| DHFR |
| ID: | 1517327157 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 187 (180) | ||
| Sequences: | 1486 (1112.3) | ||
| Seq/Len: | 8.256 | ||
| Nf(neff/√len): | 82.9 |
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: 8.256).
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_G | 145_S | 4.233 | 1.00 |
| 40_T | 70_G | 3.614 | 1.00 |
| 13_Q | 140_M | 3.209 | 1.00 |
| 55_K | 59_F | 2.886 | 1.00 |
| 76_L | 121_V | 2.727 | 1.00 |
| 50_L | 72_I | 2.680 | 1.00 |
| 34_Y | 38_M | 2.595 | 1.00 |
| 94_L | 125_A | 2.354 | 1.00 |
| 9_V | 136_V | 2.300 | 1.00 |
| 34_Y | 182_V | 2.270 | 1.00 |
| 12_S | 16_G | 2.228 | 1.00 |
| 159_L | 181_E | 2.209 | 1.00 |
| 93_S | 96_D | 2.118 | 1.00 |
| 138_R | 181_E | 2.117 | 1.00 |
| 51_V | 73_N | 2.107 | 1.00 |
| 33_R | 37_R | 2.041 | 1.00 |
| 119_S | 123_K | 2.016 | 1.00 |
| 7_C | 131_H | 2.012 | 1.00 |
| 34_Y | 135_F | 1.923 | 1.00 |
| 6_N | 135_F | 1.900 | 1.00 |
| 97_A | 125_A | 1.880 | 1.00 |
| 134_L | 152_I | 1.844 | 1.00 |
| 49_N | 114_W | 1.800 | 1.00 |
| 16_G | 148_F | 1.764 | 1.00 |
| 11_V | 15_M | 1.763 | 1.00 |
| 6_N | 112_M | 1.738 | 1.00 |
| 68_L | 71_R | 1.698 | 1.00 |
| 72_I | 88_H | 1.662 | 1.00 |
| 59_F | 82_E | 1.662 | 1.00 |
| 133_K | 184_E | 1.657 | 1.00 |
| 78_R | 120_S | 1.625 | 1.00 |
| 133_K | 182_V | 1.605 | 1.00 |
| 67_P | 73_N | 1.600 | 1.00 |
| 39_T | 71_R | 1.594 | 1.00 |
| 19_K | 144_E | 1.593 | 1.00 |
| 36_Q | 40_T | 1.571 | 1.00 |
| 35_F | 116_V | 1.567 | 1.00 |
| 53_M | 116_V | 1.559 | 1.00 |
| 6_N | 133_K | 1.523 | 1.00 |
| 115_I | 125_A | 1.495 | 1.00 |
| 120_S | 123_K | 1.467 | 0.99 |
| 160_L | 184_E | 1.466 | 0.99 |
| 14_N | 142_D | 1.460 | 0.99 |
| 52_I | 113_V | 1.459 | 0.99 |
| 24_P | 145_S | 1.451 | 0.99 |
| 77_S | 92_R | 1.451 | 0.99 |
| 29_R | 33_R | 1.430 | 0.99 |
| 91_S | 97_A | 1.415 | 0.99 |
| 6_N | 114_W | 1.404 | 0.99 |
| 119_S | 147_T | 1.394 | 0.99 |
| 38_M | 135_F | 1.393 | 0.99 |
| 56_K | 59_F | 1.382 | 0.99 |
| 52_I | 97_A | 1.345 | 0.99 |
| 9_V | 149_F | 1.342 | 0.99 |
| 12_S | 143_F | 1.336 | 0.99 |
| 52_I | 74_L | 1.324 | 0.99 |
| 49_N | 112_M | 1.320 | 0.99 |
| 159_L | 162_E | 1.300 | 0.98 |
| 53_M | 61_I | 1.299 | 0.98 |
| 30_N | 178_Y | 1.294 | 0.98 |
| 61_I | 73_N | 1.279 | 0.98 |
| 158_K | 186_N | 1.265 | 0.98 |
| 11_V | 138_R | 1.255 | 0.98 |
| 136_V | 183_Y | 1.251 | 0.98 |
| 120_S | 124_E | 1.235 | 0.98 |
| 135_F | 182_V | 1.226 | 0.97 |
| 8_I | 114_W | 1.218 | 0.97 |
| 23_L | 32_F | 1.198 | 0.97 |
| 34_Y | 114_W | 1.190 | 0.97 |
| 92_R | 96_D | 1.187 | 0.97 |
| 76_L | 125_A | 1.182 | 0.97 |
| 114_W | 135_F | 1.180 | 0.97 |
| 13_Q | 142_D | 1.174 | 0.96 |
| 94_L | 124_E | 1.159 | 0.96 |
| 73_N | 116_V | 1.148 | 0.96 |
| 77_S | 90_L | 1.144 | 0.96 |
| 158_K | 184_E | 1.133 | 0.95 |
| 140_M | 179_K | 1.123 | 0.95 |
| 121_V | 124_E | 1.122 | 0.95 |
| 58_W | 65_N | 1.118 | 0.95 |
| 51_V | 116_V | 1.112 | 0.95 |
| 11_V | 149_F | 1.111 | 0.95 |
| 7_C | 122_Y | 1.098 | 0.94 |
| 31_E | 34_Y | 1.092 | 0.94 |
| 76_L | 97_A | 1.086 | 0.94 |
| 31_E | 180_F | 1.077 | 0.93 |
| 53_M | 60_S | 1.067 | 0.93 |
| 62_P | 65_N | 1.058 | 0.93 |
| 49_N | 111_D | 1.054 | 0.92 |
| 21_G | 147_T | 1.035 | 0.92 |
| 32_F | 73_N | 1.034 | 0.91 |
| 35_F | 71_R | 1.030 | 0.91 |
| 32_F | 60_S | 1.030 | 0.91 |
| 29_R | 173_E | 1.014 | 0.90 |
| 112_M | 133_K | 1.007 | 0.90 |
| 135_F | 180_F | 1.006 | 0.90 |
| 34_Y | 180_F | 1.005 | 0.90 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4eilA | 8 | 0.9465 | 100 | 0.224 | Contact Map |
| 2bl9A | 1 | 0.9358 | 100 | 0.235 | Contact Map |
| 3irmA | 4 | 0.9733 | 100 | 0.237 | Contact Map |
| 1j3kA | 2 | 0.9519 | 100 | 0.241 | Contact Map |
| 3rg9A | 2 | 0.984 | 100 | 0.255 | Contact Map |
| 3qg2A | 2 | 0.9465 | 100 | 0.284 | Contact Map |
| 3cseA | 2 | 0.9733 | 100 | 0.305 | Contact Map |
| 1kmvA | 1 | 0.984 | 100 | 0.306 | Contact Map |
| 3nzbX | 1 | 0.9947 | 100 | 0.306 | Contact Map |
| 3ia4A | 4 | 0.861 | 100 | 0.312 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)