| T0827 212-369 |
| ID: | 1406135254 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 158 (155) | ||
| Sequences: | 434 (351.9) | ||
| Seq/Len: | 2.800 | ||
| Nf(neff/√len): | 28.3 |
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: 2.800).
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 |
| 25_P | 29_K | 2.211 | 1.00 |
| 59_G | 67_I | 1.972 | 0.99 |
| 26_L | 30_A | 1.939 | 0.99 |
| 26_L | 33_F | 1.816 | 0.99 |
| 75_S | 101_T | 1.789 | 0.99 |
| 18_S | 22_W | 1.719 | 0.98 |
| 7_Q | 14_F | 1.681 | 0.98 |
| 18_S | 23_Q | 1.612 | 0.97 |
| 48_P | 51_S | 1.611 | 0.97 |
| 56_V | 67_I | 1.607 | 0.97 |
| 7_Q | 19_A | 1.599 | 0.97 |
| 53_D | 59_G | 1.581 | 0.97 |
| 98_C | 108_V | 1.486 | 0.95 |
| 88_D | 91_G | 1.470 | 0.94 |
| 75_S | 82_G | 1.463 | 0.94 |
| 59_G | 105_R | 1.433 | 0.93 |
| 25_P | 30_A | 1.430 | 0.93 |
| 7_Q | 15_A | 1.428 | 0.93 |
| 7_Q | 18_S | 1.423 | 0.93 |
| 25_P | 31_L | 1.394 | 0.92 |
| 144_R | 151_Y | 1.368 | 0.91 |
| 110_Q | 131_E | 1.359 | 0.91 |
| 7_Q | 10_V | 1.350 | 0.90 |
| 15_A | 23_Q | 1.344 | 0.90 |
| 74_L | 101_T | 1.344 | 0.90 |
| 30_A | 33_F | 1.335 | 0.90 |
| 17_A | 20_E | 1.315 | 0.89 |
| 77_L | 82_G | 1.306 | 0.88 |
| 94_L | 97_L | 1.262 | 0.86 |
| 27_S | 33_F | 1.259 | 0.86 |
| 98_C | 116_R | 1.238 | 0.84 |
| 26_L | 32_Q | 1.232 | 0.84 |
| 10_V | 17_A | 1.221 | 0.83 |
| 11_G | 90_G | 1.218 | 0.83 |
| 46_K | 50_N | 1.217 | 0.83 |
| 99_K | 145_A | 1.214 | 0.83 |
| 72_S | 79_P | 1.213 | 0.83 |
| 7_Q | 22_W | 1.205 | 0.82 |
| 8_D | 19_A | 1.191 | 0.81 |
| 20_E | 59_G | 1.182 | 0.80 |
| 57_A | 110_Q | 1.164 | 0.79 |
| 82_G | 97_L | 1.161 | 0.79 |
| 96_I | 148_V | 1.157 | 0.78 |
| 15_A | 19_A | 1.137 | 0.77 |
| 108_V | 137_Y | 1.136 | 0.76 |
| 53_D | 98_C | 1.136 | 0.76 |
| 59_G | 108_V | 1.133 | 0.76 |
| 58_A | 66_E | 1.129 | 0.76 |
| 68_A | 93_P | 1.127 | 0.76 |
| 78_K | 117_R | 1.122 | 0.75 |
| 12_D | 19_A | 1.107 | 0.74 |
| 35_E | 56_V | 1.102 | 0.73 |
| 103_L | 143_D | 1.094 | 0.73 |
| 151_Y | 155_S | 1.092 | 0.72 |
| 84_K | 93_P | 1.071 | 0.70 |
| 85_I | 88_D | 1.066 | 0.70 |
| 5_I | 9_A | 1.064 | 0.70 |
| 16_L | 20_E | 1.062 | 0.69 |
| 30_A | 86_F | 1.056 | 0.69 |
| 85_I | 93_P | 1.056 | 0.69 |
| 41_R | 44_I | 1.055 | 0.69 |
| 4_E | 24_D | 1.053 | 0.68 |
| 9_A | 21_G | 1.052 | 0.68 |
| 27_S | 93_P | 1.048 | 0.68 |
| 5_I | 86_F | 1.048 | 0.68 |
| 104_P | 129_N | 1.046 | 0.68 |
| 101_T | 154_W | 1.046 | 0.68 |
| 53_D | 107_C | 1.036 | 0.67 |
| 79_P | 83_A | 1.035 | 0.66 |
| 65_R | 133_V | 1.033 | 0.66 |
| 8_D | 11_G | 1.032 | 0.66 |
| 57_A | 60_E | 1.027 | 0.66 |
| 35_E | 38_Q | 1.023 | 0.65 |
| 10_V | 13_V | 1.019 | 0.65 |
| 87_T | 93_P | 1.018 | 0.65 |
| 8_D | 84_K | 1.010 | 0.64 |
| 10_V | 22_W | 1.010 | 0.64 |
| 14_F | 17_A | 1.007 | 0.63 |
| 52_L | 97_L | 1.005 | 0.63 |
| 95_A | 136_V | 1.004 | 0.63 |
| 19_A | 23_Q | 1.000 | 0.63 |
| 110_Q | 127_D | 1.000 | 0.63 |
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 | |
| 1b0nA | 1 | 0.6203 | 35 | 0.898 | Contact Map |
| 3qwgA | 2 | 0.4873 | 29.8 | 0.902 | Contact Map |
| 3op9A | 1 | 0.6392 | 29.1 | 0.902 | Contact Map |
| 3pxpA | 3 | 0.7089 | 27.4 | 0.904 | Contact Map |
| 4o8bA | 1 | 0.5823 | 18.4 | 0.911 | Contact Map |
| 4jcyA | 2 | 0.538 | 15.7 | 0.914 | Contact Map |
| 3r1fA | 18 | 0.6962 | 12.4 | 0.917 | Contact Map |
| 3fmyA | 1 | 0.3987 | 12 | 0.918 | Contact Map |
| 1neqA | 1 | 0.4684 | 11.2 | 0.919 | Contact Map |
| 1y7yA | 2 | 0.4177 | 11.1 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)