| 1R84 |
| ID: | 1435840818 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 232 (225) | ||
| Sequences: | 383 (296.1) | ||
| Seq/Len: | 1.702 | ||
| Nf(neff/√len): | 19.7 |
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: 1.702).
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 |
| 52_I | 88_F | 4.562 | 1.00 |
| 19_L | 213_V | 2.681 | 1.00 |
| 90_T | 115_D | 2.252 | 0.99 |
| 85_D | 216_K | 2.175 | 0.99 |
| 14_A | 61_L | 2.102 | 0.99 |
| 27_F | 220_G | 1.993 | 0.98 |
| 59_S | 137_W | 1.794 | 0.96 |
| 24_T | 50_P | 1.725 | 0.95 |
| 80_W | 84_A | 1.660 | 0.94 |
| 189_W | 195_G | 1.657 | 0.94 |
| 89_T | 92_L | 1.634 | 0.93 |
| 118_M | 122_G | 1.624 | 0.93 |
| 85_D | 89_T | 1.596 | 0.92 |
| 53_A | 93_L | 1.596 | 0.92 |
| 66_L | 79_Y | 1.578 | 0.92 |
| 191_I | 199_V | 1.567 | 0.91 |
| 56_M | 60_M | 1.558 | 0.91 |
| 125_G | 189_W | 1.468 | 0.87 |
| 115_D | 118_M | 1.463 | 0.87 |
| 28_L | 47_T | 1.447 | 0.86 |
| 117_I | 144_A | 1.429 | 0.85 |
| 90_T | 118_M | 1.413 | 0.84 |
| 53_A | 85_D | 1.412 | 0.84 |
| 67_T | 127_L | 1.403 | 0.84 |
| 21_G | 54_F | 1.382 | 0.82 |
| 46_T | 148_I | 1.381 | 0.82 |
| 182_W | 216_K | 1.352 | 0.80 |
| 189_W | 211_L | 1.348 | 0.80 |
| 45_I | 92_L | 1.335 | 0.79 |
| 89_T | 216_K | 1.334 | 0.79 |
| 23_G | 221_L | 1.334 | 0.79 |
| 23_G | 217_V | 1.320 | 0.78 |
| 194_E | 204_E | 1.311 | 0.77 |
| 21_G | 51_A | 1.296 | 0.76 |
| 49_V | 56_M | 1.279 | 0.75 |
| 121_T | 141_S | 1.278 | 0.75 |
| 16_G | 116_G | 1.276 | 0.75 |
| 46_T | 220_G | 1.274 | 0.75 |
| 199_V | 206_L | 1.273 | 0.74 |
| 50_P | 220_G | 1.272 | 0.74 |
| 16_G | 20_M | 1.270 | 0.74 |
| 127_L | 194_E | 1.251 | 0.73 |
| 16_G | 217_V | 1.250 | 0.73 |
| 45_I | 85_D | 1.248 | 0.72 |
| 102_D | 135_F | 1.245 | 0.72 |
| 95_L | 112_V | 1.245 | 0.72 |
| 25_L | 103_A | 1.241 | 0.72 |
| 16_G | 54_F | 1.221 | 0.70 |
| 6_G | 9_E | 1.209 | 0.69 |
| 85_D | 92_L | 1.209 | 0.69 |
| 87_L | 116_G | 1.194 | 0.68 |
| 14_A | 17_T | 1.177 | 0.66 |
| 90_T | 216_K | 1.174 | 0.66 |
| 222_I | 225_R | 1.173 | 0.66 |
| 189_W | 204_E | 1.172 | 0.65 |
| 164_R | 168_A | 1.171 | 0.65 |
| 216_K | 219_F | 1.168 | 0.65 |
| 17_T | 58_L | 1.167 | 0.65 |
| 139_A | 202_N | 1.165 | 0.65 |
| 123_L | 127_L | 1.161 | 0.64 |
