| Vans1 |
| ID: | 1420470975 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 232 (222) | ||
| Sequences: | 7466 (6164.9) | ||
| Seq/Len: | 33.631 | ||
| Nf(neff/√len): | 413.8 |
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: 33.631).
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 |
| 83_G | 87_E | 3.999 | 1.00 |
| 188_R | 212_L | 3.017 | 1.00 |
| 179_R | 184_D | 2.934 | 1.00 |
| 188_R | 209_Q | 2.838 | 1.00 |
| 180_M | 208_Y | 2.808 | 1.00 |
| 180_M | 207_L | 2.561 | 1.00 |
| 7_F | 164_R | 2.538 | 1.00 |
| 195_D | 198_G | 2.520 | 1.00 |
| 174_K | 199_N | 2.338 | 1.00 |
| 188_R | 205_N | 2.336 | 1.00 |
| 5_G | 8_A | 2.302 | 1.00 |
| 80_T | 125_Q | 2.270 | 1.00 |
| 177_T | 204_I | 2.217 | 1.00 |
| 177_T | 203_Q | 2.165 | 1.00 |
| 193_S | 198_G | 2.107 | 1.00 |
| 82_K | 88_D | 2.054 | 1.00 |
| 138_Q | 142_Q | 2.047 | 1.00 |
| 27_L | 31_F | 2.025 | 1.00 |
| 191_V | 202_E | 2.017 | 1.00 |
| 190_R | 205_N | 2.002 | 1.00 |
| 186_Q | 212_L | 1.968 | 1.00 |
| 211_L | 214_V | 1.964 | 1.00 |
| 194_K | 198_G | 1.955 | 1.00 |
| 173_I | 201_K | 1.937 | 1.00 |
| 159_A | 163_A | 1.924 | 1.00 |
| 178_R | 199_N | 1.919 | 1.00 |
| 174_K | 203_Q | 1.839 | 1.00 |
| 189_L | 205_N | 1.833 | 1.00 |
| 30_Y | 141_L | 1.768 | 1.00 |
| 179_R | 187_V | 1.759 | 1.00 |
| 170_I | 200_L | 1.748 | 1.00 |
| 163_A | 167_V | 1.711 | 1.00 |
| 9_K | 195_D | 1.698 | 1.00 |
| 165_T | 168_A | 1.677 | 1.00 |
| 212_L | 216_A | 1.615 | 1.00 |
| 171_L | 174_K | 1.600 | 1.00 |
| 177_T | 200_L | 1.599 | 1.00 |
| 133_Q | 136_A | 1.579 | 1.00 |
| 156_L | 160_Y | 1.556 | 1.00 |
| 204_I | 207_L | 1.550 | 1.00 |
| 188_R | 208_Y | 1.537 | 1.00 |
| 4_T | 8_A | 1.531 | 1.00 |
| 49_A | 53_A | 1.470 | 1.00 |
| 180_M | 188_R | 1.431 | 1.00 |
| 184_D | 187_V | 1.424 | 1.00 |
| 83_G | 89_K | 1.421 | 1.00 |
| 82_K | 125_Q | 1.419 | 1.00 |
| 110_E | 113_E | 1.390 | 0.99 |
| 173_I | 189_L | 1.383 | 0.99 |
| 160_Y | 164_R | 1.363 | 0.99 |
| 170_I | 197_I | 1.358 | 0.99 |
| 7_F | 11_F | 1.358 | 0.99 |
| 177_T | 181_M | 1.311 | 0.99 |
| 177_T | 180_M | 1.298 | 0.99 |
| 201_K | 205_N | 1.280 | 0.99 |
| 161_I | 165_T | 1.266 | 0.99 |
| 164_R | 171_L | 1.265 | 0.99 |
| 178_R | 206_S | 1.259 | 0.99 |
| 189_L | 201_K | 1.244 | 0.98 |
