| TRAM1 120-260 |
| ID: | 1405502011 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (141) | ||
| Sequences: | 627 (416.3) | ||
| Seq/Len: | 4.447 | ||
| Nf(neff/√len): | 35.1 |
HHblits Results: (2013_03)
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: 4.447).
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 |
| 50_Y | 91_A | 2.799 | 1.00 |
| 118_R | 122_F | 2.540 | 1.00 |
| 50_Y | 100_G | 2.510 | 1.00 |
| 17_G | 49_F | 2.417 | 1.00 |
| 32_I | 35_R | 1.849 | 1.00 |
| 10_Y | 57_W | 1.595 | 0.99 |
| 54_L | 88_I | 1.572 | 0.99 |
| 11_L | 112_F | 1.561 | 0.99 |
| 108_Y | 111_E | 1.551 | 0.99 |
| 80_Y | 87_H | 1.548 | 0.99 |
| 81_I | 87_H | 1.522 | 0.98 |
| 10_Y | 56_Y | 1.507 | 0.98 |
| 3_S | 6_L | 1.459 | 0.98 |
| 131_F | 134_W | 1.458 | 0.98 |
| 6_L | 115_H | 1.417 | 0.97 |
| 104_L | 121_Y | 1.411 | 0.97 |
| 107_H | 115_H | 1.383 | 0.96 |
| 111_E | 114_F | 1.381 | 0.96 |
| 54_L | 85_L | 1.381 | 0.96 |
| 125_E | 128_Q | 1.379 | 0.96 |
| 33_L | 102_V | 1.379 | 0.96 |
| 3_S | 115_H | 1.350 | 0.96 |
| 121_Y | 138_F | 1.345 | 0.96 |
| 17_G | 105_V | 1.342 | 0.95 |
| 81_I | 108_Y | 1.338 | 0.95 |
| 120_F | 128_Q | 1.285 | 0.94 |
| 37_Y | 95_N | 1.272 | 0.93 |
| 107_H | 111_E | 1.254 | 0.93 |
| 30_P | 33_L | 1.249 | 0.93 |
| 28_S | 33_L | 1.242 | 0.92 |
| 67_Q | 70_K | 1.236 | 0.92 |
| 83_L | 90_G | 1.231 | 0.92 |
| 118_R | 134_W | 1.229 | 0.92 |
| 81_I | 84_Y | 1.223 | 0.92 |
| 103_L | 111_E | 1.220 | 0.91 |
| 28_S | 57_W | 1.216 | 0.91 |
| 80_Y | 84_Y | 1.207 | 0.91 |
| 3_S | 9_F | 1.184 | 0.90 |
| 80_Y | 111_E | 1.178 | 0.89 |
| 4_G | 55_A | 1.172 | 0.89 |
| 84_Y | 108_Y | 1.166 | 0.89 |
| 9_F | 104_L | 1.156 | 0.88 |
| 21_L | 27_I | 1.144 | 0.88 |
| 68_K | 102_V | 1.143 | 0.88 |
| 34_W | 99_L | 1.142 | 0.87 |
| 25_N | 32_I | 1.141 | 0.87 |
| 116_I | 133_L | 1.139 | 0.87 |
| 6_L | 10_Y | 1.137 | 0.87 |
| 4_G | 8_A | 1.133 | 0.87 |
| 91_A | 100_G | 1.120 | 0.86 |
| 11_L | 16_W | 1.114 | 0.86 |
| 19_F | 42_M | 1.095 | 0.84 |
| 117_S | 130_G | 1.094 | 0.84 |
| 111_E | 122_F | 1.083 | 0.83 |
| 8_A | 12_F | 1.074 | 0.83 |
| 114_F | 134_W | 1.073 | 0.83 |
| 82_G | 89_A | 1.071 | 0.82 |
| 25_N | 98_H | 1.060 | 0.82 |
| 6_L | 60_A | 1.055 | 0.81 |
| 135_A | 138_F | 1.054 | 0.81 |
| 24_E | 92_Y | 1.041 | 0.80 |
| 68_K | 71_K | 1.036 | 0.79 |
| 103_L | 108_Y | 1.033 | 0.79 |
| 25_N | 36_A | 1.033 | 0.79 |
| 42_M | 47_K | 1.031 | 0.79 |
| 67_Q | 71_K | 1.030 | 0.79 |
| 55_A | 98_H | 1.030 | 0.79 |
| 29_D | 32_I | 1.029 | 0.79 |
| 18_T | 105_V | 1.027 | 0.79 |
| 57_W | 60_A | 1.024 | 0.78 |
| 7_S | 20_I | 1.017 | 0.78 |
| 68_K | 114_F | 1.008 | 0.77 |
| 113_L | 133_L | 1.006 | 0.77 |
| 7_S | 11_L | 1.005 | 0.77 |
| 37_Y | 76_R | 1.003 | 0.76 |
| 48_F | 52_S | 1.002 | 0.76 |
| 111_E | 118_R | 1.001 | 0.76 |
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 | |
| 4kk0A | 10 | 0.6667 | 0.9 | 0.965 | Contact Map |
| 4f9dA | 2 | 0.3262 | 0.7 | 0.968 | Contact Map |
| 3tx3A | 2 | 0.383 | 0.6 | 0.969 | Contact Map |
| 3qilA | 24 | 0.2837 | 0.6 | 0.971 | Contact Map |
| 1nowA | 2 | 0.2482 | 0.6 | 0.971 | Contact Map |
| 3ktpB | 1 | 0.0993 | 0.5 | 0.971 | Contact Map |
| 2lx0A | 1 | 0.227 | 0.5 | 0.972 | Contact Map |
| 1u7gA | 1 | 0.7163 | 0.5 | 0.972 | Contact Map |
| 3w5aC | 1 | 0.1348 | 0.5 | 0.972 | Contact Map |
| 1wrgA | 1 | 0.2411 | 0.4 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)