| T0800 |
| ID: | 1401732168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 247 (242) | ||
| Sequences: | 509 (490.3) | ||
| Seq/Len: | 2.103 | ||
| Nf(neff/√len): | 31.5 |
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: 2.103).
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 |
| 159_V | 182_V | 5.925 | 1.00 |
| 138_T | 159_V | 5.545 | 1.00 |
| 138_T | 182_V | 4.954 | 1.00 |
| 137_G | 158_G | 4.489 | 1.00 |
| 182_V | 203_V | 4.196 | 1.00 |
| 182_V | 239_V | 4.058 | 1.00 |
| 158_G | 181_G | 3.753 | 1.00 |
| 159_V | 239_V | 3.455 | 1.00 |
| 140_E | 184_E | 3.301 | 1.00 |
| 159_V | 203_V | 3.266 | 1.00 |
| 181_G | 238_G | 3.046 | 1.00 |
| 140_E | 161_K | 3.042 | 1.00 |
| 158_G | 238_G | 3.027 | 1.00 |
| 120_W | 125_N | 3.023 | 1.00 |
| 137_G | 181_G | 3.006 | 1.00 |
| 60_V | 138_T | 2.980 | 1.00 |
| 203_V | 239_V | 2.862 | 1.00 |
| 161_K | 184_E | 2.840 | 1.00 |
| 184_E | 241_A | 2.718 | 1.00 |
| 97_G | 101_I | 2.714 | 1.00 |
| 60_V | 159_V | 2.688 | 1.00 |
| 161_K | 241_A | 2.572 | 1.00 |
| 138_T | 203_V | 2.399 | 1.00 |
| 94_D | 97_G | 2.291 | 1.00 |
| 60_V | 182_V | 2.287 | 1.00 |
| 138_T | 239_V | 2.245 | 1.00 |
| 137_G | 238_G | 2.094 | 0.99 |
| 181_G | 202_G | 2.047 | 0.99 |
| 160_G | 183_G | 2.029 | 0.99 |
| 201_K | 237_A | 1.954 | 0.99 |
| 180_G | 237_A | 1.950 | 0.99 |
| 202_G | 238_G | 1.929 | 0.99 |
| 184_E | 205_A | 1.866 | 0.98 |
| 140_E | 205_A | 1.755 | 0.97 |
| 157_M | 180_G | 1.736 | 0.97 |
| 180_G | 201_K | 1.730 | 0.97 |
| 183_G | 204_G | 1.685 | 0.96 |
| 70_E | 74_K | 1.629 | 0.95 |
| 59_G | 158_G | 1.600 | 0.95 |
| 161_K | 205_A | 1.598 | 0.95 |
| 60_V | 239_V | 1.588 | 0.94 |
| 158_G | 202_G | 1.540 | 0.93 |
| 59_G | 137_G | 1.481 | 0.91 |
| 204_G | 240_G | 1.447 | 0.90 |
| 60_V | 203_V | 1.415 | 0.88 |
| 68_N | 123_N | 1.401 | 0.88 |
| 139_G | 160_G | 1.368 | 0.86 |
| 205_A | 241_A | 1.356 | 0.85 |
| 162_V | 185_A | 1.310 | 0.83 |
| 140_E | 241_A | 1.291 | 0.81 |
| 137_G | 202_G | 1.252 | 0.78 |
| 153_L | 176_V | 1.248 | 0.78 |
| 94_D | 101_I | 1.199 | 0.74 |
| 59_G | 181_G | 1.193 | 0.74 |
| 7_F | 13_V | 1.184 | 0.73 |
| 13_V | 20_A | 1.161 | 0.71 |
| 138_T | 181_G | 1.155 | 0.70 |
| 117_R | 120_W | 1.151 | 0.70 |
| 18_A | 23_N | 1.147 | 0.69 |
| 115_N | 120_W | 1.142 | 0.69 |
| 160_G | 204_G | 1.133 | 0.68 |
| 118_N | 125_N | 1.124 | 0.67 |
| 58_F | 61_G | 1.118 | 0.67 |
| 136_L | 157_M | 1.115 | 0.66 |
| 201_K | 204_G | 1.107 | 0.65 |
| 156_G | 236_E | 1.099 | 0.65 |
| 62_K | 161_K | 1.086 | 0.63 |
| 157_M | 201_K | 1.077 | 0.62 |
| 180_G | 185_A | 1.067 | 0.61 |
| 179_E | 200_E | 1.059 | 0.60 |
| 179_E | 236_E | 1.056 | 0.60 |
| 61_G | 153_L | 1.054 | 0.60 |
| 136_L | 141_F | 1.041 | 0.58 |
| 94_D | 99_L | 1.036 | 0.58 |
| 120_W | 129_P | 1.034 | 0.58 |
| 157_M | 237_A | 1.001 | 0.54 |
| 206_V | 240_G | 1.000 | 0.54 |
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 | |
| 3lycA | 16 | 0.8016 | 99.1 | 0.676 | Contact Map |
| 3jx8A | 6 | 0.8138 | 99 | 0.698 | Contact Map |
| 4opwA | 2 | 0.7935 | 98.8 | 0.714 | Contact Map |
| 3petA | 2 | 0.7814 | 98.8 | 0.715 | Contact Map |
| 3glaA | 2 | 0.3644 | 12.5 | 0.931 | Contact Map |
| 4jg9A | 2 | 0.4858 | 12.1 | 0.932 | Contact Map |
| 2xcmC | 2 | 0.3644 | 7.9 | 0.937 | Contact Map |
| 1qleD | 1 | 0.0931 | 6.6 | 0.939 | Contact Map |
| 1m56D | 2 | 0.0931 | 6 | 0.94 | Contact Map |
| 4m5sA | 1 | 0.3239 | 5.9 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)