| MPS1 |
| ID: | 1485034691 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 135 (131) | ||
| Sequences: | 4598 (3520.7) | ||
| Seq/Len: | 35.099 | ||
| Nf(neff/√len): | 307.6 |
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: 35.099).
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 |
| 68_R | 92_E | 3.671 | 1.00 |
| 63_E | 66_D | 3.256 | 1.00 |
| 89_A | 105_L | 2.791 | 1.00 |
| 97_N | 100_K | 2.771 | 1.00 |
| 88_F | 92_E | 2.370 | 1.00 |
| 72_Q | 88_F | 2.345 | 1.00 |
| 102_K | 127_N | 2.242 | 1.00 |
| 74_A | 84_V | 2.054 | 1.00 |
| 52_Q | 74_A | 2.002 | 1.00 |
| 56_A | 67_A | 1.983 | 1.00 |
| 27_I | 59_K | 1.982 | 1.00 |
| 88_F | 104_L | 1.871 | 1.00 |
| 55_F | 59_K | 1.865 | 1.00 |
| 22_L | 25_K | 1.863 | 1.00 |
| 53_V | 87_S | 1.812 | 1.00 |
| 56_A | 71_F | 1.759 | 1.00 |
| 59_K | 66_D | 1.720 | 1.00 |
| 123_L | 127_N | 1.719 | 1.00 |
| 57_E | 87_S | 1.706 | 1.00 |
| 71_F | 87_S | 1.691 | 1.00 |
| 85_H | 104_L | 1.683 | 1.00 |
| 85_H | 108_A | 1.651 | 1.00 |
| 107_K | 111_R | 1.552 | 1.00 |
| 72_Q | 107_K | 1.550 | 1.00 |
| 89_A | 101_S | 1.438 | 1.00 |
| 55_F | 58_L | 1.422 | 1.00 |
| 102_K | 106_Q | 1.409 | 1.00 |
| 98_V | 102_K | 1.404 | 0.99 |
| 92_E | 97_N | 1.377 | 0.99 |
| 42_Y | 45_N | 1.372 | 0.99 |
| 52_Q | 70_Y | 1.368 | 0.99 |
| 75_R | 85_H | 1.348 | 0.99 |
| 81_F | 84_V | 1.339 | 0.99 |
| 73_M | 76_A | 1.304 | 0.99 |
| 7_L | 10_K | 1.296 | 0.99 |
| 75_R | 88_F | 1.287 | 0.99 |
| 30_Y | 33_A | 1.286 | 0.99 |
| 55_F | 70_Y | 1.281 | 0.99 |
| 26_L | 58_L | 1.261 | 0.99 |
| 42_Y | 46_E | 1.243 | 0.98 |
| 7_L | 11_L | 1.220 | 0.98 |
| 60_A | 94_S | 1.195 | 0.98 |
| 68_R | 91_F | 1.171 | 0.98 |
| 86_I | 90_Q | 1.171 | 0.98 |
| 107_K | 110_E | 1.142 | 0.97 |
| 32_Q | 36_A | 1.134 | 0.97 |
| 56_A | 70_Y | 1.134 | 0.97 |
| 57_E | 60_A | 1.120 | 0.96 |
| 120_E | 123_L | 1.088 | 0.96 |
| 78_C | 81_F | 1.087 | 0.96 |
| 67_A | 91_F | 1.084 | 0.96 |
| 49_A | 74_A | 1.080 | 0.95 |
| 87_S | 90_Q | 1.075 | 0.95 |
| 5_L | 9_L | 1.074 | 0.95 |
| 56_A | 59_K | 1.054 | 0.95 |
| 66_D | 69_D | 1.051 | 0.94 |
| 28_G | 32_Q | 1.043 | 0.94 |
| 119_L | 123_L | 1.040 | 0.94 |
| 4_W | 7_L | 1.037 | 0.94 |
| 32_Q | 35_E | 1.036 | 0.94 |
| 85_H | 107_K | 1.026 | 0.94 |
| 90_Q | 122_A | 1.026 | 0.94 |
| 112_G | 115_P | 1.019 | 0.93 |
| 68_R | 88_F | 1.017 | 0.93 |
| 9_L | 12_E | 1.009 | 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 | |
| 4b94A | 4 | 1 | 99.8 | 0.211 | Contact Map |
| 4h7yA | 4 | 1 | 99.7 | 0.244 | Contact Map |
| 2ooeA | 1 | 0.8963 | 99.5 | 0.362 | Contact Map |
| 2ondA | 2 | 0.8963 | 99.5 | 0.364 | Contact Map |
| 2uy1A | 1 | 0.8519 | 99.3 | 0.411 | Contact Map |
| 4aezC | 3 | 0.9556 | 99.1 | 0.465 | Contact Map |
| 4e6hA | 1 | 0.8963 | 99 | 0.493 | Contact Map |
| 2pziA | 2 | 0.8741 | 98.9 | 0.52 | Contact Map |
| 3q7aA | 1 | 0.8889 | 98.8 | 0.533 | Contact Map |
| 4ui9J | 1 | 0 | 98.8 | 0.536 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)