| TssF_454-585 |
| ID: | 1516103804 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (139) | ||
| Sequences: | 993 (645.4) | ||
| Seq/Len: | 7.144 | ||
| Nf(neff/√len): | 54.7 |
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: 7.144).
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 |
| 22_H | 44_Y | 4.148 | 1.00 |
| 104_N | 135_N | 3.785 | 1.00 |
| 58_A | 89_G | 3.350 | 1.00 |
| 80_D | 120_T | 3.082 | 1.00 |
| 65_H | 80_D | 2.760 | 1.00 |
| 100_G | 121_L | 2.754 | 1.00 |
| 58_A | 90_F | 2.523 | 1.00 |
| 87_G | 123_V | 2.200 | 1.00 |
| 78_G | 116_F | 2.194 | 1.00 |
| 103_L | 107_L | 2.191 | 1.00 |
| 81_V | 107_L | 2.170 | 1.00 |
| 82_E | 122_I | 2.080 | 1.00 |
| 106_F | 110_Y | 1.894 | 1.00 |
| 83_V | 103_L | 1.880 | 1.00 |
| 81_V | 117_N | 1.862 | 1.00 |
| 128_K | 131_R | 1.642 | 1.00 |
| 80_D | 118_Q | 1.634 | 1.00 |
| 59_I | 83_V | 1.572 | 1.00 |
| 120_T | 131_R | 1.556 | 1.00 |
| 36_V | 62_V | 1.518 | 0.99 |
| 69_R | 118_Q | 1.512 | 0.99 |
| 59_I | 85_L | 1.503 | 0.99 |
| 18_R | 39_G | 1.470 | 0.99 |
| 55_R | 95_D | 1.381 | 0.99 |
| 57_D | 125_P | 1.372 | 0.99 |
| 62_V | 83_V | 1.363 | 0.98 |
| 87_G | 125_P | 1.340 | 0.98 |
| 63_Q | 82_E | 1.308 | 0.98 |
| 26_G | 114_N | 1.299 | 0.98 |
| 63_Q | 84_T | 1.254 | 0.97 |
| 60_L | 86_D | 1.253 | 0.97 |
| 22_H | 43_L | 1.245 | 0.97 |
| 120_T | 128_K | 1.238 | 0.97 |
| 77_R | 137_N | 1.234 | 0.97 |
| 41_L | 56_L | 1.222 | 0.96 |
| 97_H | 130_I | 1.192 | 0.96 |
| 85_L | 99_F | 1.181 | 0.95 |
| 26_G | 30_M | 1.170 | 0.95 |
| 83_V | 119_L | 1.169 | 0.95 |
| 98_L | 113_M | 1.158 | 0.95 |
| 101_E | 132_W | 1.149 | 0.94 |
| 47_R | 52_N | 1.146 | 0.94 |
| 60_L | 84_T | 1.127 | 0.94 |
| 23_L | 27_F | 1.123 | 0.94 |
| 79_L | 119_L | 1.099 | 0.93 |
| 70_F | 89_G | 1.098 | 0.93 |
| 45_N | 53_H | 1.097 | 0.92 |
| 43_L | 56_L | 1.093 | 0.92 |
| 92_G | 95_D | 1.092 | 0.92 |
| 80_D | 131_R | 1.091 | 0.92 |
| 105_R | 139_R | 1.055 | 0.90 |
| 88_N | 108_A | 1.033 | 0.89 |
| 85_L | 121_L | 1.032 | 0.89 |
| 62_V | 81_V | 1.028 | 0.89 |
| 118_Q | 134_E | 1.021 | 0.88 |
| 34_A | 72_K | 1.017 | 0.88 |
| 25_T | 39_G | 1.013 | 0.88 |
| 37_L | 103_L | 1.011 | 0.88 |
| 104_N | 117_N | 1.008 | 0.88 |
| 59_I | 79_L | 1.007 | 0.88 |
| 45_N | 52_N | 1.002 | 0.87 |
| 96_I | 121_L | 1.001 | 0.87 |
| 26_G | 29_N | 1.001 | 0.87 |
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 | |
| 1qvrA | 3 | 0.662 | 3 | 0.946 | Contact Map |
| 2d96A | 1 | 0.6127 | 2.8 | 0.947 | Contact Map |
| 2ee7A | 1 | 0.6056 | 2.6 | 0.947 | Contact Map |
| 2xgaA | 2 | 0.669 | 2.5 | 0.948 | Contact Map |
| 2izvA | 1 | 0.338 | 2.2 | 0.95 | Contact Map |
| 1ry9A | 4 | 0.669 | 2.1 | 0.95 | Contact Map |
| 4icsA | 2 | 0.838 | 2 | 0.951 | Contact Map |
| 1z21A | 1 | 0.493 | 1.8 | 0.952 | Contact Map |
| 3g5bA | 1 | 0.507 | 1.8 | 0.952 | Contact Map |
| 3u85B | 1 | 0.0634 | 1.6 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)