| T0826 1-220 |
| ID: | 1403943265 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 220 (213) | ||
| Sequences: | 485 (384.5) | ||
| Seq/Len: | 2.277 | ||
| Nf(neff/√len): | 26.3 |
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: 2.277).
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 |
| 131_G | 135_A | 3.057 | 1.00 |
| 62_N | 162_S | 3.016 | 1.00 |
| 82_L | 138_Y | 2.704 | 1.00 |
| 52_T | 177_Y | 2.371 | 1.00 |
| 87_A | 127_I | 2.346 | 1.00 |
| 79_P | 139_I | 2.244 | 1.00 |
| 173_Q | 177_Y | 2.137 | 1.00 |
| 23_S | 65_F | 2.081 | 0.99 |
| 79_P | 138_Y | 2.072 | 0.99 |
| 15_L | 138_Y | 2.021 | 0.99 |
| 79_P | 135_A | 2.019 | 0.99 |
| 91_Q | 118_L | 1.978 | 0.99 |
| 59_F | 165_C | 1.920 | 0.99 |
| 22_Y | 27_L | 1.845 | 0.98 |
| 49_F | 177_Y | 1.837 | 0.98 |
| 104_L | 203_K | 1.775 | 0.98 |
| 92_E | 99_F | 1.767 | 0.98 |
| 151_E | 155_R | 1.736 | 0.97 |
| 91_Q | 99_F | 1.736 | 0.97 |
| 71_P | 75_K | 1.688 | 0.97 |
| 108_L | 203_K | 1.653 | 0.96 |
| 152_L | 160_A | 1.565 | 0.95 |
| 24_S | 58_F | 1.545 | 0.94 |
| 19_L | 78_I | 1.545 | 0.94 |
| 94_F | 138_Y | 1.517 | 0.93 |
| 62_N | 158_L | 1.449 | 0.91 |
| 188_T | 198_G | 1.444 | 0.91 |
| 31_F | 35_V | 1.416 | 0.90 |
| 63_F | 159_A | 1.414 | 0.90 |
| 31_F | 185_K | 1.404 | 0.89 |
| 20_S | 27_L | 1.364 | 0.87 |
| 165_C | 168_G | 1.344 | 0.86 |
| 95_F | 153_L | 1.341 | 0.86 |
| 161_V | 164_L | 1.311 | 0.84 |
| 75_K | 79_P | 1.307 | 0.84 |
| 15_L | 78_I | 1.298 | 0.84 |
| 145_Y | 151_E | 1.291 | 0.83 |
| 92_E | 95_F | 1.288 | 0.83 |
| 99_F | 214_Y | 1.288 | 0.83 |
| 137_A | 217_L | 1.286 | 0.83 |
| 30_A | 93_I | 1.270 | 0.82 |
| 68_I | 77_L | 1.266 | 0.81 |
| 23_S | 172_L | 1.260 | 0.81 |
| 103_M | 106_N | 1.259 | 0.81 |
| 100_N | 103_M | 1.259 | 0.81 |
| 31_F | 57_L | 1.248 | 0.80 |
| 31_F | 192_V | 1.246 | 0.80 |
| 192_V | 198_G | 1.239 | 0.79 |
| 75_K | 81_I | 1.217 | 0.78 |
| 63_F | 163_F | 1.211 | 0.77 |
| 31_F | 198_G | 1.209 | 0.77 |
| 140_A | 144_K | 1.206 | 0.77 |
| 10_L | 18_F | 1.202 | 0.77 |
| 31_F | 92_E | 1.199 | 0.76 |
| 129_C | 136_L | 1.197 | 0.76 |
| 49_F | 173_Q | 1.193 | 0.76 |
| 99_F | 118_L | 1.183 | 0.75 |
| 63_F | 166_A | 1.183 | 0.75 |
| 127_I | 132_V | 1.171 | 0.74 |
| 23_S | 81_I | 1.166 | 0.73 |
| 163_F | 167_L | 1.160 | 0.73 |
| 136_L | 140_A | 1.152 | 0.72 |
| 204_Y | 208_K | 1.151 | 0.72 |
| 156_L | 160_A | 1.139 | 0.71 |
| 43_G | 46_A | 1.138 | 0.71 |
| 175_Q | 183_N | 1.118 | 0.69 |
| 174_Y | 178_A | 1.118 | 0.69 |
| 52_T | 57_L | 1.116 | 0.69 |
| 170_A | 183_N | 1.100 | 0.67 |
| 190_L | 195_N | 1.099 | 0.67 |
| 94_F | 122_G | 1.093 | 0.66 |
| 125_L | 152_L | 1.090 | 0.66 |
| 24_S | 27_L | 1.085 | 0.66 |
| 179_S | 183_N | 1.081 | 0.65 |
| 59_F | 169_I | 1.078 | 0.65 |
| 71_P | 190_L | 1.072 | 0.64 |
| 86_A | 161_V | 1.068 | 0.64 |
| 11_G | 84_I | 1.066 | 0.64 |
| 63_F | 155_R | 1.066 | 0.64 |
| 21_L | 58_F | 1.056 | 0.62 |
| 91_Q | 214_Y | 1.054 | 0.62 |
| 128_V | 132_V | 1.043 | 0.61 |
| 10_L | 14_A | 1.038 | 0.60 |
| 132_V | 164_L | 1.035 | 0.60 |
| 33_A | 120_T | 1.035 | 0.60 |
| 126_W | 130_L | 1.034 | 0.60 |
| 185_K | 194_S | 1.032 | 0.60 |
| 95_F | 100_N | 1.030 | 0.60 |
| 111_T | 188_T | 1.023 | 0.59 |
| 86_A | 131_G | 1.022 | 0.59 |
| 63_F | 216_Q | 1.021 | 0.59 |
| 92_E | 217_L | 1.012 | 0.58 |
| 29_Y | 85_S | 1.005 | 0.57 |
| 20_S | 61_S | 1.003 | 0.57 |
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 | |
| 1fmeA | 1 | 0.1045 | 3.9 | 0.969 | Contact Map |
| 2ww9C | 1 | 0.0955 | 2.8 | 0.971 | Contact Map |
| 2wwbC | 1 | 0.1591 | 2.6 | 0.971 | Contact Map |
| 2hi2A | 1 | 0.3 | 2.4 | 0.972 | Contact Map |
| 4lz6A | 1 | 0.8455 | 2.2 | 0.972 | Contact Map |
| 2a65A | 1 | 0.55 | 2 | 0.973 | Contact Map |
| 4humA | 1 | 0.8455 | 1.8 | 0.973 | Contact Map |
| 4httA | 2 | 0.2727 | 1.8 | 0.974 | Contact Map |
| 4m48A | 1 | 0.6455 | 1.6 | 0.974 | Contact Map |
| 3cx5G | 2 | 0.1955 | 1.6 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)