| PSEA8_1_159 |
| ID: | 1496596501 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 159 (156) | ||
| Sequences: | 4537 (2609.9) | ||
| Seq/Len: | 29.083 | ||
| Nf(neff/√len): | 209.0 |
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: 29.083).
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 |
| 30_H | 65_E | 4.626 | 1.00 |
| 67_V | 76_F | 3.506 | 1.00 |
| 13_I | 54_A | 3.354 | 1.00 |
| 3_R | 30_H | 3.160 | 1.00 |
| 67_V | 80_Q | 3.135 | 1.00 |
| 24_A | 86_L | 2.930 | 1.00 |
| 22_E | 60_H | 2.638 | 1.00 |
| 25_S | 63_N | 2.430 | 1.00 |
| 57_V | 148_A | 2.086 | 1.00 |
| 107_Q | 143_K | 2.084 | 1.00 |
| 13_I | 21_I | 2.004 | 1.00 |
| 5_L | 77_V | 1.998 | 1.00 |
| 51_V | 55_Q | 1.965 | 1.00 |
| 46_S | 49_Q | 1.947 | 1.00 |
| 9_T | 43_P | 1.945 | 1.00 |
| 53_L | 152_A | 1.944 | 1.00 |
| 150_A | 154_A | 1.837 | 1.00 |
| 71_T | 79_E | 1.775 | 1.00 |
| 134_I | 139_G | 1.755 | 1.00 |
| 78_K | 109_A | 1.706 | 1.00 |
| 52_A | 55_Q | 1.692 | 1.00 |
| 87_R | 101_L | 1.676 | 1.00 |
| 78_K | 111_D | 1.665 | 1.00 |
| 18_G | 146_H | 1.622 | 1.00 |
| 58_T | 61_L | 1.589 | 1.00 |
| 32_I | 80_Q | 1.560 | 1.00 |
| 56_E | 148_A | 1.558 | 1.00 |
| 23_R | 113_E | 1.556 | 1.00 |
| 51_V | 68_G | 1.531 | 1.00 |
| 75_H | 78_K | 1.516 | 1.00 |
| 18_G | 58_T | 1.516 | 1.00 |
| 76_F | 80_Q | 1.472 | 1.00 |
| 77_V | 112_V | 1.472 | 1.00 |
| 49_Q | 156_R | 1.459 | 1.00 |
| 45_F | 53_L | 1.442 | 1.00 |
| 52_A | 56_E | 1.441 | 1.00 |
| 71_T | 75_H | 1.439 | 1.00 |
| 56_E | 152_A | 1.438 | 1.00 |
| 74_A | 109_A | 1.436 | 1.00 |
| 19_D | 120_S | 1.433 | 1.00 |
| 47_L | 68_G | 1.417 | 1.00 |
| 28_F | 31_V | 1.405 | 0.99 |
| 151_D | 155_E | 1.398 | 0.99 |
| 104_M | 130_L | 1.395 | 0.99 |
| 36_A | 69_F | 1.389 | 0.99 |
| 4_V | 31_V | 1.382 | 0.99 |
| 85_F | 112_V | 1.381 | 0.99 |
| 56_E | 59_K | 1.377 | 0.99 |
| 40_K | 133_E | 1.371 | 0.99 |
| 73_L | 85_F | 1.356 | 0.99 |
| 21_I | 33_I | 1.351 | 0.99 |
| 104_M | 134_I | 1.331 | 0.99 |
| 34_A | 69_F | 1.328 | 0.99 |
| 27_L | 115_M | 1.297 | 0.99 |
| 152_A | 155_E | 1.297 | 0.99 |
| 133_E | 137_L | 1.255 | 0.99 |
| 3_R | 32_I | 1.205 | 0.98 |
| 74_A | 112_V | 1.169 | 0.97 |
| 22_E | 61_L | 1.154 | 0.97 |
| 89_L | 116_F | 1.142 | 0.97 |
| 34_A | 76_F | 1.140 | 0.97 |
| 25_S | 61_L | 1.114 | 0.96 |
| 89_L | 95_F | 1.110 | 0.96 |
| 5_L | 76_F | 1.104 | 0.96 |
| 28_F | 84_V | 1.093 | 0.96 |
| 142_S | 150_A | 1.087 | 0.96 |
| 61_L | 64_V | 1.087 | 0.96 |
| 15_K | 146_H | 1.081 | 0.95 |
| 92_V | 96_E | 1.077 | 0.95 |
| 57_V | 146_H | 1.075 | 0.95 |
| 7_P | 85_F | 1.072 | 0.95 |
| 3_R | 82_A | 1.071 | 0.95 |
| 123_Y | 126_I | 1.056 | 0.95 |
| 147_P | 151_D | 1.050 | 0.94 |
| 44_L | 157_F | 1.048 | 0.94 |
| 145_V | 149_V | 1.033 | 0.94 |
| 141_I | 153_L | 1.033 | 0.94 |
| 32_I | 82_A | 1.027 | 0.94 |
| 65_E | 80_Q | 1.026 | 0.94 |
| 27_L | 117_L | 1.023 | 0.93 |
| 136_A | 157_F | 1.023 | 0.93 |
| 2_N | 83_N | 1.017 | 0.93 |
| 35_V | 51_V | 1.008 | 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 | |
| 3k9wA | 1 | 1 | 100 | 0.47 | Contact Map |
| 1vlhA | 6 | 0.9937 | 100 | 0.471 | Contact Map |
| 3nbkA | 4 | 0.9874 | 100 | 0.479 | Contact Map |
| 4natA | 3 | 0.9686 | 100 | 0.482 | Contact Map |
| 3nd5A | 6 | 0.9434 | 100 | 0.485 | Contact Map |
| 1od6A | 1 | 0.9623 | 100 | 0.489 | Contact Map |
| 1qjcA | 2 | 0.9874 | 100 | 0.493 | Contact Map |
| 3nv7A | 1 | 0.9748 | 100 | 0.497 | Contact Map |
| 1o6bA | 1 | 1 | 100 | 0.498 | Contact Map |
| 4f3rA | 3 | 0.9308 | 100 | 0.512 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)