| 47_Rpt_Regions |
| ID: | 1476387777 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (138) | ||
| Sequences: | 511 (316) | ||
| Seq/Len: | 3.703 | ||
| Nf(neff/√len): | 26.9 |
HHblits Results: (2016_02)
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: 3.703).
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 |
| 26_W | 38_F | 2.467 | 1.00 |
| 20_L | 42_L | 2.188 | 1.00 |
| 36_E | 62_R | 2.103 | 1.00 |
| 85_K | 98_Q | 1.806 | 0.99 |
| 95_L | 117_L | 1.737 | 0.99 |
| 115_L | 128_V | 1.697 | 0.99 |
| 133_Y | 137_G | 1.664 | 0.99 |
| 23_A | 130_T | 1.643 | 0.99 |
| 35_P | 39_S | 1.635 | 0.99 |
| 58_A | 62_R | 1.625 | 0.98 |
| 87_N | 94_S | 1.616 | 0.98 |
| 50_P | 74_L | 1.589 | 0.98 |
| 7_V | 65_I | 1.565 | 0.98 |
| 47_D | 120_E | 1.516 | 0.97 |
| 4_E | 78_S | 1.501 | 0.97 |
| 36_E | 58_A | 1.404 | 0.95 |
| 39_S | 48_L | 1.401 | 0.95 |
| 12_D | 15_I | 1.390 | 0.95 |
| 88_I | 99_F | 1.315 | 0.93 |
| 9_I | 65_I | 1.303 | 0.92 |
| 113_F | 135_I | 1.302 | 0.92 |
| 12_D | 69_P | 1.293 | 0.92 |
| 19_K | 24_F | 1.281 | 0.91 |
| 2_Q | 25_T | 1.277 | 0.91 |
| 118_C | 125_G | 1.270 | 0.91 |
| 23_A | 129_T | 1.262 | 0.91 |
| 105_E | 108_N | 1.228 | 0.89 |
| 103_M | 134_S | 1.228 | 0.89 |
| 103_M | 139_L | 1.227 | 0.89 |
| 25_T | 132_A | 1.209 | 0.88 |
| 35_P | 61_I | 1.207 | 0.88 |
| 102_D | 105_E | 1.201 | 0.88 |
| 12_D | 81_R | 1.189 | 0.87 |
| 61_I | 120_E | 1.187 | 0.87 |
| 111_E | 136_R | 1.187 | 0.87 |
| 57_I | 71_D | 1.183 | 0.86 |
| 11_L | 60_A | 1.170 | 0.86 |
| 65_I | 68_Y | 1.170 | 0.86 |
| 56_A | 63_Q | 1.168 | 0.86 |
| 12_D | 21_R | 1.167 | 0.85 |
| 4_E | 27_N | 1.165 | 0.85 |
| 122_G | 126_E | 1.158 | 0.85 |
| 56_A | 120_E | 1.157 | 0.85 |
| 67_S | 133_Y | 1.135 | 0.83 |
| 127_F | 130_T | 1.131 | 0.83 |
| 56_A | 59_S | 1.123 | 0.82 |
| 106_K | 132_A | 1.120 | 0.82 |
| 90_V | 95_L | 1.118 | 0.82 |
| 17_G | 117_L | 1.116 | 0.82 |
| 81_R | 133_Y | 1.109 | 0.81 |
| 135_I | 138_Q | 1.105 | 0.81 |
| 39_S | 43_C | 1.094 | 0.80 |
| 83_I | 124_G | 1.083 | 0.79 |
| 48_L | 92_N | 1.079 | 0.79 |
| 7_V | 107_E | 1.070 | 0.78 |
| 84_I | 99_F | 1.066 | 0.78 |
| 103_M | 108_N | 1.058 | 0.77 |
| 4_E | 120_E | 1.049 | 0.76 |
| 132_A | 136_R | 1.049 | 0.76 |
| 39_S | 49_N | 1.046 | 0.76 |
| 129_T | 136_R | 1.045 | 0.76 |
| 7_V | 16_D | 1.044 | 0.75 |
| 97_D | 101_W | 1.043 | 0.75 |
| 39_S | 134_S | 1.035 | 0.75 |
| 88_I | 129_T | 1.033 | 0.74 |
| 79_D | 104_S | 1.033 | 0.74 |
| 14_E | 59_S | 1.030 | 0.74 |
| 31_K | 47_D | 1.029 | 0.74 |
| 17_G | 78_S | 1.028 | 0.74 |
| 10_R | 100_E | 1.023 | 0.73 |
| 99_F | 113_F | 1.022 | 0.73 |
| 37_M | 44_D | 1.012 | 0.72 |
| 29_N | 41_I | 1.011 | 0.72 |
| 56_A | 87_N | 1.010 | 0.72 |
| 15_I | 20_L | 1.007 | 0.72 |
| 39_S | 58_A | 1.001 | 0.71 |
| 21_R | 125_G | 1.001 | 0.71 |
| 10_R | 16_D | 1.000 | 0.71 |
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 | |
| 2lruA | 1 | 0.5714 | 66.4 | 0.921 | Contact Map |
| 2v3sA | 2 | 0.4 | 24.1 | 0.94 | Contact Map |
| 2k89A | 1 | 0.4643 | 21.2 | 0.941 | Contact Map |
| 1fc3A | 3 | 0.6929 | 14.8 | 0.945 | Contact Map |
| 2hqsA | 4 | 0.3929 | 11.5 | 0.948 | Contact Map |
| 4bjtA | 3 | 0.55 | 8.9 | 0.95 | Contact Map |
| 2dplA | 2 | 0.6357 | 8.6 | 0.951 | Contact Map |
| 4bm5A | 1 | 0.8643 | 6.9 | 0.953 | Contact Map |
| 2fi9A | 1 | 0.5357 | 6.6 | 0.953 | Contact Map |
| 2d6fC | 2 | 0.7643 | 6.2 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)