| tssaa |
| ID: | 1430314752 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 137 (130) | ||
| Sequences: | 275 (183.5) | ||
| Seq/Len: | 2.115 | ||
| Nf(neff/√len): | 16.1 |
Jackhmmer Results: (2015_01_07)
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: 2.115).
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 |
| 37_R | 79_E | 2.841 | 1.00 |
| 47_A | 63_L | 1.956 | 0.99 |
| 90_R | 111_D | 1.911 | 0.99 |
| 47_A | 59_A | 1.760 | 0.97 |
| 19_G | 22_A | 1.722 | 0.97 |
| 47_A | 90_R | 1.559 | 0.94 |
| 102_E | 107_R | 1.428 | 0.89 |
| 41_L | 126_R | 1.426 | 0.89 |
| 63_L | 90_R | 1.403 | 0.88 |
| 15_A | 27_L | 1.384 | 0.87 |
| 33_I | 38_S | 1.379 | 0.87 |
| 50_A | 90_R | 1.357 | 0.86 |
| 64_A | 111_D | 1.349 | 0.85 |
| 93_L | 97_K | 1.347 | 0.85 |
| 2_A | 42_L | 1.340 | 0.85 |
| 67_D | 87_K | 1.317 | 0.83 |
| 12_L | 19_G | 1.317 | 0.83 |
| 20_T | 53_T | 1.296 | 0.82 |
| 47_A | 50_A | 1.293 | 0.82 |
| 25_S | 39_N | 1.286 | 0.81 |
| 66_L | 119_L | 1.286 | 0.81 |
| 27_L | 94_L | 1.280 | 0.81 |
| 4_I | 53_T | 1.231 | 0.77 |
| 71_T | 96_M | 1.228 | 0.77 |
| 39_N | 123_D | 1.227 | 0.77 |
| 70_A | 114_H | 1.217 | 0.76 |
| 39_N | 122_I | 1.205 | 0.75 |
| 21_E | 50_A | 1.187 | 0.73 |
| 11_A | 14_I | 1.180 | 0.73 |
| 43_R | 55_K | 1.169 | 0.72 |
| 43_R | 46_M | 1.154 | 0.70 |
| 15_A | 93_L | 1.133 | 0.68 |
| 38_S | 54_G | 1.123 | 0.67 |
| 42_L | 121_A | 1.123 | 0.67 |
| 106_V | 130_L | 1.108 | 0.66 |
| 13_Q | 128_A | 1.103 | 0.65 |
| 20_T | 49_V | 1.102 | 0.65 |
| 46_M | 82_L | 1.096 | 0.64 |
| 25_S | 53_T | 1.092 | 0.64 |
| 101_T | 118_G | 1.087 | 0.64 |
| 98_S | 121_A | 1.082 | 0.63 |
| 46_M | 62_L | 1.082 | 0.63 |
| 40_W | 89_R | 1.075 | 0.62 |
| 79_E | 119_L | 1.073 | 0.62 |
| 43_R | 69_R | 1.070 | 0.62 |
| 98_S | 101_T | 1.069 | 0.62 |
| 94_L | 127_A | 1.067 | 0.61 |
| 70_A | 119_L | 1.066 | 0.61 |
| 45_L | 128_A | 1.065 | 0.61 |
| 4_I | 29_A | 1.062 | 0.61 |
| 62_L | 91_L | 1.058 | 0.60 |
| 91_L | 119_L | 1.056 | 0.60 |
| 36_D | 49_V | 1.045 | 0.59 |
| 49_V | 87_K | 1.043 | 0.59 |
| 46_M | 88_A | 1.037 | 0.58 |
| 6_S | 14_I | 1.034 | 0.58 |
| 63_L | 89_R | 1.030 | 0.57 |
| 90_R | 123_D | 1.028 | 0.57 |
| 106_V | 110_P | 1.027 | 0.57 |
| 48_R | 85_E | 1.015 | 0.56 |
| 14_I | 18_E | 1.015 | 0.56 |
| 48_R | 59_A | 1.014 | 0.56 |
| 86_V | 113_E | 1.013 | 0.55 |
| 8_E | 45_L | 1.012 | 0.55 |
| 26_W | 84_F | 1.012 | 0.55 |
| 37_R | 78_W | 1.012 | 0.55 |
| 110_P | 118_G | 1.004 | 0.54 |
| 38_S | 79_E | 1.002 | 0.54 |
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 | |
| 2mhkA | 1 | 0.9489 | 76.7 | 0.879 | Contact Map |
| 3urzA | 2 | 0.8467 | 74 | 0.882 | Contact Map |
| 4kvmA | 4 | 0.8467 | 67 | 0.887 | Contact Map |
| 2r5sA | 2 | 0.8248 | 65.4 | 0.888 | Contact Map |
| 4ja7A | 1 | 0.7883 | 63.6 | 0.889 | Contact Map |
| 4rg9A | 2 | 0.8905 | 62.9 | 0.89 | Contact Map |
| 4f3vA | 2 | 0.854 | 60.8 | 0.892 | Contact Map |
| 4gywA | 2 | 0.8467 | 59.7 | 0.892 | Contact Map |
| 4r7sA | 1 | 0.8613 | 56.8 | 0.894 | Contact Map |
| 3mkrA | 1 | 0.7956 | 56 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)