| 1rx4 |
| ID: | 1476310576 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (157) | ||
| Sequences: | 19685 (13638.9) | ||
| Seq/Len: | 125.382 | ||
| Nf(neff/√len): | 1088.5 |
Jackhmmer Results: (2016_04)
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: 125.382).
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 |
| 44_R | 48_E | 3.203 | 1.00 |
| 13_V | 121_G | 2.486 | 1.00 |
| 10_V | 116_D | 2.465 | 1.00 |
| 4_L | 107_A | 2.392 | 1.00 |
| 58_K | 73_T | 2.376 | 1.00 |
| 4_L | 100_Y | 2.329 | 1.00 |
| 14_I | 97_G | 1.998 | 1.00 |
| 98_R | 102_Q | 1.884 | 1.00 |
| 3_S | 111_Y | 1.880 | 1.00 |
| 135_S | 154_E | 1.872 | 1.00 |
| 114_H | 154_E | 1.805 | 1.00 |
| 8_L | 114_H | 1.792 | 1.00 |
| 36_L | 56_G | 1.787 | 1.00 |
| 104_L | 110_L | 1.755 | 1.00 |
| 135_S | 138_S | 1.728 | 1.00 |
| 8_L | 12_R | 1.727 | 1.00 |
| 39_P | 60_I | 1.698 | 1.00 |
| 79_D | 106_K | 1.691 | 1.00 |
| 9_A | 13_V | 1.680 | 1.00 |
| 93_V | 103_F | 1.634 | 1.00 |
| 33_R | 37_D | 1.634 | 1.00 |
| 62_L | 99_V | 1.583 | 1.00 |
| 109_K | 157_E | 1.559 | 1.00 |
| 10_V | 118_E | 1.559 | 1.00 |
| 38_K | 89_P | 1.551 | 1.00 |
| 143_A | 150_S | 1.541 | 1.00 |
| 77_S | 80_E | 1.538 | 1.00 |
| 116_D | 152_C | 1.529 | 1.00 |
| 138_S | 152_C | 1.526 | 1.00 |
| 38_K | 90_E | 1.521 | 1.00 |
| 6_A | 112_L | 1.516 | 1.00 |
| 78_V | 103_F | 1.505 | 1.00 |
| 84_A | 87_D | 1.504 | 1.00 |
| 9_A | 119_V | 1.503 | 1.00 |
| 30_W | 34_N | 1.473 | 1.00 |
| 30_W | 113_T | 1.461 | 1.00 |
| 140_F | 152_C | 1.460 | 1.00 |
| 136_V | 157_E | 1.454 | 1.00 |
| 6_A | 100_Y | 1.444 | 1.00 |
| 3_S | 90_E | 1.441 | 1.00 |
| 65_Q | 68_T | 1.438 | 1.00 |
| 109_K | 155_I | 1.428 | 1.00 |
| 38_K | 92_M | 1.410 | 1.00 |
| 75_V | 84_A | 1.389 | 0.99 |
| 8_L | 112_L | 1.385 | 0.99 |
| 39_P | 58_K | 1.357 | 0.99 |
| 32_K | 36_L | 1.341 | 0.99 |
| 41_I | 91_I | 1.332 | 0.99 |
| 32_K | 35_T | 1.324 | 0.99 |
| 98_R | 101_E | 1.313 | 0.99 |
| 97_G | 101_E | 1.277 | 0.99 |
| 54_L | 57_R | 1.261 | 0.99 |
| 81_A | 84_A | 1.252 | 0.99 |
| 80_E | 83_A | 1.243 | 0.98 |
| 76_K | 80_E | 1.239 | 0.98 |
| 11_D | 118_E | 1.207 | 0.98 |
| 80_E | 84_A | 1.175 | 0.98 |
| 138_S | 154_E | 1.165 | 0.97 |
| 129_E | 132_D | 1.155 | 0.97 |
| 116_D | 150_S | 1.144 | 0.97 |
| 45_H | 49_S | 1.143 | 0.97 |
| 45_H | 98_R | 1.141 | 0.97 |
| 144_D | 147_N | 1.136 | 0.97 |
| 26_A | 151_Y | 1.135 | 0.97 |
| 44_R | 64_S | 1.125 | 0.97 |
| 16_M | 19_A | 1.121 | 0.97 |
| 60_I | 75_V | 1.119 | 0.96 |
| 64_S | 98_R | 1.110 | 0.96 |
| 34_N | 111_Y | 1.108 | 0.96 |
| 40_V | 59_N | 1.101 | 0.96 |
| 30_W | 155_I | 1.100 | 0.96 |
| 16_M | 120_E | 1.081 | 0.95 |
| 123_T | 126_P | 1.079 | 0.95 |
| 3_S | 109_K | 1.078 | 0.95 |
| 33_R | 36_L | 1.078 | 0.95 |
| 45_H | 48_E | 1.074 | 0.95 |
| 24_L | 27_D | 1.057 | 0.95 |
| 134_E | 157_E | 1.054 | 0.95 |
| 13_V | 124_H | 1.053 | 0.95 |
| 30_W | 111_Y | 1.051 | 0.94 |
| 39_P | 88_V | 1.050 | 0.94 |
| 107_A | 110_L | 1.041 | 0.94 |
| 137_F | 155_I | 1.035 | 0.94 |
| 42_M | 47_W | 1.021 | 0.93 |
| 141_H | 151_Y | 1.014 | 0.93 |
| 102_Q | 106_K | 1.012 | 0.93 |
| 82_I | 86_G | 1.000 | 0.92 |
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 | |
| 4pssA | 1 | 0.7296 | 100 | 0.111 | Contact Map |
| 3tq8A | 1 | 0.9874 | 100 | 0.119 | Contact Map |
| 1zdrA | 2 | 1 | 100 | 0.128 | Contact Map |
| 3ia4A | 4 | 1 | 100 | 0.133 | Contact Map |
| 2w9hA | 1 | 0.9811 | 100 | 0.138 | Contact Map |
| 3s9uA | 2 | 1 | 100 | 0.146 | Contact Map |
| 4m7uA | 1 | 1 | 100 | 0.149 | Contact Map |
| 3rg9A | 2 | 1 | 100 | 0.15 | Contact Map |
| 3ix9A | 2 | 1 | 100 | 0.161 | Contact Map |
| 4eilA | 8 | 0.9874 | 100 | 0.164 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)