| T0814 1-120 |
| ID: | 1404851054 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (115) | ||
| Sequences: | 219 (208.3) | ||
| Seq/Len: | 1.904 | ||
| Nf(neff/√len): | 19.4 |
Jackhmmer Results: (2014_04_16)
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: 1.904).
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 |
| 82_N | 86_T | 4.569 | 1.00 |
| 66_G | 74_Y | 2.492 | 1.00 |
| 11_M | 51_Y | 2.381 | 1.00 |
| 38_L | 62_I | 2.361 | 1.00 |
| 40_V | 62_I | 2.302 | 1.00 |
| 40_V | 60_I | 2.158 | 0.99 |
| 80_H | 88_S | 1.952 | 0.99 |
| 28_T | 31_N | 1.828 | 0.98 |
| 92_P | 100_Q | 1.801 | 0.97 |
| 52_I | 60_I | 1.626 | 0.94 |
| 47_I | 119_N | 1.538 | 0.92 |
| 69_S | 116_Q | 1.484 | 0.90 |
| 75_A | 100_Q | 1.374 | 0.84 |
| 76_Y | 98_G | 1.358 | 0.83 |
| 52_I | 67_L | 1.332 | 0.82 |
| 66_G | 114_T | 1.309 | 0.80 |
| 42_V | 60_I | 1.294 | 0.79 |
| 14_F | 19_G | 1.250 | 0.76 |
| 115_T | 120_Y | 1.245 | 0.75 |
| 35_I | 74_Y | 1.235 | 0.74 |
| 47_I | 51_Y | 1.233 | 0.74 |
| 77_N | 108_A | 1.209 | 0.72 |
| 36_K | 74_Y | 1.204 | 0.72 |
| 75_A | 103_T | 1.197 | 0.71 |
| 14_F | 89_Q | 1.186 | 0.70 |
| 73_R | 103_T | 1.186 | 0.70 |
| 9_L | 16_L | 1.184 | 0.70 |
| 38_L | 41_K | 1.184 | 0.70 |
| 39_Q | 63_N | 1.158 | 0.67 |
| 82_N | 94_E | 1.149 | 0.67 |
| 49_E | 80_H | 1.143 | 0.66 |
| 26_F | 81_C | 1.138 | 0.66 |
| 9_L | 78_V | 1.135 | 0.65 |
| 84_D | 88_S | 1.120 | 0.64 |
| 30_V | 61_E | 1.107 | 0.62 |
| 48_S | 56_G | 1.099 | 0.62 |
| 70_G | 108_A | 1.088 | 0.60 |
| 109_N | 118_S | 1.070 | 0.58 |
| 71_Y | 75_A | 1.064 | 0.58 |
| 61_E | 78_V | 1.063 | 0.58 |
| 73_R | 83_A | 1.062 | 0.58 |
| 66_G | 115_T | 1.060 | 0.57 |
| 38_L | 93_I | 1.030 | 0.54 |
| 7_S | 16_L | 1.021 | 0.53 |
| 10_F | 17_S | 1.013 | 0.52 |
| 71_Y | 109_N | 1.011 | 0.52 |
| 82_N | 97_N | 1.006 | 0.52 |
| 95_Y | 106_D | 1.003 | 0.51 |
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 | |
| 4dw1A | 1 | 0.975 | 21.8 | 0.93 | Contact Map |
| 2qgmA | 1 | 0.775 | 9.9 | 0.941 | Contact Map |
| 4jg9A | 2 | 0.425 | 9 | 0.941 | Contact Map |
| 1utrA | 2 | 0.4333 | 8.8 | 0.942 | Contact Map |
| 4bbwA | 1 | 0.6417 | 8.6 | 0.942 | Contact Map |
| 1v10A | 1 | 0.75 | 5.4 | 0.947 | Contact Map |
| 1ygpA | 2 | 0.9667 | 4.8 | 0.949 | Contact Map |
| 4n4rB | 2 | 0.725 | 4.7 | 0.949 | Contact Map |
| 4nnrA | 2 | 0.5417 | 4.5 | 0.949 | Contact Map |
| 2dckA | 1 | 0.725 | 3.8 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)