| Subset500 |
| ID: | 1478300791 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (92) | ||
| