| salbiii |
| ID: | 1513976230 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 134 (126) | ||
| Sequences: | 11857 (8277.2) | ||
| Seq/Len: | 94.103 | ||
| Nf(neff/√len): | 737.4 |
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: 94.103).
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 |
| 107_T | 116_S | 2.853 | 1.00 |
| 27_V | 52_R | 2.658 | 1.00 |
| 83_L | 102_A | 2.600 | 1.00 |
| 22_D | 25_A | 2.506 | 1.00 |
| 32_E | 48_R | 2.335 | 1.00 |
| 31_T | 115_D | 2.223 | 1.00 |
| 86_E | 99_K | 2.055 | 1.00 |
| 37_E | 118_R | 2.046 | 1.00 |
| 84_A | 99_K | 2.015 | 1.00 |
| 8_K | 12_A | 1.980 | 1.00 |
| 69_H | 84_A | 1.965 | 1.00 |
| 35_T | 116_S | 1.890 | 1.00 |
| 34_A | 51_Q | 1.772 | 1.00 |
| 16_R | 20_E | 1.753 | 1.00 |
| 9_E | 13_E | 1.741 | 1.00 |
| 13_E | 16_R | 1.717 | 1.00 |
| 10_I | 108_L | 1.696 | 1.00 |
| 27_V | 48_R | 1.685 | 1.00 |
| 78_S | 107_T | 1.645 | 1.00 |
| 83_L | 104_D | 1.626 | 1.00 |
| 25_A | 28_E | 1.612 | 1.00 |
| 47_G | 50_A | 1.606 | 1.00 |
| 104_D | 119_V | 1.595 | 1.00 |
| 30_F | 34_A | 1.588 | 1.00 |
| 21_G | 59_V | 1.575 | 1.00 |
| 13_E | 29_M | 1.573 | 1.00 |
| 24_D | 52_R | 1.564 | 1.00 |
| 80_A | 105_V | 1.526 | 1.00 |
| 70_L | 78_S | 1.507 | 1.00 |
| 52_R | 56_N | 1.501 | 1.00 |
| 6_K | 9_E | 1.483 | 1.00 |
| 33_N | 115_D | 1.454 | 1.00 |
| 109_T | 115_D | 1.451 | 1.00 |
| 110_P | 115_D | 1.431 | 1.00 |
| 35_T | 46_E | 1.429 | 1.00 |
| 37_E | 116_S | 1.400 | 0.99 |
| 7_R | 108_L | 1.396 | 0.99 |
| 37_E | 44_V | 1.370 | 0.99 |
| 23_V | 27_V | 1.348 | 0.99 |
| 49_A | 53_E | 1.327 | 0.99 |
| 86_E | 97_R | 1.317 | 0.99 |
| 70_L | 82_A | 1.306 | 0.99 |
| 23_V | 56_N | 1.264 | 0.99 |
| 84_A | 101_N | 1.250 | 0.99 |
| 31_T | 109_T | 1.248 | 0.99 |
| 53_E | 56_N | 1.246 | 0.98 |
| 72_A | 80_A | 1.240 | 0.98 |
| 12_A | 16_R | 1.238 | 0.98 |
| 53_E | 57_S | 1.187 | 0.98 |
| 104_D | 117_M | 1.180 | 0.98 |
| 78_S | 105_V | 1.171 | 0.98 |
| 66_E | 86_E | 1.170 | 0.97 |
| 79_V | 108_L | 1.167 | 0.97 |
| 24_D | 27_V | 1.150 | 0.97 |
| 13_E | 25_A | 1.142 | 0.97 |
| 68_G | 84_A | 1.133 | 0.97 |
| 38_D | 119_V | 1.126 | 0.97 |
| 30_F | 117_M | 1.125 | 0.97 |
| 11_V | 79_V | 1.107 | 0.96 |
| 30_F | 51_Q | 1.106 | 0.96 |
| 13_E | 28_E | 1.099 | 0.96 |
| 7_R | 79_V | 1.083 | 0.96 |
| 88_T | 94_N | 1.082 | 0.96 |
| 77_K | 110_P | 1.079 | 0.95 |
| 107_T | 115_D | 1.077 | 0.95 |
| 68_G | 86_E | 1.062 | 0.95 |
| 36_I | 117_M | 1.061 | 0.95 |
| 49_A | 52_R | 1.058 | 0.95 |
| 11_V | 106_F | 1.052 | 0.95 |
| 82_A | 118_R | 1.048 | 0.94 |
| 7_R | 73_G | 1.044 | 0.94 |
| 57_S | 61_A | 1.034 | 0.94 |
| 109_T | 113_K | 1.018 | 0.93 |
| 106_F | 114_I | 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 | |
| 3rgaA | 1 | 0.9701 | 99.7 | 0.137 | Contact Map |
| 3wmdA | 2 | 0.9701 | 99.7 | 0.151 | Contact Map |
| 1ohpA | 4 | 0.9328 | 99.7 | 0.167 | Contact Map |
| 1oh0A | 2 | 0.9403 | 99.7 | 0.181 | Contact Map |
| 1tuhA | 1 | 0.9403 | 99.7 | 0.188 | Contact Map |
| 2gexA | 2 | 0.9701 | 99.7 | 0.192 | Contact Map |
| 2f99A | 4 | 0.9627 | 99.7 | 0.197 | Contact Map |
| 3ebtA | 1 | 0.9328 | 99.6 | 0.201 | Contact Map |
| 3kkgA | 1 | 0.9776 | 99.6 | 0.201 | Contact Map |
| 3g8zA | 1 | 0.9179 | 99.6 | 0.204 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)