| 5p21 |
| ID: | 1408342783 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (162) | ||
| Sequences: | 24939 (15196.1) | ||
| Seq/Len: | 153.944 | ||
| Nf(neff/√len): | 1193.9 |
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: 153.944).
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 | 3.278 | 1.00 |
| 11_A | 92_D | 2.949 | 1.00 |
| 142_I | 158_T | 2.709 | 1.00 |
| 158_T | 161_R | 2.588 | 1.00 |
| 114_V | 155_A | 2.544 | 1.00 |
| 84_I | 115_G | 2.511 | 1.00 |
| 19_L | 81_V | 2.510 | 1.00 |
| 81_V | 116_N | 2.364 | 1.00 |
| 79_L | 114_V | 2.259 | 1.00 |
| 140_P | 158_T | 2.244 | 1.00 |
| 131_Q | 135_R | 2.194 | 1.00 |
| 151_G | 154_D | 2.032 | 1.00 |
| 116_N | 146_A | 2.007 | 1.00 |
| 7_V | 75_G | 1.988 | 1.00 |
| 82_F | 141_Y | 1.951 | 1.00 |
| 115_G | 143_E | 1.943 | 1.00 |
| 8_V | 20_T | 1.868 | 1.00 |
| 87_T | 129_Q | 1.850 | 1.00 |
| 18_A | 146_A | 1.844 | 1.00 |
| 118_C | 143_E | 1.832 | 1.00 |
| 127_S | 131_Q | 1.826 | 1.00 |
| 84_I | 118_C | 1.804 | 1.00 |
| 158_T | 162_E | 1.743 | 1.00 |
| 118_C | 150_Q | 1.733 | 1.00 |
| 19_L | 155_A | 1.719 | 1.00 |
| 77_G | 159_L | 1.715 | 1.00 |
| 8_V | 79_L | 1.683 | 1.00 |
| 112_V | 142_I | 1.648 | 1.00 |
| 144_T | 155_A | 1.647 | 1.00 |
| 114_V | 144_T | 1.635 | 1.00 |
| 112_V | 158_T | 1.633 | 1.00 |
| 19_L | 152_V | 1.599 | 1.00 |
| 130_A | 134_A | 1.593 | 1.00 |
| 83_A | 86_N | 1.578 | 1.00 |
| 82_F | 113_L | 1.476 | 1.00 |
| 86_N | 89_S | 1.461 | 1.00 |
| 22_Q | 152_V | 1.434 | 1.00 |
| 132_D | 136_S | 1.423 | 1.00 |
| 79_L | 159_L | 1.418 | 1.00 |
| 80_C | 97_R | 1.392 | 0.99 |
| 154_D | 157_Y | 1.356 | 0.99 |
| 114_V | 142_I | 1.336 | 0.99 |
| 53_L | 160_V | 1.333 | 0.99 |
| 83_A | 117_K | 1.294 | 0.99 |
| 94_H | 136_S | 1.287 | 0.99 |
| 45_V | 50_T | 1.272 | 0.99 |
| 133_L | 137_Y | 1.263 | 0.99 |
| 88_K | 91_E | 1.249 | 0.99 |
| 85_N | 120_L | 1.236 | 0.98 |
| 97_R | 111_M | 1.219 | 0.98 |
| 153_E | 157_Y | 1.218 | 0.98 |
| 117_K | 120_L | 1.217 | 0.98 |
| 4_Y | 163_I | 1.203 | 0.98 |
| 98_E | 101_K | 1.179 | 0.98 |
| 130_A | 141_Y | 1.173 | 0.98 |
| 19_L | 23_L | 1.167 | 0.97 |
| 45_V | 48_G | 1.147 | 0.97 |
| 115_G | 141_Y | 1.146 | 0.97 |
| 157_Y | 161_R | 1.133 | 0.97 |
| 154_D | 158_T | 1.131 | 0.97 |
| 6_L | 77_G | 1.125 | 0.97 |
| 126_E | 129_Q | 1.117 | 0.96 |
| 11_A | 14_V | 1.114 | 0.96 |
| 98_E | 102_R | 1.110 | 0.96 |
| 129_Q | 132_D | 1.109 | 0.96 |
| 5_K | 54_D | 1.101 | 0.96 |
| 80_C | 93_I | 1.081 | 0.95 |
| 79_L | 155_A | 1.069 | 0.95 |
| 97_R | 101_K | 1.066 | 0.95 |
| 82_F | 115_G | 1.065 | 0.95 |
| 41_R | 54_D | 1.062 | 0.95 |
| 34_P | 37_E | 1.052 | 0.95 |
| 59_A | 62_E | 1.039 | 0.94 |
| 21_I | 29_V | 1.035 | 0.94 |
| 82_F | 130_A | 1.026 | 0.94 |
| 123_R | 143_E | 1.017 | 0.93 |
| 12_G | 61_Q | 1.009 | 0.93 |
| 79_L | 112_V | 1.007 | 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 | |
| 3conA | 1 | 0.9337 | 100 | 0.137 | Contact Map |
| 1m7bA | 1 | 0.9819 | 100 | 0.138 | Contact Map |
| 2ce2X | 1 | 1 | 100 | 0.139 | Contact Map |
| 3kkqA | 1 | 1 | 100 | 0.147 | Contact Map |
| 3c5cA | 4 | 0.988 | 100 | 0.149 | Contact Map |
| 2bovA | 1 | 1 | 100 | 0.15 | Contact Map |
| 4ku4A | 2 | 0.9759 | 100 | 0.15 | Contact Map |
| 1u8zA | 2 | 0.9819 | 100 | 0.151 | Contact Map |
| 4kvgA | 2 | 0.9759 | 100 | 0.151 | Contact Map |
| 3oesA | 1 | 0.9398 | 100 | 0.152 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)