| spind |
| ID: | 1446645932 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 120 (114) | ||
| Sequences: | 1121 (822.3) | ||
| Seq/Len: | 9.833 | ||
| Nf(neff/√len): | 77.0 |
Jackhmmer Results: (2015_08)
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: 9.833).
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 |
| 91_L | 94_L | 2.591 | 1.00 |
| 24_A | 27_G | 2.557 | 1.00 |
| 106_V | 109_L | 2.312 | 1.00 |
| 23_A | 27_G | 2.225 | 1.00 |
| 27_G | 31_V | 2.144 | 1.00 |
| 55_Y | 58_E | 2.049 | 1.00 |
| 34_Q | 37_L | 1.976 | 1.00 |
| 48_M | 51_M | 1.752 | 1.00 |
| 22_K | 26_Y | 1.658 | 1.00 |
| 33_S | 38_Q | 1.625 | 1.00 |
| 38_Q | 42_D | 1.610 | 1.00 |
| 98_L | 102_H | 1.583 | 1.00 |
| 113_I | 116_L | 1.550 | 1.00 |
| 84_K | 87_Q | 1.542 | 1.00 |
| 41_L | 44_C | 1.495 | 1.00 |
| 35_N | 50_T | 1.493 | 1.00 |
| 105_E | 110_K | 1.476 | 1.00 |
| 90_H | 95_E | 1.458 | 1.00 |
| 112_K | 117_K | 1.436 | 1.00 |
| 107_N | 111_T | 1.432 | 1.00 |
| 108_E | 112_K | 1.355 | 0.99 |
| 110_K | 119_E | 1.323 | 0.99 |
| 40_Q | 43_K | 1.321 | 0.99 |
| 28_L | 34_Q | 1.317 | 0.99 |
| 7_T | 10_R | 1.312 | 0.99 |
| 6_I | 10_R | 1.311 | 0.99 |
| 13_L | 16_A | 1.256 | 0.99 |
| 60_Y | 64_R | 1.233 | 0.98 |
| 54_S | 58_E | 1.212 | 0.98 |
| 28_L | 31_V | 1.202 | 0.98 |
| 29_Q | 33_S | 1.186 | 0.98 |
| 65_E | 70_S | 1.149 | 0.97 |
| 103_G | 110_K | 1.139 | 0.97 |
| 5_I | 8_N | 1.126 | 0.97 |
| 46_N | 50_T | 1.125 | 0.96 |
| 66_V | 69_K | 1.124 | 0.96 |
| 73_L | 76_L | 1.121 | 0.96 |
| 83_I | 87_Q | 1.121 | 0.96 |
| 63_Q | 70_S | 1.117 | 0.96 |
| 24_A | 31_V | 1.115 | 0.96 |
| 92_E | 95_E | 1.112 | 0.96 |
| 91_L | 95_E | 1.101 | 0.96 |
| 65_E | 69_K | 1.101 | 0.96 |
| 23_A | 31_V | 1.100 | 0.96 |
| 100_R | 110_K | 1.092 | 0.96 |
| 90_H | 93_K | 1.084 | 0.95 |
| 20_R | 30_L | 1.082 | 0.95 |
| 12_R | 17_E | 1.070 | 0.95 |
| 102_H | 106_V | 1.065 | 0.95 |
| 100_R | 108_E | 1.061 | 0.95 |
| 47_E | 51_M | 1.056 | 0.95 |
| 22_K | 28_L | 1.051 | 0.94 |
| 110_K | 113_I | 1.040 | 0.94 |
| 36_E | 40_Q | 1.040 | 0.94 |
| 57_Q | 61_T | 1.034 | 0.94 |
| 5_I | 12_R | 1.029 | 0.93 |
| 54_S | 59_K | 1.023 | 0.93 |
| 64_R | 67_E | 1.018 | 0.93 |
| 112_K | 115_K | 1.017 | 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 | |
| 3vkgA | 2 | 0.8917 | 93.8 | 0.581 | Contact Map |
| 1i84S | 2 | 0 | 91.2 | 0.615 | Contact Map |
| 4ll8A | 1 | 0.2667 | 90.6 | 0.62 | Contact Map |
| 2dfsA | 2 | 0.7833 | 90.5 | 0.62 | Contact Map |
| 4q4gX | 1 | 0 | 90.4 | 0.622 | Contact Map |
| 3ojaB | 1 | 0.9833 | 86.6 | 0.647 | Contact Map |
| 4rsiB | 1 | 0.8917 | 86.1 | 0.649 | Contact Map |
| 4linA | 12 | 0.9917 | 85.8 | 0.651 | Contact Map |
| 1c1gA | 4 | 0.9917 | 81.9 | 0.667 | Contact Map |
| 4rsiA | 1 | 0.4333 | 73.4 | 0.691 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)