| shuangxi |
| ID: | 1491915863 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (165) | ||
| Sequences: | 2489 (1954.9) | ||
| Seq/Len: | 15.085 | ||
| Nf(neff/√len): | 152.2 |
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: 15.085).
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 |
| 46_Y | 50_Q | 3.867 | 1.00 |
| 56_M | 76_F | 3.156 | 1.00 |
| 90_L | 127_G | 3.118 | 1.00 |
| 69_G | 91_F | 2.981 | 1.00 |
| 35_T | 40_M | 2.573 | 1.00 |
| 62_D | 68_F | 2.402 | 1.00 |
| 73_S | 85_T | 2.282 | 1.00 |
| 70_A | 119_F | 2.271 | 1.00 |
| 36_S | 160_D | 2.253 | 1.00 |
| 49_M | 163_I | 2.223 | 1.00 |
| 44_T | 48_A | 2.054 | 1.00 |
| 32_A | 165_S | 2.011 | 1.00 |
| 83_Y | 112_G | 2.002 | 1.00 |
| 38_H | 48_A | 1.973 | 1.00 |
| 63_S | 157_F | 1.923 | 1.00 |
| 61_K | 159_Q | 1.920 | 1.00 |
| 69_G | 89_F | 1.853 | 1.00 |
| 54_S | 75_P | 1.820 | 1.00 |
| 33_F | 161_I | 1.707 | 1.00 |
| 130_L | 158_V | 1.677 | 1.00 |
| 123_S | 128_L | 1.657 | 1.00 |
| 90_L | 128_L | 1.629 | 1.00 |
| 56_M | 75_P | 1.595 | 1.00 |
| 71_L | 89_F | 1.557 | 1.00 |
| 62_D | 66_Q | 1.527 | 1.00 |
| 72_A | 76_F | 1.512 | 1.00 |
| 35_T | 160_D | 1.507 | 1.00 |
| 72_A | 110_I | 1.469 | 1.00 |
| 124_G | 127_G | 1.455 | 1.00 |
| 30_N | 165_S | 1.450 | 1.00 |
| 103_T | 109_F | 1.431 | 1.00 |
| 33_F | 40_M | 1.415 | 1.00 |
| 72_A | 119_F | 1.411 | 1.00 |
| 74_E | 85_T | 1.393 | 0.99 |
| 86_G | 102_W | 1.375 | 0.99 |
| 34_S | 160_D | 1.365 | 0.99 |
| 141_S | 149_M | 1.355 | 0.99 |
| 145_F | 150_L | 1.353 | 0.99 |
| 61_K | 160_D | 1.344 | 0.99 |
| 31_L | 34_S | 1.337 | 0.99 |
| 42_I | 46_Y | 1.307 | 0.99 |
| 63_S | 159_Q | 1.286 | 0.99 |
| 55_P | 75_P | 1.285 | 0.99 |
| 9_E | 12_Q | 1.259 | 0.99 |
| 35_T | 161_I | 1.256 | 0.99 |
| 73_S | 88_T | 1.255 | 0.99 |
| 88_T | 145_F | 1.242 | 0.98 |
| 45_L | 163_I | 1.233 | 0.98 |
| 60_I | 158_V | 1.230 | 0.98 |
| 45_L | 49_M | 1.211 | 0.98 |
| 105_D | 146_G | 1.194 | 0.98 |
| 60_I | 128_L | 1.184 | 0.98 |
| 60_I | 130_L | 1.172 | 0.98 |
| 32_A | 56_M | 1.157 | 0.97 |
| 31_L | 38_H | 1.141 | 0.97 |
| 103_T | 106_N | 1.138 | 0.97 |
| 149_M | 152_M | 1.126 | 0.97 |
| 15_K | 19_H | 1.109 | 0.96 |
| 33_F | 130_L | 1.107 | 0.96 |
| 12_Q | 93_F | 1.105 | 0.96 |
| 61_K | 67_I | 1.094 | 0.96 |
| 12_Q | 59_V | 1.091 | 0.96 |
| 156_F | 162_E | 1.075 | 0.95 |
| 84_G | 144_T | 1.056 | 0.95 |
| 62_D | 151_S | 1.055 | 0.95 |
| 76_F | 110_I | 1.054 | 0.95 |
| 44_T | 47_R | 1.053 | 0.95 |
| 85_T | 88_T | 1.048 | 0.94 |
| 147_N | 150_L | 1.042 | 0.94 |
| 17_A | 29_W | 1.042 | 0.94 |
| 35_T | 39_G | 1.042 | 0.94 |
| 3_E | 13_I | 1.040 | 0.94 |
| 129_W | 132_G | 1.034 | 0.94 |
| 16_L | 20_L | 1.027 | 0.94 |
| 87_E | 102_W | 1.016 | 0.93 |
| 142_C | 147_N | 1.015 | 0.93 |
| 66_Q | 94_Y | 1.014 | 0.93 |
| 102_W | 109_F | 1.012 | 0.93 |
| 41_S | 44_T | 1.010 | 0.93 |
| 111_K | 118_A | 1.009 | 0.93 |
| 45_L | 134_L | 1.004 | 0.93 |
| 58_L | 163_I | 1.000 | 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 | |
| 4acjA | 1 | 1 | 100 | 0.014 | Contact Map |
| 3g40A | 1 | 0.3293 | 4.2 | 0.945 | Contact Map |
| 4bpxB | 2 | 0.2036 | 3.1 | 0.948 | Contact Map |
| 3j60Z | 1 | 0.4371 | 1.9 | 0.954 | Contact Map |
| 4ociA | 1 | 0.3353 | 1.9 | 0.954 | Contact Map |
| 4y21A | 1 | 0 | 1.9 | 0.954 | Contact Map |
| 4lyaA | 1 | 0.5689 | 1.8 | 0.954 | Contact Map |
| 3zeyU | 1 | 0.4251 | 1.8 | 0.954 | Contact Map |
| 1bjfA | 2 | 0.3653 | 1.7 | 0.955 | Contact Map |
| 4ujpa | 1 | 0.4192 | 1.7 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)