| 53_A | 92_L | 1.158 | 0.64 |
| 53_A | 216_K | 1.158 | 0.64 |
| 56_M | 126_A | 1.157 | 0.64 |
| 122_G | 216_K | 1.153 | 0.64 |
| 146_L | 225_R | 1.151 | 0.63 |
| 152_L | 179_V | 1.151 | 0.63 |
| 119_I | 216_K | 1.148 | 0.63 |
| 90_T | 122_G | 1.146 | 0.63 |
| 191_I | 207_L | 1.143 | 0.63 |
| 57_Y | 92_L | 1.126 | 0.61 |
| 20_M | 122_G | 1.125 | 0.61 |
| 216_K | 220_G | 1.113 | 0.60 |
| 117_I | 138_W | 1.112 | 0.59 |
| 169_S | 173_V | 1.111 | 0.59 |
| 153_F | 179_V | 1.104 | 0.59 |
| 22_L | 213_V | 1.097 | 0.58 |
| 64_Y | 133_Y | 1.088 | 0.57 |
| 27_F | 46_T | 1.087 | 0.57 |
| 19_L | 217_V | 1.087 | 0.57 |
| 115_D | 119_I | 1.084 | 0.57 |
| 53_A | 89_T | 1.083 | 0.56 |
| 53_A | 118_M | 1.082 | 0.56 |
| 25_L | 51_A | 1.081 | 0.56 |
| 82_R | 118_M | 1.079 | 0.56 |
| 62_L | 77_P | 1.074 | 0.55 |
| 58_L | 136_V | 1.069 | 0.55 |
| 53_A | 152_L | 1.067 | 0.55 |
| 16_G | 213_V | 1.062 | 0.54 |
| 52_I | 164_R | 1.061 | 0.54 |
| 25_L | 28_L | 1.061 | 0.54 |
| 146_L | 176_N | 1.059 | 0.54 |
| 52_I | 111_L | 1.056 | 0.54 |
| 122_G | 186_P | 1.053 | 0.53 |
| 49_V | 174_L | 1.048 | 0.53 |
| 121_T | 215_A | 1.042 | 0.52 |
| 86_W | 185_Y | 1.035 | 0.51 |
| 13_L | 205_T | 1.032 | 0.51 |
| 124_V | 187_V | 1.029 | 0.51 |
| 196_A | 203_I | 1.028 | 0.51 |
| 53_A | 60_M | 1.026 | 0.50 |
| 46_T | 96_D | 1.024 | 0.50 |
| 86_W | 122_G | 1.017 | 0.49 |
| 77_P | 201_L | 1.017 | 0.49 |
| 89_T | 122_G | 1.016 | 0.49 |
| 78_I | 126_A | 1.014 | 0.49 |
| 82_R | 122_G | 1.010 | 0.49 |
| 90_T | 211_L | 1.008 | 0.48 |
| 83_Y | 86_W | 1.007 | 0.48 |
| 21_G | 221_L | 1.006 | 0.48 |
| 61_L | 211_L | 1.001 | 0.48 |
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 | |
| 1m0kA | 1 | 0.9569 | 100 | 0.127 | Contact Map |
| 3wqjA | 1 | 0.9871 | 100 | 0.134 | Contact Map |
| 4l35A | 1 | 0.9914 | 100 | 0.142 | Contact Map |
| 4fbzA | 1 | 0.9957 | 100 | 0.15 | Contact Map |
| 3qapA | 1 | 0.944 | 100 | 0.172 | Contact Map |
| 3am6A | 4 | 0.9612 | 100 | 0.177 | Contact Map |
| 1xioA | 1 | 0.9181 | 100 | 0.179 | Contact Map |
| 3qbgA | 3 | 0.9828 | 100 | 0.192 | Contact Map |
| 2jafA | 1 | 0.9784 | 100 | 0.203 | Contact Map |
| 3ddlA | 2 | 0.9871 | 100 | 0.233 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)