| 5P21 |
| ID: | 1447750557 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (163) | ||
| Sequences: | 39845 (22424.6) | ||
| Seq/Len: | 244.448 | ||
| Nf(neff/√len): | 1756.4 |
HHblits Results: (2015_06)
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: 244.448).
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 |
| 22_Q | 149_R | 3.208 | 1.00 |
| 142_I | 158_T | 3.159 | 1.00 |
| 84_I | 115_G | 2.651 | 1.00 |
| 11_A | 92_D | 2.572 | 1.00 |
| 140_P | 158_T | 2.461 | 1.00 |
| 79_L | 114_V | 2.459 | 1.00 |
| 158_T | 161_R | 2.392 | 1.00 |
| 114_V | 144_T | 2.284 | 1.00 |
| 114_V | 155_A | 2.268 | 1.00 |
| 158_T | 162_E | 2.235 | 1.00 |
| 81_V | 116_N | 2.185 | 1.00 |
| 19_L | 81_V | 2.094 | 1.00 |
| 118_C | 143_E | 2.035 | 1.00 |
| 115_G | 143_E | 1.955 | 1.00 |
| 5_K | 54_D | 1.820 | 1.00 |
| 18_A | 146_A | 1.762 | 1.00 |
| 118_C | 150_Q | 1.722 | 1.00 |
| 7_V | 75_G | 1.683 | 1.00 |
| 151_G | 154_D | 1.671 | 1.00 |
| 77_G | 159_L | 1.664 | 1.00 |
| 8_V | 20_T | 1.659 | 1.00 |
| 53_L | 160_V | 1.658 | 1.00 |
| 41_R | 54_D | 1.633 | 1.00 |
| 79_L | 159_L | 1.617 | 1.00 |
| 22_Q | 152_V | 1.604 | 1.00 |
| 84_I | 118_C | 1.599 | 1.00 |
| 97_R | 111_M | 1.581 | 1.00 |
| 19_L | 155_A | 1.536 | 1.00 |
| 4_Y | 163_I | 1.531 | 1.00 |
| 112_V | 142_I | 1.526 | 1.00 |
| 80_C | 97_R | 1.520 | 1.00 |
| 131_Q | 135_R | 1.507 | 1.00 |
| 82_F | 141_Y | 1.506 | 1.00 |
| 116_N | 146_A | 1.504 | 1.00 |
| 82_F | 115_G | 1.497 | 1.00 |
| 119_D | 145_S | 1.493 | 1.00 |
| 3_E | 54_D | 1.492 | 1.00 |
| 97_R | 101_K | 1.472 | 1.00 |
| 112_V | 158_T | 1.467 | 1.00 |
| 144_T | 155_A | 1.459 | 1.00 |
| 115_G | 141_Y | 1.453 | 1.00 |
| 82_F | 113_L | 1.430 | 1.00 |
| 87_T | 129_Q | 1.394 | 0.99 |
| 19_L | 152_V | 1.386 | 0.99 |
| 85_N | 120_L | 1.374 | 0.99 |
| 8_V | 79_L | 1.360 | 0.99 |
| 132_D | 136_S | 1.314 | 0.99 |
| 77_G | 112_V | 1.314 | 0.99 |
| 127_S | 131_Q | 1.295 | 0.99 |
| 79_L | 112_V | 1.291 | 0.99 |
| 130_A | 134_A | 1.273 | 0.99 |
| 154_D | 157_Y | 1.252 | 0.99 |
| 80_C | 93_I | 1.245 | 0.98 |
| 43_Q | 52_L | 1.239 | 0.98 |
| 83_A | 117_K | 1.234 | 0.98 |
| 140_P | 162_E | 1.224 | 0.98 |
| 6_L | 77_G | 1.219 | 0.98 |
| 45_V | 50_T | 1.215 | 0.98 |
| 79_L | 155_A | 1.214 | 0.98 |
| 3_E | 52_L | 1.189 | 0.98 |
| 83_A | 86_N | 1.174 | 0.98 |
| 69_D | 99_Q | 1.162 | 0.97 |
| 86_N | 89_S | 1.157 | 0.97 |
| 126_E | 129_Q | 1.150 | 0.97 |
| 130_A | 143_E | 1.147 | 0.97 |
| 133_L | 137_Y | 1.145 | 0.97 |
| 152_V | 156_F | 1.143 | 0.97 |
| 21_I | 29_V | 1.142 | 0.97 |
| 68_R | 72_M | 1.134 | 0.97 |
| 117_K | 120_L | 1.133 | 0.97 |
| 98_E | 102_R | 1.123 | 0.97 |
| 154_D | 158_T | 1.121 | 0.97 |
| 39_S | 56_L | 1.119 | 0.96 |
| 110_P | 162_E | 1.100 | 0.96 |
| 153_E | 157_Y | 1.085 | 0.96 |
| 43_Q | 54_D | 1.074 | 0.95 |
| 5_K | 56_L | 1.068 | 0.95 |
| 113_L | 141_Y | 1.061 | 0.95 |
| 157_Y | 161_R | 1.059 | 0.95 |
| 77_G | 163_I | 1.052 | 0.95 |
| 11_A | 14_V | 1.043 | 0.94 |
| 88_K | 91_E | 1.040 | 0.94 |
| 21_I | 25_Q | 1.034 | 0.94 |
| 23_L | 156_F | 1.033 | 0.94 |
| 19_L | 146_A | 1.026 | 0.94 |
| 51_C | 160_V | 1.005 | 0.93 |
| 144_T | 152_V | 1.002 | 0.92 |
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 | |
| 2ce2X | 1 | 1 | 100 | 0.064 | Contact Map |
| 3conA | 1 | 0.9337 | 100 | 0.069 | Contact Map |
| 1u8zA | 2 | 0.9819 | 100 | 0.078 | Contact Map |
| 1m7bA | 1 | 0.9819 | 100 | 0.078 | Contact Map |
| 4klzA | 1 | 0.9337 | 99.9 | 0.081 | Contact Map |
| 3regA | 2 | 0.988 | 99.9 | 0.084 | Contact Map |
| 3t5gA | 1 | 0.9759 | 99.9 | 0.085 | Contact Map |
| 3x1xA | 1 | 0 | 99.9 | 0.085 | Contact Map |
| 3kkqA | 1 | 1 | 99.9 | 0.087 | Contact Map |
| 2bovA | 1 | 1 | 99.9 | 0.088 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)