| SMARCC2_500_900 65-200 |
| ID: | 1490395851 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (132) | ||
| Sequences: | 301 (176.7) | ||
| Seq/Len: | 2.280 | ||
| Nf(neff/√len): | 15.4 |
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: 2.280).
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 |
| 42_T | 74_H | 1.988 | 0.99 |
| 122_P | 126_S | 1.811 | 0.98 |
| 93_G | 97_Y | 1.753 | 0.98 |
| 14_R | 17_M | 1.654 | 0.96 |
| 79_P | 132_A | 1.645 | 0.96 |
| 48_A | 62_H | 1.615 | 0.96 |
| 125_A | 132_A | 1.590 | 0.95 |
| 43_L | 46_L | 1.547 | 0.94 |
| 124_V | 127_A | 1.485 | 0.92 |
| 126_S | 129_A | 1.471 | 0.92 |
| 55_D | 58_K | 1.442 | 0.91 |
| 101_P | 108_P | 1.368 | 0.88 |
| 53_K | 66_R | 1.360 | 0.87 |
| 79_P | 114_A | 1.355 | 0.87 |
| 128_A | 132_A | 1.352 | 0.87 |
| 101_P | 124_V | 1.331 | 0.86 |
| 51_M | 84_Y | 1.310 | 0.84 |
| 114_A | 132_A | 1.309 | 0.84 |
| 58_K | 70_E | 1.307 | 0.84 |
| 40_Q | 47_E | 1.297 | 0.84 |
| 67_T | 103_S | 1.283 | 0.83 |
| 75_F | 107_N | 1.278 | 0.82 |
| 24_P | 27_S | 1.240 | 0.80 |
| 46_L | 113_V | 1.240 | 0.80 |
| 125_A | 129_A | 1.239 | 0.80 |
| 40_Q | 44_L | 1.232 | 0.79 |
| 36_E | 66_R | 1.227 | 0.79 |
| 38_T | 41_E | 1.217 | 0.78 |
| 39_E | 110_M | 1.215 | 0.78 |
| 92_L | 97_Y | 1.211 | 0.77 |
| 44_L | 57_N | 1.211 | 0.77 |
| 54_D | 131_S | 1.199 | 0.76 |
| 99_P | 112_T | 1.192 | 0.76 |
| 73_L | 77_R | 1.188 | 0.75 |
| 39_E | 43_L | 1.187 | 0.75 |
| 23_V | 28_K | 1.182 | 0.75 |
| 72_I | 79_P | 1.181 | 0.75 |
| 13_L | 16_D | 1.179 | 0.75 |
| 8_M | 22_N | 1.174 | 0.74 |
| 18_Y | 67_T | 1.156 | 0.73 |
| 44_L | 47_E | 1.151 | 0.72 |
| 107_N | 115_F | 1.149 | 0.72 |
| 17_M | 23_V | 1.146 | 0.72 |
| 59_V | 130_K | 1.137 | 0.71 |
| 64_G | 116_L | 1.136 | 0.71 |
| 107_N | 111_S | 1.132 | 0.70 |
| 47_E | 62_H | 1.124 | 0.70 |
| 34_T | 131_S | 1.120 | 0.69 |
| 22_N | 25_S | 1.119 | 0.69 |
| 59_V | 113_V | 1.117 | 0.69 |
| 41_E | 65_S | 1.117 | 0.69 |
| 109_V | 115_F | 1.114 | 0.69 |
| 5_P | 22_N | 1.107 | 0.68 |
| 74_H | 93_G | 1.095 | 0.67 |
| 9_Q | 20_K | 1.070 | 0.64 |
| 48_A | 89_E | 1.065 | 0.63 |
| 67_T | 134_E | 1.064 | 0.63 |
| 41_E | 45_L | 1.059 | 0.63 |
| 13_L | 18_Y | 1.044 | 0.61 |
| 67_T | 121_D | 1.036 | 0.60 |
| 53_K | 112_T | 1.034 | 0.60 |
| 111_S | 115_F | 1.032 | 0.60 |
| 44_L | 62_H | 1.030 | 0.60 |
| 104_Q | 112_T | 1.018 | 0.58 |
| 6_T | 9_Q | 1.017 | 0.58 |
| 35_R | 70_E | 1.010 | 0.57 |
| 10_N | 18_Y | 1.009 | 0.57 |
| 20_K | 25_S | 1.006 | 0.57 |
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 | |
| 3zn0B | 1 | 0.6397 | 99.2 | 0.728 | Contact Map |
| 2yusA | 1 | 0.5809 | 99.1 | 0.738 | Contact Map |
| 2elkA | 1 | 0.4118 | 98.8 | 0.771 | Contact Map |
| 4czzB | 1 | 0.6471 | 98.6 | 0.78 | Contact Map |
| 1x41A | 1 | 0.4338 | 98.6 | 0.782 | Contact Map |
| 2cqrA | 1 | 0.5074 | 98.5 | 0.79 | Contact Map |
| 2cqqA | 1 | 0.5 | 98.5 | 0.79 | Contact Map |
| 2iw5B | 1 | 0.6544 | 98.5 | 0.79 | Contact Map |
| 2yqkA | 1 | 0.4559 | 98.5 | 0.791 | Contact Map |
| 4a69C | 2 | 0.4779 | 98.4 | 0.793 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)