| T0831 109-352 Tp831 -force run |
| ID: | 1407214705 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 244 (244) | ||
| Sequences: | 116 (90.8) | ||
| Seq/Len: | 0.475 | ||
| Nf(neff/√len): | 5.8 |
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: 0.475).
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 |
| 136_F | 242_V | 2.110 | 0.89 |
| 125_R | 136_F | 1.875 | 0.79 |
| 125_R | 131_L | 1.838 | 0.77 |
| 125_R | 238_L | 1.825 | 0.76 |
| 125_R | 242_V | 1.824 | 0.76 |
| 231_L | 242_V | 1.770 | 0.73 |
| 136_F | 231_L | 1.746 | 0.72 |
| 125_R | 231_L | 1.663 | 0.66 |
| 183_G | 229_K | 1.662 | 0.66 |
| 131_L | 242_V | 1.578 | 0.61 |
| 191_E | 228_Y | 1.526 | 0.57 |
| 55_V | 114_N | 1.521 | 0.56 |
| 52_V | 212_D | 1.512 | 0.56 |
| 79_C | 86_L | 1.494 | 0.54 |
| 185_W | 228_Y | 1.492 | 0.54 |
| 119_A | 126_P | 1.484 | 0.54 |
| 147_E | 185_W | 1.465 | 0.52 |
| 226_K | 232_H | 1.458 | 0.52 |
| 125_R | 185_W | 1.442 | 0.50 |
| 123_H | 242_V | 1.429 | 0.49 |
| 229_K | 235_W | 1.429 | 0.49 |
| 35_W | 227_E | 1.402 | 0.47 |
| 124_L | 242_V | 1.399 | 0.47 |
| 191_E | 225_K | 1.398 | 0.47 |
| 124_L | 229_K | 1.363 | 0.44 |
| 97_Q | 131_L | 1.361 | 0.44 |
| 93_L | 188_S | 1.361 | 0.44 |
| 193_S | 221_F | 1.349 | 0.43 |
| 98_K | 117_E | 1.348 | 0.43 |
| 104_V | 237_A | 1.323 | 0.41 |
| 85_L | 228_Y | 1.309 | 0.40 |
| 111_P | 131_L | 1.302 | 0.40 |
| 161_I | 167_E | 1.300 | 0.40 |
| 7_V | 16_P | 1.289 | 0.39 |
| 161_I | 168_D | 1.282 | 0.38 |
| 55_V | 112_S | 1.264 | 0.37 |
| 238_L | 242_V | 1.256 | 0.37 |
| 119_A | 124_L | 1.254 | 0.36 |
| 124_L | 183_G | 1.246 | 0.36 |
| 58_E | 193_S | 1.240 | 0.35 |
| 162_F | 167_E | 1.240 | 0.35 |
| 6_E | 233_E | 1.239 | 0.35 |
| 213_E | 235_W | 1.227 | 0.34 |
| 225_K | 243_S | 1.214 | 0.34 |
| 91_E | 199_S | 1.213 | 0.34 |
| 42_A | 145_E | 1.207 | 0.33 |
| 34_W | 191_E | 1.205 | 0.33 |
| 222_E | 225_K | 1.204 | 0.33 |
| 126_P | 214_G | 1.203 | 0.33 |
| 214_G | 225_K | 1.202 | 0.33 |
| 235_W | 238_L | 1.198 | 0.33 |
| 120_T | 125_R | 1.196 | 0.32 |
| 87_T | 202_K | 1.193 | 0.32 |
| 115_V | 221_F | 1.188 | 0.32 |
| 170_E | 177_A | 1.186 | 0.32 |
| 78_D | 84_F | 1.184 | 0.32 |
| 12_Q | 19_Q | 1.181 | 0.31 |
| 135_V | 197_I | 1.174 | 0.31 |
| 166_I | 170_E | 1.168 | 0.31 |
| 7_V | 14_L | 1.161 | 0.30 |
| 168_D | 171_G | 1.160 | 0.30 |
| 55_V | 105_K | 1.159 | 0.30 |
| 123_H | 136_F | 1.159 | 0.30 |
| 55_V | 196_A | 1.159 | 0.30 |
| 119_A | 147_E | 1.151 | 0.29 |
| 38_V | 55_V | 1.150 | 0.29 |
| 59_I | 230_L | 1.135 | 0.28 |
