| 3eji |
| ID: | 1453737418 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (134) | ||
| Sequences: | 2999 (2280.9) | ||
| Seq/Len: | 22.381 | ||
| Nf(neff/√len): | 197.0 |
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: 22.381).
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 |
| 95_E | 122_A | 3.168 | 1.00 |
| 55_F | 100_Q | 2.550 | 1.00 |
| 24_K | 33_T | 2.448 | 1.00 |
| 56_T | 93_V | 2.349 | 1.00 |
| 96_A | 99_R | 2.256 | 1.00 |
| 23_V | 86_I | 2.196 | 1.00 |
| 92_M | 119_L | 2.135 | 1.00 |
| 18_I | 24_K | 2.074 | 1.00 |
| 36_K | 94_N | 1.987 | 1.00 |
| 125_Q | 129_E | 1.981 | 1.00 |
| 96_A | 100_Q | 1.950 | 1.00 |
| 37_L | 83_L | 1.939 | 1.00 |
| 36_K | 56_T | 1.891 | 1.00 |
| 95_E | 118_L | 1.845 | 1.00 |
| 85_Y | 92_M | 1.831 | 1.00 |
| 12_A | 25_L | 1.791 | 1.00 |
| 53_S | 57_K | 1.764 | 1.00 |
| 99_R | 125_Q | 1.761 | 1.00 |
| 123_E | 127_K | 1.725 | 1.00 |
| 91_K | 96_A | 1.691 | 1.00 |
| 55_F | 97_L | 1.660 | 1.00 |
| 98_V | 119_L | 1.639 | 1.00 |
| 40_D | 43_E | 1.626 | 1.00 |
| 55_F | 59_M | 1.542 | 1.00 |
| 61_E | 64_K | 1.486 | 1.00 |
| 60_V | 93_V | 1.458 | 1.00 |
| 124_A | 128_K | 1.417 | 1.00 |
| 105_V | 120_R | 1.416 | 1.00 |
| 44_F | 53_S | 1.390 | 0.99 |
| 16_K | 24_K | 1.345 | 0.99 |
| 105_V | 123_E | 1.340 | 0.99 |
| 55_F | 96_A | 1.329 | 0.99 |
| 56_T | 97_L | 1.327 | 0.99 |
| 59_M | 93_V | 1.320 | 0.99 |
| 19_D | 43_E | 1.306 | 0.99 |
| 68_V | 84_A | 1.288 | 0.99 |
| 21_D | 43_E | 1.283 | 0.99 |
| 44_F | 50_P | 1.249 | 0.99 |
| 32_M | 76_T | 1.247 | 0.99 |
| 75_R | 83_L | 1.240 | 0.98 |
| 19_D | 22_T | 1.233 | 0.98 |
| 9_K | 67_E | 1.227 | 0.98 |
| 14_L | 66_I | 1.226 | 0.98 |
| 23_V | 36_K | 1.225 | 0.98 |
| 57_K | 61_E | 1.225 | 0.98 |
| 22_T | 33_T | 1.216 | 0.98 |
| 59_M | 96_A | 1.211 | 0.98 |
| 14_L | 17_A | 1.208 | 0.98 |
| 48_Y | 102_L | 1.207 | 0.98 |
| 123_E | 134_W | 1.198 | 0.98 |
| 87_Y | 92_M | 1.191 | 0.98 |
| 41_T | 52_A | 1.179 | 0.98 |
| 23_V | 60_V | 1.177 | 0.98 |
| 98_V | 105_V | 1.177 | 0.98 |
| 52_A | 97_L | 1.171 | 0.98 |
| 37_L | 85_Y | 1.162 | 0.97 |
| 55_F | 58_K | 1.121 | 0.97 |
| 100_Q | 131_L | 1.120 | 0.96 |
| 69_E | 87_Y | 1.113 | 0.96 |
| 24_K | 31_P | 1.113 | 0.96 |
| 95_E | 99_R | 1.113 | 0.96 |
| 39_V | 97_L | 1.107 | 0.96 |
| 41_T | 103_A | 1.095 | 0.96 |
| 35_R | 79_Y | 1.093 | 0.96 |
| 20_G | 52_A | 1.085 | 0.96 |
| 110_K | 123_E | 1.068 | 0.95 |
| 104_K | 133_I | 1.060 | 0.95 |
| 99_R | 129_E | 1.057 | 0.95 |
| 11_P | 67_E | 1.057 | 0.95 |
| 35_R | 81_R | 1.051 | 0.94 |
| 44_F | 49_G | 1.040 | 0.94 |
| 41_T | 56_T | 1.035 | 0.94 |
| 54_A | 58_K | 1.022 | 0.93 |
| 56_T | 60_V | 1.014 | 0.93 |
| 125_Q | 131_L | 1.011 | 0.93 |
| 98_V | 103_A | 1.009 | 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 | |
| 4eqpA | 1 | 0.9021 | 100 | 0.023 | Contact Map |
| 3bdlA | 1 | 0.958 | 100 | 0.123 | Contact Map |
| 4qmgA | 5 | 0.9301 | 100 | 0.15 | Contact Map |
| 2wacA | 2 | 0.9161 | 99.8 | 0.4 | Contact Map |
| 2hqxA | 2 | 0.2168 | 99.8 | 0.402 | Contact Map |
| 4b9wA | 2 | 0.6993 | 97.3 | 0.766 | Contact Map |
| 4q5yA | 1 | 0.6503 | 95.2 | 0.811 | Contact Map |
| 4b9xA | 1 | 0.6993 | 92.1 | 0.834 | Contact Map |
| 3ntkA | 2 | 0.6434 | 92.1 | 0.834 | Contact Map |
| 4q5wA | 2 | 0.7273 | 80.8 | 0.862 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)