| 36_T | 40_H | 1.216 | 0.98 |
| 205_N | 208_Y | 1.209 | 0.98 |
| 44_T | 128_A | 1.206 | 0.98 |
| 163_A | 166_I | 1.203 | 0.98 |
| 141_L | 144_L | 1.203 | 0.98 |
| 168_A | 171_L | 1.199 | 0.98 |
| 142_Q | 146_Y | 1.197 | 0.98 |
| 185_S | 211_L | 1.195 | 0.98 |
| 176_V | 189_L | 1.179 | 0.98 |
| 207_L | 211_L | 1.179 | 0.98 |
| 174_K | 178_R | 1.165 | 0.97 |
| 221_K | 224_A | 1.163 | 0.97 |
| 34_P | 38_L | 1.162 | 0.97 |
| 173_I | 204_I | 1.162 | 0.97 |
| 209_Q | 213_T | 1.161 | 0.97 |
| 14_T | 163_A | 1.161 | 0.97 |
| 81_V | 124_L | 1.148 | 0.97 |
| 22_V | 26_H | 1.147 | 0.97 |
| 80_T | 88_D | 1.143 | 0.97 |
| 6_L | 197_I | 1.136 | 0.97 |
| 41_R | 133_Q | 1.134 | 0.97 |
| 46_G | 50_T | 1.132 | 0.97 |
| 10_I | 14_T | 1.131 | 0.97 |
| 149_L | 153_L | 1.125 | 0.97 |
| 141_L | 145_P | 1.123 | 0.97 |
| 111_E | 125_Q | 1.123 | 0.97 |
| 82_K | 123_I | 1.121 | 0.97 |
| 171_L | 199_N | 1.119 | 0.96 |
| 181_M | 206_S | 1.109 | 0.96 |
| 38_L | 42_Q | 1.106 | 0.96 |
| 176_V | 187_V | 1.105 | 0.96 |
| 191_V | 198_G | 1.102 | 0.96 |
| 11_F | 15_F | 1.101 | 0.96 |
| 106_S | 109_I | 1.091 | 0.96 |
| 42_Q | 108_F | 1.076 | 0.95 |
| 88_D | 92_V | 1.070 | 0.95 |
| 171_L | 175_R | 1.068 | 0.95 |
| 43_E | 46_G | 1.063 | 0.95 |
| 208_Y | 212_L | 1.058 | 0.95 |
| 174_K | 177_T | 1.056 | 0.95 |
| 172_E | 190_R | 1.050 | 0.94 |
| 181_M | 210_H | 1.049 | 0.94 |
| 164_R | 168_A | 1.047 | 0.94 |
| 155_S | 159_A | 1.037 | 0.94 |
| 14_T | 159_A | 1.034 | 0.94 |
| 185_S | 208_Y | 1.019 | 0.93 |
| 145_P | 149_L | 1.017 | 0.93 |
| 138_Q | 141_L | 1.014 | 0.93 |
| 37_Y | 41_R | 1.006 | 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 | |
| 4cq4A | 4 | 0.3879 | 99.5 | 0.536 | Contact Map |
| 2f95B | 1 | 0.2284 | 99.3 | 0.588 | Contact Map |
| 4i5sA | 2 | 0.3276 | 99.2 | 0.609 | Contact Map |
| 4gycB | 1 | 0.2629 | 98.9 | 0.656 | Contact Map |
| 4i3mA | 1 | 0.3017 | 98.7 | 0.672 | Contact Map |
| 2kseA | 1 | 0.3147 | 98.7 | 0.676 | Contact Map |
| 3zx6A | 2 | 0.2974 | 98.4 | 0.705 | Contact Map |
| 3zccA | 2 | 0.2888 | 98.3 | 0.711 | Contact Map |
| 4bixA | 2 | 0.1466 | 98.1 | 0.725 | Contact Map |
| 4ctiA | 4 | 0.2845 | 97.6 | 0.757 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)