| T20 |
| ID: | 1447599582 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (161) | ||
| Sequences: | 227 (165.9) | ||
| Seq/Len: | 1.410 | ||
| Nf(neff/√len): | 13.1 |
HHblits Results: (2015_06)
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: 1.410).
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 |
| 29_Y | 33_N | 2.728 | 1.00 |
| 30_K | 34_D | 2.582 | 1.00 |
| 37_F | 41_L | 2.304 | 0.99 |
| 43_R | 50_R | 2.124 | 0.99 |
| 18_T | 21_L | 1.697 | 0.93 |
| 30_K | 83_S | 1.645 | 0.91 |
| 70_M | 91_L | 1.628 | 0.90 |
| 91_L | 95_Q | 1.604 | 0.90 |
| 10_T | 14_A | 1.531 | 0.86 |
| 107_A | 139_I | 1.513 | 0.86 |
| 16_V | 35_P | 1.477 | 0.84 |
| 67_I | 146_M | 1.449 | 0.82 |
| 35_P | 49_A | 1.438 | 0.81 |
| 128_I | 144_A | 1.410 | 0.80 |
| 86_K | 93_Q | 1.372 | 0.77 |
| 132_D | 145_E | 1.372 | 0.77 |
| 22_A | 25_V | 1.367 | 0.77 |
| 115_Y | 143_L | 1.348 | 0.75 |
| 34_D | 104_P | 1.348 | 0.75 |
| 118_L | 131_Y | 1.338 | 0.74 |
| 38_R | 111_S | 1.330 | 0.74 |
| 74_A | 128_I | 1.321 | 0.73 |
| 91_L | 113_A | 1.320 | 0.73 |
| 114_F | 121_Y | 1.309 | 0.72 |
| 112_L | 142_I | 1.273 | 0.69 |
| 39_R | 155_I | 1.270 | 0.69 |
| 53_K | 57_E | 1.264 | 0.68 |
| 94_V | 134_T | 1.261 | 0.68 |
| 89_Y | 93_Q | 1.253 | 0.67 |
| 25_V | 94_V | 1.237 | 0.66 |
| 89_Y | 104_P | 1.207 | 0.63 |
| 39_R | 52_E | 1.205 | 0.63 |
| 132_D | 140_L | 1.195 | 0.62 |
| 52_E | 72_D | 1.192 | 0.62 |
| 48_Q | 146_M | 1.180 | 0.60 |
| 14_A | 93_Q | 1.160 | 0.59 |
| 37_F | 111_S | 1.150 | 0.58 |
| 137_K | 141_D | 1.138 | 0.56 |
| 36_E | 57_E | 1.133 | 0.56 |
| 91_L | 134_T | 1.133 | 0.56 |
| 16_V | 102_Q | 1.130 | 0.56 |
| 111_S | 146_M | 1.125 | 0.55 |
| 19_G | 22_A | 1.122 | 0.55 |
| 15_A | 56_A | 1.112 | 0.54 |
| 118_L | 121_Y | 1.099 | 0.52 |
| 96_A | 123_T | 1.092 | 0.52 |
| 128_I | 150_D | 1.090 | 0.51 |
| 147_I | 155_I | 1.085 | 0.51 |
| 47_R | 153_L | 1.085 | 0.51 |
| 24_A | 113_A | 1.084 | 0.51 |
| 9_T | 62_A | 1.082 | 0.51 |
| 74_A | 77_E | 1.080 | 0.50 |
| 12_A | 53_K | 1.079 | 0.50 |
| 48_Q | 149_Y | 1.077 | 0.50 |
| 33_N | 72_D | 1.075 | 0.50 |
| 93_Q | 120_V | 1.074 | 0.50 |
| 61_Q | 65_Q | 1.066 | 0.49 |
| 51_Q | 58_L | 1.065 | 0.49 |
| 95_Q | 113_A | 1.065 | 0.49 |
| 156_G | 160_T | 1.062 | 0.49 |
| 30_K | 33_N | 1.059 | 0.48 |
| 161_G | 164_D | 1.056 | 0.48 |
| 131_Y | 135_V | 1.056 | 0.48 |
| 141_D | 147_I | 1.055 | 0.48 |
| 127_L | 131_Y | 1.055 | 0.48 |
| 37_F | 130_I | 1.051 | 0.48 |
| 35_P | 73_E | 1.051 | 0.48 |
| 140_L | 144_A | 1.045 | 0.47 |
| 37_F | 115_Y | 1.044 | 0.47 |
| 74_A | 78_G | 1.041 | 0.47 |
| 129_S | 140_L | 1.040 | 0.46 |
| 121_Y | 131_Y | 1.039 | 0.46 |
| 17_A | 141_D | 1.039 | 0.46 |
| 13_V | 52_E | 1.028 | 0.45 |
| 132_D | 143_L | 1.020 | 0.44 |
| 78_G | 144_A | 1.015 | 0.44 |
| 57_E | 61_Q | 1.014 | 0.44 |
| 11_A | 138_P | 1.013 | 0.44 |
| 159_Y | 162_G | 1.005 | 0.43 |
| 137_K | 145_E | 1.003 | 0.43 |
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 | |
| 1om2A | 1 | 0.5249 | 99.9 | 0.606 | Contact Map |
| 3ax2A | 4 | 0.3867 | 99.9 | 0.62 | Contact Map |
| 5a2fA | 1 | 0 | 25.9 | 0.952 | Contact Map |
| 4grdA | 4 | 0.3204 | 18.7 | 0.955 | Contact Map |
| 2kc7A | 1 | 0.4641 | 18.2 | 0.955 | Contact Map |
| 3trhA | 16 | 0.3481 | 17.5 | 0.956 | Contact Map |
| 4pypA | 1 | 0.1602 | 16.4 | 0.956 | Contact Map |
| 4djkA | 2 | 0.2265 | 16 | 0.957 | Contact Map |
| 3rg8A | 8 | 0.3094 | 15.1 | 0.957 | Contact Map |
| 2k1kA | 2 | 0.1823 | 14.5 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)