.302 | 0.78 |
| 6_L | 62_L | 1.286 | 0.77 |
| 79_K | 150_T | 1.274 | 0.76 |
| 54_H | 58_F | 1.271 | 0.76 |
| 152_E | 160_D | 1.260 | 0.75 |
| 105_T | 133_E | 1.259 | 0.75 |
| 16_E | 135_E | 1.249 | 0.74 |
| 99_V | 166_I | 1.248 | 0.74 |
| 168_A | 186_V | 1.235 | 0.73 |
| 4_K | 66_F | 1.232 | 0.73 |
| 17_Q | 179_I | 1.231 | 0.73 |
| 196_T | 199_A | 1.231 | 0.73 |
| 90_T | 179_I | 1.228 | 0.73 |
| 155_L | 185_E | 1.225 | 0.72 |
| 89_E | 149_V | 1.217 | 0.72 |
| 26_A | 69_K | 1.211 | 0.71 |
| 94_T | 167_K | 1.207 | 0.71 |
| 73_A | 181_E | 1.198 | 0.70 |
| 111_I | 154_F | 1.194 | 0.69 |
| 98_Q | 167_K | 1.189 | 0.69 |
| 80_Y | 98_Q | 1.186 | 0.69 |
| 152_E | 156_D | 1.181 | 0.68 |
| 71_L | 178_R | 1.175 | 0.68 |
| 7_I | 62_L | 1.166 | 0.67 |
| 151_R | 154_F | 1.154 | 0.66 |
| 53_L | 179_I | 1.153 | 0.66 |
| 62_L | 164_I | 1.144 | 0.65 |
| 8_R | 148_T | 1.136 | 0.64 |
| 132_T | 154_F | 1.133 | 0.64 |
| 60_W | 136_W | 1.130 | 0.63 |
| 40_P | 73_A | 1.122 | 0.62 |
| 70_K | 81_A | 1.121 | 0.62 |
| 104_G | 159_Y | 1.121 | 0.62 |
| 6_L | 20_L | 1.115 | 0.62 |
| 153_D | 201_L | 1.108 | 0.61 |
| 159_Y | 201_L | 1.097 | 0.60 |
| 66_F | 136_W | 1.095 | 0.60 |
| 73_A | 182_I | 1.093 | 0.59 |
| 141_D | 162_H | 1.086 | 0.59 |
| 61_K | 83_Y | 1.079 | 0.58 |
| 129_I | 193_T | 1.078 | 0.58 |
| 22_L | 169_T | 1.072 | 0.57 |
| 23_V | 59_Y | 1.070 | 0.57 |
| 77_K | 130_E | 1.068 | 0.57 |
| 29_H | 129_I | 1.066 | 0.57 |
| 95_Y | 179_I | 1.066 | 0.57 |
| 187_A | 199_A | 1.065 | 0.56 |
| 4_K | 14_K | 1.062 | 0.56 |
| 14_K | 62_L | 1.059 | 0.56 |
| 43_V | 46_M | 1.057 | 0.56 |
| 164_I | 185_E | 1.057 | 0.56 |
| 82_I | 89_E | 1.042 | 0.54 |
| 47_D | 161_I | 1.041 | 0.54 |
| 41_E | 183_S | 1.040 | 0.54 |
| 89_E | 175_R | 1.038 | 0.54 |
| 19_I | 32_T | 1.034 | 0.53 |
| 91_G | 150_T | 1.034 | 0.53 |
| 111_I | 115_H | 1.033 | 0.53 |
| 138_Y | 153_D | 1.031 | 0.53 |
| 7_I | 20_L | 1.029 | 0.53 |
| 111_I | 157_I | 1.024 | 0.52 |
| 33_K | 141_D | 1.017 | 0.51 |
| 57_P | 77_K | 1.015 | 0.51 |
| 38_Q | 122_G | 1.013 | 0.51 |
| 56_E | 71_L | 1.011 | 0.51 |
| 111_I | 151_R | 1.009 | 0.50 |
| 191_R | 199_A | 1.006 | 0.50 |
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 | |
| 4a0tA | 3 | 0.4657 | 5.1 | 0.964 | Contact Map |
| 2brfA | 1 | 0.3186 | 4.1 | 0.965 | Contact Map |
| 3kt9A | 1 | 0.3235 | 3.8 | 0.966 | Contact Map |
| 1wfxA | 1 | 0.4363 | 3.6 | 0.966 | Contact Map |
| 2aqjA | 1 | 0.5294 | 3.1 | 0.968 | Contact Map |
| 1cjcA | 1 | 0.4804 | 2.5 | 0.969 | Contact Map |
| 2jwkA | 2 | 0.3235 | 2.3 | 0.97 | Contact Map |
| 2qa1A | 1 | 0.5 | 2.2 | 0.97 | Contact Map |
| 1ujxA | 1 | 0.3431 | 2.2 | 0.97 | Contact Map |
| 2pfuA | 1 | 0.402 | 2.2 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)