| aktm |
| ID: | 1405072743 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 163 (152) | ||
| Sequences: | 4877 (3473.9) | ||
| Seq/Len: | 32.086 | ||
| Nf(neff/√len): | 281.8 |
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: 32.086).
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 |
| 31_I | 54_K | 2.994 | 1.00 |
| 43_I | 57_G | 2.958 | 1.00 |
| 119_L | 123_T | 2.809 | 1.00 |
| 33_Y | 96_A | 2.659 | 1.00 |
| 56_V | 96_A | 2.487 | 1.00 |
| 59_E | 65_I | 2.354 | 1.00 |
| 62_D | 85_K | 2.322 | 1.00 |
| 56_V | 84_V | 2.295 | 1.00 |
| 37_C | 57_G | 2.278 | 1.00 |
| 97_T | 120_K | 2.272 | 1.00 |
| 54_K | 82_S | 2.131 | 1.00 |
| 44_I | 72_I | 2.106 | 1.00 |
| 65_I | 83_I | 2.077 | 1.00 |
| 62_D | 66_R | 1.943 | 1.00 |
| 37_C | 68_A | 1.900 | 1.00 |
| 59_E | 64_R | 1.778 | 1.00 |
| 72_I | 83_I | 1.748 | 1.00 |
| 114_K | 117_K | 1.746 | 1.00 |
| 48_K | 75_N | 1.734 | 1.00 |
| 65_I | 85_K | 1.717 | 1.00 |
| 17_V | 41_R | 1.678 | 1.00 |
| 47_A | 81_A | 1.645 | 1.00 |
| 101_M | 125_V | 1.623 | 1.00 |
| 31_I | 56_V | 1.615 | 1.00 |
| 72_I | 81_A | 1.600 | 1.00 |
| 109_E | 113_P | 1.574 | 1.00 |
| 60_I | 87_N | 1.552 | 1.00 |
| 114_K | 118_E | 1.548 | 1.00 |
| 18_R | 22_E | 1.546 | 1.00 |
| 115_L | 125_V | 1.532 | 1.00 |
| 31_I | 96_A | 1.488 | 1.00 |
| 44_I | 71_N | 1.473 | 1.00 |
| 18_R | 45_T | 1.460 | 1.00 |
| 57_G | 68_A | 1.450 | 1.00 |
| 66_R | 70_A | 1.437 | 1.00 |
| 43_I | 55_A | 1.427 | 1.00 |
| 68_A | 83_I | 1.420 | 1.00 |
| 66_R | 69_L | 1.398 | 0.99 |
| 31_I | 97_T | 1.380 | 0.99 |
| 87_N | 90_E | 1.365 | 0.99 |
| 70_A | 74_K | 1.363 | 0.99 |
| 18_R | 49_D | 1.327 | 0.99 |
| 129_E | 153_Y | 1.318 | 0.99 |
| 73_E | 78_T | 1.305 | 0.99 |
| 58_V | 91_V | 1.291 | 0.99 |
| 56_V | 82_S | 1.287 | 0.99 |
| 30_D | 98_V | 1.258 | 0.99 |
| 144_E | 148_M | 1.253 | 0.99 |
| 32_V | 46_A | 1.252 | 0.99 |
| 20_M | 152_V | 1.251 | 0.99 |
| 37_C | 59_E | 1.233 | 0.98 |
| 57_G | 81_A | 1.212 | 0.98 |
| 57_G | 83_I | 1.210 | 0.98 |
| 65_I | 69_L | 1.198 | 0.98 |
| 42_I | 100_T | 1.182 | 0.98 |
| 20_M | 128_H | 1.173 | 0.98 |
| 27_S | 30_D | 1.162 | 0.97 |
| 32_V | 42_I | 1.154 | 0.97 |
| 99_V | 115_L | 1.149 | 0.97 |
| 33_Y | 56_V | 1.146 | 0.97 |
| 37_C | 43_I | 1.140 | 0.97 |
| 32_V | 98_V | 1.136 | 0.97 |
| 47_A | 55_A | 1.134 | 0.97 |
| 19_R | 22_E | 1.126 | 0.97 |
| 32_V | 100_T | 1.111 | 0.96 |
| 35_L | 58_V | 1.105 | 0.96 |
| 137_P | 140_V | 1.096 | 0.96 |
| 70_A | 73_E | 1.089 | 0.96 |
| 35_L | 88_F | 1.083 | 0.96 |
| 99_V | 118_E | 1.047 | 0.94 |
| 115_L | 123_T | 1.045 | 0.94 |
| 39_D | 71_N | 1.034 | 0.94 |
| 110_M | 113_P | 1.033 | 0.94 |
| 120_K | 123_T | 1.029 | 0.94 |
| 63_E | 66_R | 1.026 | 0.94 |
| 45_T | 49_D | 1.025 | 0.93 |
| 34_D | 37_C | 1.016 | 0.93 |
| 21_L | 46_A | 1.013 | 0.93 |
| 99_V | 123_T | 1.007 | 0.93 |
| 137_P | 155_Y | 1.003 | 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 | |
| 2fk8A | 1 | 0.9877 | 99.8 | 0.437 | Contact Map |
| 1kpgA | 4 | 0.9877 | 99.8 | 0.44 | Contact Map |
| 3busA | 2 | 0.9939 | 99.8 | 0.44 | Contact Map |
| 3hemA | 1 | 0.9877 | 99.8 | 0.441 | Contact Map |
| 1u2zA | 3 | 1 | 99.8 | 0.442 | Contact Map |
| 3uwpA | 1 | 1 | 99.8 | 0.443 | Contact Map |
| 3fpfA | 2 | 0.9693 | 99.8 | 0.452 | Contact Map |
| 2o57A | 4 | 0.9816 | 99.8 | 0.454 | Contact Map |
| 1nkvA | 3 | 0.9816 | 99.8 | 0.455 | Contact Map |
| 1l3iA | 6 | 0.9693 | 99.8 | 0.458 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)