| L20_L21 |
| ID: | 1484908139 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 219 (218) | ||
| Sequences: | 1204 (655.8) | ||
| Seq/Len: | 5.523 | ||
| Nf(neff/√len): | 44.4 |
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: 5.523).
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 |
| 96_A | 100_V | 4.198 | 1.00 |
| 178_E | 215_K | 3.537 | 1.00 |
| 124_K | 155_V | 3.314 | 1.00 |
| 134_P | 216_E | 3.101 | 1.00 |
| 69_C | 79_F | 2.924 | 1.00 |
| 21_A | 39_L | 2.858 | 1.00 |
| 145_A | 179_V | 2.831 | 1.00 |
| 133_E | 136_L | 2.678 | 1.00 |
| 184_R | 208_P | 2.622 | 1.00 |
| 152_E | 174_S | 2.566 | 1.00 |
| 189_L | 202_K | 2.520 | 1.00 |
| 177_A | 214_I | 2.501 | 1.00 |
| 6_T | 10_R | 2.498 | 1.00 |
| 72_H | 107_A | 2.475 | 1.00 |
| 81_H | 85_K | 2.459 | 1.00 |
| 178_E | 213_L | 2.393 | 1.00 |
| 153_L | 212_L | 2.390 | 1.00 |
| 177_A | 212_L | 2.336 | 1.00 |
| 140_V | 212_L | 2.327 | 1.00 |
| 38_T | 42_A | 2.040 | 1.00 |
| 94_N | 97_D | 2.008 | 1.00 |
| 146_E | 149_A | 1.995 | 1.00 |
| 194_K | 199_Y | 1.986 | 1.00 |
| 139_R | 211_E | 1.966 | 1.00 |
| 40_F | 193_F | 1.940 | 1.00 |
| 91_D | 124_K | 1.917 | 1.00 |
| 174_S | 218_R | 1.909 | 1.00 |
| 37_E | 41_A | 1.874 | 1.00 |
| 49_H | 52_R | 1.841 | 1.00 |
| 150_T | 176_V | 1.816 | 1.00 |
| 66_N | 70_R | 1.781 | 1.00 |
| 48_A | 52_R | 1.767 | 1.00 |
| 52_R | 55_R | 1.738 | 1.00 |
| 123_V | 153_L | 1.707 | 1.00 |
| 53_R | 56_D | 1.693 | 1.00 |
| 102_E | 120_F | 1.685 | 1.00 |
| 138_L | 212_L | 1.684 | 1.00 |
| 34_K | 37_E | 1.661 | 1.00 |
| 158_L | 163_T | 1.656 | 1.00 |
| 128_K | 141_E | 1.652 | 1.00 |
| 88_I | 112_R | 1.648 | 0.99 |
| 183_G | 209_Y | 1.618 | 0.99 |
| 75_N | 78_T | 1.609 | 0.99 |
| 125_T | 140_V | 1.587 | 0.99 |
| 27_L | 30_K | 1.582 | 0.99 |
| 36_R | 200_R | 1.557 | 0.99 |
| 28_R | 38_T | 1.545 | 0.99 |
| 107_A | 111_E | 1.534 | 0.99 |
| 43_G | 189_L | 1.524 | 0.99 |
| 69_C | 72_H | 1.495 | 0.99 |
| 153_L | 177_A | 1.484 | 0.99 |
| 31_S | 34_K | 1.474 | 0.99 |
| 139_R | 185_G | 1.468 | 0.99 |
| 137_K | 211_E | 1.458 | 0.98 |
| 102_E | 105_V | 1.404 | 0.98 |
| 125_T | 141_E | 1.379 | 0.98 |
| 152_E | 176_V | 1.361 | 0.97 |
| 108_E | 111_E | 1.349 | 0.97 |
| 90_V | 94_N | 1.349 | 0.97 |
| 40_F | 191_S | 1.347 | 0.97 |
| 97_D | 101_R | 1.345 | 0.97 |
| 124_K | 169_V | 1.333 | 0.97 |
| 137_K | 213_L | 1.319 | 0.97 |
| 193_F | 196_K | 1.316 | 0.97 |
| 158_L | 165_V | 1.314 | 0.97 |
| 111_E | 114_K | 1.296 | 0.96 |
| 8_V | 12_R | 1.295 | 0.96 |
| 108_E | 162_K | 1.282 | 0.96 |
| 181_G | 211_E | 1.276 | 0.96 |
| 190_V | 199_Y | 1.265 | 0.95 |
| 155_V | 169_V | 1.260 | 0.95 |
| 20_L | 43_G | 1.242 | 0.95 |
| 101_R | 131_R | 1.230 | 0.94 |
| 42_A | 45_Y | 1.217 | 0.94 |
| 27_L | 31_S | 1.209 | 0.94 |
| 176_V | 216_E | 1.195 | 0.93 |
| 52_R | 56_D | 1.193 | 0.93 |
| 78_T | 81_H | 1.182 | 0.93 |
| 168_P | 172_G | 1.181 | 0.93 |
| 165_V | 168_P | 1.176 | 0.93 |
| 8_V | 14_H | 1.168 | 0.92 |
| 47_Y | 192_K | 1.168 | 0.92 |
| 69_C | 110_V | 1.164 | 0.92 |
| 80_I | 84_K | 1.161 | 0.92 |
| 9_V | 14_H | 1.159 | 0.92 |
| 190_V | 203_K | 1.159 | 0.92 |
| 98_L | 102_E | 1.150 | 0.91 |
| 83_L | 109_L | 1.141 | 0.91 |
| 41_A | 45_Y | 1.135 | 0.91 |
| 9_V | 12_R | 1.133 | 0.91 |
| 104_Q | 107_A | 1.130 | 0.90 |
| 47_Y | 199_Y | 1.129 | 0.90 |
| 111_E | 115_A | 1.124 | 0.90 |
| 140_V | 143_L | 1.114 | 0.90 |
| 142_K | 208_P | 1.096 | 0.89 |
| 108_E | 112_R | 1.093 | 0.88 |
| 93_K | 130_Y | 1.065 | 0.87 |
| 150_T | 178_E | 1.048 | 0.85 |
| 20_L | 189_L | 1.047 | 0.85 |
| 192_K | 199_Y | 1.046 | 0.85 |
| 32_F | 36_R | 1.036 | 0.84 |
| 125_T | 130_Y | 1.033 | 0.84 |
| 79_F | 109_L | 1.030 | 0.84 |
| 98_L | 105_V | 1.019 | 0.83 |
| 89_E | 124_K | 1.015 | 0.83 |
| 126_G | 141_E | 1.015 | 0.83 |
| 113_A | 116_A | 1.014 | 0.83 |
| 91_D | 94_N | 1.013 | 0.83 |
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 | |
| 4rb6U | 1 | 0.5297 | 100 | 0.454 | Contact Map |
| 2zjrN | 1 | 0.5342 | 100 | 0.455 | Contact Map |
| 4tp9Q | 1 | 0.5342 | 100 | 0.465 | Contact Map |
| 3j3wQ | 1 | 0.5342 | 100 | 0.468 | Contact Map |
| 2ghjA | 4 | 0.4612 | 100 | 0.474 | Contact Map |
| 3bboS | 1 | 0.5342 | 100 | 0.478 | Contact Map |
| 3j7yR | 1 | 0.6393 | 100 | 0.499 | Contact Map |
| 4tp9R | 1 | 0.4612 | 100 | 0.625 | Contact Map |
| 3j3wR | 1 | 0.4612 | 100 | 0.628 | Contact Map |
| 4rb6V | 1 | 0.4566 | 100 | 0.629 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)