| model_256_4q2eB_NOTaligned_region |
| ID: | 1488116445 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (108) | ||
| Sequences: | 474 (326.3) | ||
| Seq/Len: | 4.389 | ||
| Nf(neff/√len): | 31.4 |
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: 4.389).
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 |
| 84_K | 87_Q | 1.956 | 1.00 |
| 43_L | 51_A | 1.871 | 1.00 |
| 45_A | 49_A | 1.798 | 1.00 |
| 77_G | 80_A | 1.788 | 1.00 |
| 74_F | 111_A | 1.779 | 1.00 |
| 107_I | 110_S | 1.753 | 0.99 |
| 50_A | 107_I | 1.687 | 0.99 |
| 73_Y | 109_S | 1.651 | 0.99 |
| 115_V | 119_L | 1.635 | 0.99 |
| 82_K | 85_M | 1.598 | 0.99 |
| 50_A | 103_P | 1.573 | 0.99 |
| 72_A | 75_V | 1.547 | 0.98 |
| 68_L | 90_A | 1.496 | 0.98 |
| 37_P | 74_F | 1.465 | 0.98 |
| 33_V | 71_A | 1.385 | 0.96 |
| 25_V | 68_L | 1.385 | 0.96 |
| 27_N | 67_F | 1.377 | 0.96 |
| 96_K | 100_R | 1.359 | 0.96 |
| 44_S | 58_T | 1.341 | 0.95 |
| 51_A | 55_G | 1.335 | 0.95 |
| 31_I | 105_S | 1.312 | 0.95 |
| 35_G | 39_L | 1.293 | 0.94 |
| 54_L | 66_G | 1.285 | 0.94 |
| 54_L | 110_S | 1.237 | 0.92 |
| 70_V | 73_Y | 1.233 | 0.92 |
| 37_P | 108_G | 1.231 | 0.92 |
| 61_A | 72_A | 1.217 | 0.91 |
| 42_G | 105_S | 1.215 | 0.91 |
| 77_G | 124_V | 1.186 | 0.90 |
| 80_A | 92_G | 1.168 | 0.89 |
| 43_L | 47_G | 1.160 | 0.88 |
| 86_T | 90_A | 1.156 | 0.88 |
| 38_L | 48_I | 1.152 | 0.88 |
| 81_T | 102_G | 1.151 | 0.88 |
| 46_S | 50_A | 1.141 | 0.87 |
| 49_A | 57_L | 1.108 | 0.85 |
| 40_V | 43_L | 1.103 | 0.85 |
| 75_V | 122_Y | 1.096 | 0.84 |
| 118_F | 122_Y | 1.094 | 0.84 |
| 53_L | 118_F | 1.079 | 0.83 |
| 57_L | 114_C | 1.072 | 0.82 |
| 105_S | 109_S | 1.069 | 0.82 |
| 61_A | 84_K | 1.052 | 0.81 |
| 66_G | 91_Q | 1.051 | 0.80 |
| 45_A | 75_V | 1.047 | 0.80 |
| 77_G | 94_A | 1.040 | 0.80 |
| 110_S | 113_G | 1.038 | 0.79 |
| 54_L | 114_C | 1.031 | 0.79 |
| 49_A | 118_F | 1.030 | 0.79 |
| 21_W | 60_R | 1.021 | 0.78 |
| 24_A | 61_A | 1.020 | 0.78 |
| 50_A | 106_V | 1.018 | 0.77 |
| 80_A | 90_A | 1.014 | 0.77 |
| 53_L | 122_Y | 1.014 | 0.77 |
| 19_P | 26_A | 1.008 | 0.76 |
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 | |
| 2xq2A | 1 | 0.9453 | 65.2 | 0.894 | Contact Map |
| 3dh4A | 4 | 0.9297 | 60.8 | 0.897 | Contact Map |
| 2ks1B | 1 | 0.3438 | 21.4 | 0.921 | Contact Map |
| 2jwaA | 2 | 0.3359 | 17.8 | 0.923 | Contact Map |
| 2kluA | 1 | 0.4844 | 7.5 | 0.935 | Contact Map |
| 2yevB | 2 | 0.6797 | 4.9 | 0.941 | Contact Map |
| 2l2tA | 2 | 0.3438 | 4.5 | 0.942 | Contact Map |
| 2m20A | 2 | 0.4688 | 4.2 | 0.942 | Contact Map |
| 4qtnA | 3 | 0.9688 | 4.2 | 0.942 | Contact Map |
| 2k1kA | 2 | 0.2969 | 3.4 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)