| 162_F | 171_G | 1.124 | 0.28 |
| 82_L | 131_L | 1.123 | 0.28 |
| 170_E | 173_V | 1.121 | 0.28 |
| 86_L | 156_K | 1.117 | 0.27 |
| 173_V | 177_A | 1.116 | 0.27 |
| 185_W | 191_E | 1.115 | 0.27 |
| 53_Q | 196_A | 1.113 | 0.27 |
| 40_H | 48_D | 1.112 | 0.27 |
| 125_R | 183_G | 1.111 | 0.27 |
| 147_E | 151_F | 1.111 | 0.27 |
| 191_E | 214_G | 1.107 | 0.27 |
| 41_R | 84_F | 1.100 | 0.26 |
| 7_V | 55_V | 1.099 | 0.26 |
| 19_Q | 26_R | 1.097 | 0.26 |
| 26_R | 39_I | 1.092 | 0.26 |
| 170_E | 175_D | 1.089 | 0.26 |
| 55_V | 239_R | 1.085 | 0.25 |
| 66_Q | 69_K | 1.085 | 0.25 |
| 62_N | 100_V | 1.076 | 0.25 |
| 121_V | 242_V | 1.075 | 0.25 |
| 32_S | 119_A | 1.072 | 0.25 |
| 129_L | 194_M | 1.067 | 0.24 |
| 158_Q | 193_S | 1.064 | 0.24 |
| 61_S | 225_K | 1.059 | 0.24 |
| 167_E | 173_V | 1.059 | 0.24 |
| 153_N | 181_T | 1.058 | 0.24 |
| 54_R | 84_F | 1.056 | 0.24 |
| 119_A | 123_H | 1.055 | 0.24 |
| 32_S | 227_E | 1.048 | 0.23 |
| 38_V | 128_R | 1.046 | 0.23 |
| 172_L | 176_R | 1.045 | 0.23 |
| 107_L | 239_R | 1.044 | 0.23 |
| 2_K | 5_T | 1.043 | 0.23 |
| 60_T | 90_M | 1.043 | 0.23 |
| 140_D | 143_F | 1.042 | 0.23 |
| 13_A | 20_T | 1.041 | 0.23 |
| 11_Q | 92_E | 1.038 | 0.23 |
| 39_I | 215_S | 1.036 | 0.23 |
| 116_I | 119_A | 1.036 | 0.23 |
| 42_A | 73_S | 1.031 | 0.22 |
| 119_A | 185_W | 1.031 | 0.22 |
| 125_R | 226_K | 1.031 | 0.22 |
| 10_A | 115_V | 1.027 | 0.22 |
| 86_L | 119_A | 1.026 | 0.22 |
| 167_E | 177_A | 1.024 | 0.22 |
| 85_L | 192_R | 1.022 | 0.22 |
| 195_K | 215_S | 1.021 | 0.22 |
| 52_V | 85_L | 1.019 | 0.22 |
| 24_L | 81_G | 1.016 | 0.22 |
| 39_I | 72_M | 1.013 | 0.22 |
| 105_K | 144_T | 1.011 | 0.21 |
| 50_E | 214_G | 1.011 | 0.21 |
| 139_A | 240_N | 1.010 | 0.21 |
| 143_F | 149_K | 1.006 | 0.21 |
| 81_G | 200_F | 1.005 | 0.21 |
| 15_Y | 146_Y | 1.005 | 0.21 |
| 46_T | 53_Q | 1.003 | 0.21 |
| 113_R | 201_A | 1.003 | 0.21 |
| 86_L | 193_S | 1.000 | 0.21 |
| 120_T | 214_G | 1.000 | 0.21 |
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 | |
| 4lvhA | 4 | 0.0574 | 19.4 | 0.952 | Contact Map |
| 2yp5A | 1 | 0.5615 | 16.3 | 0.953 | Contact Map |
| 2wr1A | 3 | 0.5656 | 16.3 | 0.953 | Contact Map |
| 3ghgC | 4 | 0.5164 | 11.3 | 0.957 | Contact Map |
| 1m1jC | 2 | 0.5082 | 10.9 | 0.957 | Contact Map |
| 2w83C | 2 | 0.2746 | 7.6 | 0.96 | Contact Map |
| 4f23A | 3 | 0.6148 | 7.3 | 0.96 | Contact Map |
| 4mc5A | 3 | 0.5779 | 6.5 | 0.961 | Contact Map |
| 3ghgA | 4 | 0.4303 | 6.2 | 0.962 | Contact Map |
| 2v0oA | 3 | 0.4549 | 5.1 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)