| Sin3A |
| ID: | 1494876200 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (142) | ||
| Sequences: | 471 (297.8) | ||
| Seq/Len: | 3.317 | ||
| Nf(neff/√len): | 25.0 |
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: 3.317).
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 |
| 16_K | 19_E | 2.242 | 1.00 |
| 5_A | 9_V | 2.114 | 1.00 |
| 110_H | 113_K | 2.064 | 1.00 |
| 1_N | 6_V | 1.965 | 1.00 |
| 106_A | 127_K | 1.841 | 0.99 |
| 46_Q | 68_E | 1.747 | 0.99 |
| 24_Q | 29_K | 1.683 | 0.99 |
| 74_R | 90_H | 1.578 | 0.98 |
| 35_N | 38_Y | 1.569 | 0.97 |
| 34_Q | 38_Y | 1.550 | 0.97 |
| 17_E | 21_R | 1.532 | 0.97 |
| 10_L | 14_K | 1.529 | 0.97 |
| 61_K | 95_Y | 1.492 | 0.96 |
| 129_I | 133_F | 1.483 | 0.96 |
| 81_D | 84_G | 1.480 | 0.96 |
| 11_K | 17_E | 1.463 | 0.96 |
| 66_E | 124_Y | 1.453 | 0.96 |
| 27_F | 55_T | 1.419 | 0.95 |
| 15_M | 45_H | 1.413 | 0.95 |
| 91_L | 100_I | 1.406 | 0.94 |
| 17_E | 28_N | 1.401 | 0.94 |
| 20_W | 31_W | 1.390 | 0.94 |
| 7_P | 12_R | 1.370 | 0.93 |
| 50_F | 59_R | 1.352 | 0.93 |
| 122_D | 131_H | 1.350 | 0.93 |
| 36_E | 57_V | 1.338 | 0.92 |
| 18_E | 41_K | 1.291 | 0.90 |
| 15_M | 19_E | 1.284 | 0.90 |
| 50_F | 56_K | 1.256 | 0.89 |
| 64_L | 106_A | 1.246 | 0.88 |
| 97_D | 103_D | 1.238 | 0.88 |
| 88_G | 137_L | 1.236 | 0.87 |
| 37_K | 125_K | 1.226 | 0.87 |
| 12_R | 45_H | 1.201 | 0.85 |
| 52_Q | 126_I | 1.200 | 0.85 |
| 33_E | 37_K | 1.190 | 0.85 |
| 18_E | 54_D | 1.158 | 0.82 |
| 46_Q | 69_S | 1.136 | 0.81 |
| 68_E | 111_H | 1.131 | 0.80 |
| 42_S | 45_H | 1.128 | 0.80 |
| 38_Y | 50_F | 1.128 | 0.80 |
| 78_A | 85_V | 1.125 | 0.80 |
| 14_K | 18_E | 1.119 | 0.79 |
| 62_S | 95_Y | 1.108 | 0.78 |
| 90_H | 97_D | 1.107 | 0.78 |
| 9_V | 13_L | 1.106 | 0.78 |
| 66_E | 117_G | 1.103 | 0.78 |
| 14_K | 27_F | 1.092 | 0.77 |
| 3_S | 77_Q | 1.090 | 0.77 |
| 93_L | 97_D | 1.087 | 0.77 |
| 34_Q | 40_L | 1.078 | 0.76 |
| 25_R | 30_V | 1.072 | 0.75 |
| 39_Y | 113_K | 1.068 | 0.75 |
| 16_K | 20_W | 1.051 | 0.73 |
| 3_S | 76_E | 1.046 | 0.73 |
| 42_S | 136_D | 1.041 | 0.72 |
| 86_P | 100_I | 1.038 | 0.72 |
| 40_L | 47_G | 1.027 | 0.71 |
| 73_E | 137_L | 1.027 | 0.71 |
| 50_F | 58_L | 1.024 | 0.70 |
| 32_R | 37_K | 1.021 | 0.70 |
| 37_K | 88_G | 1.020 | 0.70 |
| 72_D | 125_K | 1.019 | 0.70 |
| 37_K | 66_E | 1.017 | 0.70 |
| 24_Q | 32_R | 1.017 | 0.70 |
| 75_Q | 106_A | 1.009 | 0.69 |
| 41_K | 44_D | 1.007 | 0.68 |
| 114_R | 135_P | 1.005 | 0.68 |
| 86_P | 92_S | 1.005 | 0.68 |
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 | |
| 2n2hB | 1 | 0 | 99.7 | 0.622 | Contact Map |
| 1fsuA | 1 | 0.3357 | 7.8 | 0.95 | Contact Map |
| 2ve7C | 2 | 0.3706 | 6.5 | 0.952 | Contact Map |
| 2zy9A | 2 | 0.3287 | 5.3 | 0.954 | Contact Map |
| 4wlpB | 1 | 0.3077 | 5.1 | 0.954 | Contact Map |
| 4d6kA | 6 | 0.3147 | 5.1 | 0.954 | Contact Map |
| 3mstA | 1 | 0.3986 | 5 | 0.954 | Contact Map |
| 4bjsA | 3 | 0.3846 | 4.4 | 0.955 | Contact Map |
| 2p90A | 3 | 0.3706 | 4.2 | 0.956 | Contact Map |
| 3mb2A | 6 | 0.2587 | 4.1 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)