| SrtA_sa |
| ID: | 1402323133 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (199) | ||
| Sequences: | 3064 (2695.1) | ||
| Seq/Len: | 15.397 | ||
| Nf(neff/√len): | 191.1 |
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: 15.397).
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 |
| 132_N | 135_A | 3.426 | 1.00 |
| 114_N | 180_T | 3.353 | 1.00 |
| 179_L | 202_A | 3.123 | 1.00 |
| 156_T | 203_T | 2.870 | 1.00 |
| 75_Y | 84_K | 2.607 | 1.00 |
| 74_G | 87_V | 2.573 | 1.00 |
| 101_V | 117_I | 2.528 | 1.00 |
| 141_M | 152_K | 2.480 | 1.00 |
| 142_V | 202_A | 2.392 | 1.00 |
| 79_P | 143_Y | 2.365 | 1.00 |
| 142_V | 179_L | 2.331 | 1.00 |
| 95_E | 99_R | 2.271 | 1.00 |
| 144_F | 179_L | 2.116 | 1.00 |
| 154_K | 203_T | 2.111 | 1.00 |
| 80_D | 140_S | 2.105 | 1.00 |
| 178_Q | 201_V | 2.075 | 1.00 |
| 101_V | 119_G | 2.070 | 1.00 |
| 77_E | 145_K | 2.006 | 1.00 |
| 121_T | 134_K | 1.983 | 1.00 |
| 77_E | 84_K | 1.871 | 1.00 |
| 74_G | 144_F | 1.867 | 1.00 |
| 115_I | 179_L | 1.863 | 1.00 |
| 157_S | 201_V | 1.848 | 1.00 |
| 80_D | 136_A | 1.832 | 1.00 |
| 141_M | 154_K | 1.824 | 1.00 |
| 159_R | 201_V | 1.800 | 1.00 |
| 96_Q | 102_S | 1.733 | 1.00 |
| 156_T | 178_Q | 1.693 | 1.00 |
| 158_I | 198_K | 1.661 | 1.00 |
| 87_V | 144_F | 1.653 | 1.00 |
| 159_R | 168_V | 1.634 | 1.00 |
| 77_E | 143_Y | 1.631 | 1.00 |
| 130_F | 181_L | 1.627 | 1.00 |
| 175_K | 203_T | 1.616 | 1.00 |
| 78_I | 81_A | 1.611 | 1.00 |
| 92_A | 96_Q | 1.605 | 1.00 |
| 155_M | 200_F | 1.601 | 1.00 |
| 120_H | 184_C | 1.579 | 1.00 |
| 143_Y | 152_K | 1.566 | 1.00 |
| 20_A | 24_F | 1.559 | 1.00 |
| 88_Y | 96_Q | 1.554 | 1.00 |
| 89_P | 103_F | 1.519 | 1.00 |
| 136_A | 155_M | 1.502 | 1.00 |
| 91_P | 105_E | 1.499 | 1.00 |
| 85_E | 129_Q | 1.479 | 1.00 |
| 125_R | 128_Y | 1.474 | 1.00 |
| 76_I | 142_V | 1.457 | 1.00 |
| 151_R | 204_E | 1.448 | 1.00 |
| 180_T | 201_V | 1.416 | 1.00 |
| 133_L | 136_A | 1.414 | 1.00 |
| 128_Y | 132_N | 1.382 | 0.99 |
| 108_E | 112_D | 1.374 | 0.99 |
| 162_K | 196_K | 1.370 | 0.99 |
| 103_F | 107_N | 1.347 | 0.99 |
| 108_E | 171_E | 1.300 | 0.99 |
| 81_A | 132_N | 1.260 | 0.99 |
| 156_T | 201_V | 1.254 | 0.99 |
| 146_V | 149_E | 1.251 | 0.99 |
| 81_A | 136_A | 1.247 | 0.99 |
| 73_A | 89_P | 1.214 | 0.98 |
| 115_I | 144_F | 1.207 | 0.98 |
| 133_L | 198_K | 1.200 | 0.98 |
| 172_Q | 178_Q | 1.197 | 0.98 |
| 114_N | 201_V | 1.195 | 0.98 |
| 22_Y | 26_K | 1.182 | 0.98 |
| 13_G | 17_I | 1.168 | 0.97 |
| 116_S | 182_I | 1.165 | 0.97 |
| 36_K | 40_E | 1.165 | 0.97 |
| 185_D | 196_K | 1.155 | 0.97 |
| 24_F | 28_H | 1.154 | 0.97 |
| 136_A | 140_S | 1.146 | 0.97 |
| 145_K | 150_T | 1.144 | 0.97 |
| 28_H | 31_N | 1.134 | 0.97 |
| 80_D | 137_K | 1.132 | 0.97 |
| 141_M | 205_V | 1.131 | 0.97 |
| 121_T | 131_T | 1.114 | 0.96 |
| 154_K | 205_V | 1.114 | 0.96 |
| 97_L | 100_G | 1.103 | 0.96 |
| 182_I | 199_I | 1.100 | 0.96 |
| 61_A | 64_Q | 1.099 | 0.96 |
| 191_T | 196_K | 1.091 | 0.96 |
| 38_K | 41_K | 1.088 | 0.96 |
| 160_D | 185_D | 1.087 | 0.96 |
| 102_S | 117_I | 1.082 | 0.96 |
| 61_A | 65_I | 1.075 | 0.95 |
| 86_P | 101_V | 1.052 | 0.95 |
| 100_G | 103_F | 1.048 | 0.94 |
| 143_Y | 150_T | 1.045 | 0.94 |
| 78_I | 83_I | 1.044 | 0.94 |
| 175_K | 178_Q | 1.036 | 0.94 |
| 188_N | 191_T | 1.035 | 0.94 |
| 32_Y | 36_K | 1.034 | 0.94 |
| 94_P | 98_N | 1.032 | 0.94 |
| 133_L | 200_F | 1.024 | 0.93 |
| 186_D | 190_K | 1.023 | 0.93 |
| 104_A | 115_I | 1.022 | 0.93 |
| 183_T | 198_K | 1.015 | 0.93 |
| 161_V | 182_I | 1.010 | 0.93 |
| 153_Y | 202_A | 1.005 | 0.93 |
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 | |
| 1rz2A | 1 | 0.7961 | 100 | 0.241 | Contact Map |
| 2xwgA | 5 | 0.7233 | 100 | 0.273 | Contact Map |
| 1t2wA | 3 | 0.7039 | 100 | 0.315 | Contact Map |
| 3fn5A | 2 | 0.6553 | 100 | 0.34 | Contact Map |
| 3rccA | 18 | 0.6165 | 100 | 0.343 | Contact Map |
| 2kw8A | 1 | 0.7282 | 100 | 0.344 | Contact Map |
| 2w1jA | 2 | 0.8398 | 100 | 0.349 | Contact Map |
| 2w1kA | 2 | 0.8641 | 100 | 0.349 | Contact Map |
| 3g66A | 2 | 0.835 | 100 | 0.35 | Contact Map |
| 4g1hA | 1 | 0.7767 | 100 | 0.35 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)