| Tau_RDs_5854_nr_noisoform_mafft |
| ID: | 1494987233 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (125) | ||
| Sequences: | 194 (102.3) | ||
| Seq/Len: | 1.552 | ||
| Nf(neff/√len): | 9.1 |
HHblits Results: (2016_02)
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: 1.552).
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 |
| 119_H | 123_G | 1.806 | 0.96 |
| 51_K | 55_K | 1.701 | 0.94 |
| 9_D | 20_T | 1.485 | 0.86 |
| 64_Q | 85_I | 1.470 | 0.85 |
| 49_G | 53_N | 1.467 | 0.85 |
| 56_H | 59_G | 1.463 | 0.85 |
| 116_N | 119_H | 1.461 | 0.85 |
| 9_D | 24_K | 1.460 | 0.85 |
| 20_T | 26_Q | 1.453 | 0.84 |
| 72_L | 110_K | 1.453 | 0.84 |
| 56_H | 60_G | 1.387 | 0.80 |
| 12_N | 24_K | 1.385 | 0.80 |
| 68_K | 79_C | 1.383 | 0.80 |
| 50_S | 53_N | 1.372 | 0.79 |
| 18_G | 30_G | 1.372 | 0.79 |
| 11_K | 17_I | 1.339 | 0.77 |
| 25_H | 29_G | 1.318 | 0.76 |
| 116_N | 123_G | 1.306 | 0.75 |
| 28_G | 31_K | 1.300 | 0.74 |
| 28_G | 51_K | 1.255 | 0.70 |
| 42_S | 45_Q | 1.249 | 0.70 |
| 73_S | 79_C | 1.248 | 0.70 |
| 74_K | 86_H | 1.246 | 0.70 |
| 19_S | 29_G | 1.231 | 0.68 |
| 113_S | 116_N | 1.226 | 0.68 |
| 42_S | 46_S | 1.226 | 0.68 |
| 104_K | 110_K | 1.221 | 0.67 |
| 48_C | 52_D | 1.211 | 0.66 |
| 64_Q | 79_C | 1.206 | 0.66 |
| 32_V | 36_N | 1.201 | 0.65 |
| 74_K | 95_E | 1.183 | 0.64 |
| 23_L | 94_V | 1.181 | 0.64 |
| 67_Y | 117_I | 1.180 | 0.63 |
| 116_N | 124_G | 1.173 | 0.63 |
| 25_H | 108_Q | 1.162 | 0.62 |
| 43_N | 47_K | 1.157 | 0.61 |
| 97_K | 111_I | 1.153 | 0.61 |
| 46_S | 50_S | 1.148 | 0.60 |
| 33_Q | 48_C | 1.142 | 0.60 |
| 6_P | 25_H | 1.135 | 0.59 |
| 118_T | 126_K | 1.135 | 0.59 |
| 82_L | 86_H | 1.135 | 0.59 |
| 88_K | 93_Q | 1.133 | 0.59 |
| 46_S | 56_H | 1.132 | 0.59 |
| 64_Q | 73_S | 1.123 | 0.58 |
| 15_S | 19_S | 1.122 | 0.58 |
| 112_G | 116_N | 1.122 | 0.58 |
| 49_G | 56_H | 1.114 | 0.57 |
| 51_K | 57_V | 1.106 | 0.56 |
| 9_D | 52_D | 1.101 | 0.55 |
| 10_L | 13_V | 1.099 | 0.55 |
| 69_P | 82_L | 1.091 | 0.54 |
| 56_H | 87_H | 1.084 | 0.54 |
| 21_E | 25_H | 1.084 | 0.54 |
| 16_K | 29_G | 1.079 | 0.53 |
| 51_K | 54_I | 1.076 | 0.53 |
| 62_S | 79_C | 1.068 | 0.52 |
| 19_S | 22_N | 1.059 | 0.51 |
| 86_H | 93_Q | 1.056 | 0.51 |
| 19_S | 25_H | 1.054 | 0.51 |
| 111_I | 114_L | 1.051 | 0.50 |
| 26_Q | 42_S | 1.047 | 0.50 |
| 95_E | 126_K | 1.043 | 0.49 |
| 41_L | 51_K | 1.041 | 0.49 |
| 110_K | 113_S | 1.039 | 0.49 |
| 9_D | 26_Q | 1.038 | 0.49 |
| 110_K | 116_N | 1.038 | 0.49 |
| 52_D | 55_K | 1.034 | 0.49 |
| 72_L | 76_T | 1.029 | 0.48 |
| 19_S | 30_G | 1.027 | 0.48 |
| 16_K | 30_G | 1.025 | 0.48 |
| 103_F | 107_V | 1.023 | 0.47 |
| 69_P | 73_S | 1.012 | 0.46 |
| 14_K | 21_E | 1.008 | 0.46 |
| 18_G | 28_G | 1.003 | 0.45 |
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 | |
| 2mz7A | 1 | 0 | 99.8 | 0.675 | Contact Map |
| 3qr8A | 1 | 0.4646 | 6.3 | 0.96 | Contact Map |
| 1lq7A | 1 | 0.4016 | 3.1 | 0.966 | Contact Map |
| 3nngA | 2 | 0.2835 | 1.6 | 0.97 | Contact Map |
| 4r29A | 4 | 0.3543 | 1.6 | 0.971 | Contact Map |
| 5bxvB | 2 | 0 | 1.6 | 0.971 | Contact Map |
| 3zey5 | 1 | 0.5433 | 1.5 | 0.971 | Contact Map |
| 2gbbA | 4 | 0.5197 | 1.2 | 0.972 | Contact Map |
| 4uedB | 1 | 0.1181 | 1.2 | 0.973 | Contact Map |
| 3tqmA | 4 | 0.4488 | 1 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)