| Janice M Reimer |
| ID: | 1498242875 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 179 (169) | ||
| Sequences: | 25194 (20233.6) | ||
| Seq/Len: | 149.077 | ||
| Nf(neff/√len): | 1556.4 |
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: 149.077).
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 |
| 150_T | 163_V | 4.102 | 1.00 |
| 29_D | 68_R | 2.514 | 1.00 |
| 57_R | 60_Q | 2.490 | 1.00 |
| 19_H | 48_Q | 2.464 | 1.00 |
| 3_V | 29_D | 2.458 | 1.00 |
| 60_Q | 73_L | 2.377 | 1.00 |
| 31_H | 65_P | 2.334 | 1.00 |
| 152_H | 161_R | 2.314 | 1.00 |
| 64_H | 73_L | 2.263 | 1.00 |
| 32_F | 37_G | 2.116 | 1.00 |
| 93_E | 159_V | 2.064 | 1.00 |
| 17_W | 67_I | 2.054 | 1.00 |
| 66_T | 69_Q | 2.031 | 1.00 |
| 146_G | 149_S | 2.023 | 1.00 |
| 129_D | 132_Q | 1.990 | 1.00 |
| 6_T | 28_I | 1.990 | 1.00 |
| 12_Q | 52_I | 1.901 | 1.00 |
| 9_L | 75_T | 1.864 | 1.00 |
| 9_L | 12_Q | 1.823 | 1.00 |
| 138_E | 142_L | 1.803 | 1.00 |
| 134_R | 138_E | 1.791 | 1.00 |
| 27_G | 30_D | 1.771 | 1.00 |
| 12_Q | 15_Q | 1.769 | 1.00 |
| 14_A | 67_I | 1.750 | 1.00 |
| 139_Q | 142_L | 1.733 | 1.00 |
| 64_H | 69_Q | 1.729 | 1.00 |
| 10_E | 28_I | 1.708 | 1.00 |
| 7_D | 28_I | 1.699 | 1.00 |
| 16_V | 45_L | 1.681 | 1.00 |
| 50_K | 55_S | 1.677 | 1.00 |
| 31_H | 34_E | 1.670 | 1.00 |
| 8_E | 11_Q | 1.655 | 1.00 |
| 17_W | 37_G | 1.592 | 1.00 |
| 28_I | 67_I | 1.573 | 1.00 |
| 14_A | 18_S | 1.567 | 1.00 |
| 142_L | 165_R | 1.536 | 1.00 |
| 128_V | 133_I | 1.502 | 1.00 |
| 13_L | 71_K | 1.501 | 1.00 |
| 93_E | 154_R | 1.494 | 1.00 |
| 130_T | 134_R | 1.487 | 1.00 |
| 28_I | 68_R | 1.479 | 1.00 |
| 13_L | 49_L | 1.424 | 1.00 |
| 38_D | 41_K | 1.423 | 1.00 |
| 96_T | 158_I | 1.412 | 1.00 |
| 7_D | 11_Q | 1.376 | 0.99 |
| 18_S | 25_Q | 1.370 | 0.99 |
| 13_L | 67_I | 1.361 | 0.99 |
| 154_R | 159_V | 1.345 | 0.99 |
| 11_Q | 15_Q | 1.333 | 0.99 |
| 3_V | 28_I | 1.322 | 0.99 |
| 15_Q | 52_I | 1.321 | 0.99 |
| 45_L | 61_L | 1.320 | 0.99 |
| 149_S | 160_K | 1.309 | 0.99 |
| 12_Q | 51_N | 1.282 | 0.99 |
| 14_A | 28_I | 1.281 | 0.99 |
| 54_L | 74_L | 1.270 | 0.99 |
| 59_D | 63_T | 1.256 | 0.99 |
| 17_W | 45_L | 1.247 | 0.99 |
| 16_V | 49_L | 1.245 | 0.98 |
| 108_Q | 153_M | 1.223 | 0.98 |
| 7_D | 75_T | 1.213 | 0.98 |
| 14_A | 26_M | 1.211 | 0.98 |
| 61_L | 70_L | 1.198 | 0.98 |
| 8_E | 12_Q | 1.181 | 0.98 |
| 105_I | 109_Q | 1.177 | 0.98 |
| 60_Q | 63_T | 1.158 | 0.97 |
| 20_V | 45_L | 1.157 | 0.97 |
| 149_S | 162_I | 1.153 | 0.97 |
| 3_V | 68_R | 1.148 | 0.97 |
| 48_Q | 51_N | 1.139 | 0.97 |
| 42_V | 61_L | 1.138 | 0.97 |
| 100_E | 160_K | 1.137 | 0.97 |
| 153_M | 158_I | 1.133 | 0.97 |
| 101_K | 157_E | 1.126 | 0.97 |
| 154_R | 157_E | 1.116 | 0.96 |
| 6_T | 10_E | 1.102 | 0.96 |
| 33_L | 62_F | 1.100 | 0.96 |
| 93_E | 161_R | 1.096 | 0.96 |
| 135_V | 138_E | 1.094 | 0.96 |
| 46_I | 50_K | 1.086 | 0.96 |
| 16_V | 48_Q | 1.076 | 0.95 |
| 97_S | 100_E | 1.072 | 0.95 |
| 49_L | 56_L | 1.068 | 0.95 |
| 6_T | 68_R | 1.065 | 0.95 |
| 56_L | 70_L | 1.065 | 0.95 |
| 15_Q | 18_S | 1.058 | 0.95 |
| 91_Q | 164_P | 1.055 | 0.95 |
| 42_V | 58_Y | 1.051 | 0.94 |
| 10_E | 71_K | 1.051 | 0.94 |
| 16_V | 19_H | 1.049 | 0.94 |
| 17_W | 70_L | 1.048 | 0.94 |
| 150_T | 161_R | 1.040 | 0.94 |
| 60_Q | 77_Q | 1.022 | 0.93 |
| 9_L | 74_L | 1.021 | 0.93 |
| 138_E | 167_E | 1.011 | 0.93 |
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 | |
| 2jgpA | 1 | 1 | 100 | 0.154 | Contact Map |
| 4oqjA | 1 | 0 | 99.7 | 0.559 | Contact Map |
| 4r0mB | 2 | 0.419 | 99.7 | 0.559 | Contact Map |
| 4dg8A | 1 | 0 | 99.7 | 0.578 | Contact Map |
| 2cq8A | 1 | 0.5028 | 99.6 | 0.595 | Contact Map |
| 1dnyA | 1 | 0.419 | 99.6 | 0.605 | Contact Map |
| 3tejA | 2 | 0.9609 | 99.6 | 0.606 | Contact Map |
| 4pxhB | 3 | 0.4134 | 99.6 | 0.607 | Contact Map |
| 4tx3B | 1 | 0.5698 | 99.5 | 0.615 | Contact Map |
| 4iz6A | 2 | 0.4413 | 99.5 | 0.62 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)