| 104l |
| ID: | 1427811678 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 164 (149) | ||
| Sequences: | 446 (332.9) | ||
| Seq/Len: | 2.993 | ||
| Nf(neff/√len): | 27.3 |
HHblits Results: (2013_03)
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: 2.993).
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 |
| 95_A | 99_A | 3.745 | 1.00 |
| 31_H | 72_D | 3.320 | 1.00 |
| 127_R | 130_E | 3.307 | 1.00 |
| 94_D | 97_R | 2.810 | 1.00 |
| 79_G | 110_E | 2.396 | 1.00 |
| 134_N | 137_K | 2.271 | 1.00 |
| 19_K | 25_Y | 2.123 | 1.00 |
| 31_H | 106_F | 2.041 | 1.00 |
| 24_Y | 32_L | 1.944 | 1.00 |
| 28_G | 65_A | 1.853 | 0.99 |
| 122_M | 134_N | 1.850 | 0.99 |
| 93_L | 123_L | 1.848 | 0.99 |
| 103_N | 150_R | 1.803 | 0.99 |
| 10_D | 145_P | 1.735 | 0.99 |
| 8_R | 29_I | 1.650 | 0.98 |
| 17_I | 58_G | 1.642 | 0.98 |
| 119_S | 134_N | 1.631 | 0.98 |
| 107_Q | 144_T | 1.620 | 0.98 |
| 29_I | 65_A | 1.619 | 0.98 |
| 29_I | 69_F | 1.615 | 0.97 |
| 27_I | 60_I | 1.594 | 0.97 |
| 122_M | 127_R | 1.578 | 0.97 |
| 13_L | 65_A | 1.570 | 0.97 |
| 145_P | 149_K | 1.542 | 0.96 |
| 72_D | 106_F | 1.518 | 0.96 |
| 119_S | 137_K | 1.493 | 0.95 |
| 122_M | 130_E | 1.464 | 0.95 |
| 15_L | 65_A | 1.424 | 0.94 |
| 60_I | 68_L | 1.418 | 0.94 |
| 127_R | 133_V | 1.414 | 0.93 |
| 21_T | 143_Q | 1.411 | 0.93 |
| 18_Y | 26_T | 1.401 | 0.93 |
| 17_I | 27_I | 1.388 | 0.93 |
| 31_H | 68_L | 1.385 | 0.93 |
| 10_D | 149_K | 1.370 | 0.92 |
| 119_S | 138_S | 1.346 | 0.91 |
| 15_L | 60_I | 1.335 | 0.91 |
| 20_D | 25_Y | 1.335 | 0.91 |
| 107_Q | 147_R | 1.310 | 0.89 |
| 15_L | 62_K | 1.280 | 0.88 |
| 60_I | 65_A | 1.270 | 0.87 |
| 78_R | 125_Q | 1.257 | 0.87 |
| 8_R | 66_E | 1.257 | 0.87 |
| 64_E | 68_L | 1.223 | 0.85 |
| 62_K | 65_A | 1.223 | 0.85 |
| 104_M | 116_F | 1.211 | 0.84 |
| 148_A | 152_I | 1.172 | 0.81 |
| 13_L | 29_I | 1.171 | 0.81 |
| 27_I | 68_L | 1.151 | 0.79 |
| 20_D | 23_G | 1.147 | 0.79 |
| 119_S | 122_M | 1.140 | 0.79 |
| 104_M | 108_M | 1.139 | 0.78 |
| 7_L | 29_I | 1.138 | 0.78 |
| 123_L | 131_A | 1.117 | 0.77 |
| 108_M | 138_S | 1.114 | 0.76 |
| 108_M | 116_F | 1.114 | 0.76 |
| 61_T | 64_E | 1.112 | 0.76 |
| 107_Q | 145_P | 1.108 | 0.76 |
| 6_M | 10_D | 1.102 | 0.75 |
| 77_V | 102_I | 1.079 | 0.73 |
| 133_V | 151_V | 1.077 | 0.73 |
| 16_K | 59_V | 1.076 | 0.73 |
| 33_L | 36_S | 1.071 | 0.72 |
| 116_F | 120_L | 1.069 | 0.72 |
| 132_A | 154_T | 1.066 | 0.72 |
| 107_Q | 150_R | 1.051 | 0.70 |
| 146_N | 150_R | 1.038 | 0.69 |
| 134_N | 138_S | 1.029 | 0.68 |
| 97_R | 104_M | 1.026 | 0.67 |
| 62_K | 66_E | 1.022 | 0.67 |
| 28_G | 72_D | 1.003 | 0.65 |
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 | |
| 2qb0B | 2 | 0.9878 | 100 | 0.199 | Contact Map |
| 4epiA | 1 | 0.9878 | 100 | 0.215 | Contact Map |
| 1swyA | 1 | 0.9878 | 100 | 0.217 | Contact Map |
| 4plaA | 1 | 0.9878 | 100 | 0.218 | Contact Map |
| 4e97A | 2 | 0.9878 | 100 | 0.219 | Contact Map |
| 1wthA | 1 | 0.9878 | 100 | 0.221 | Contact Map |
| 4httA | 2 | 0 | 100 | 0.235 | Contact Map |
| 4tn3A | 2 | 0.9878 | 100 | 0.242 | Contact Map |
| 4iapA | 2 | 0.9878 | 100 | 0.28 | Contact Map |
| 4ldeA | 1 | 0.9878 | 100 | 0.289 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)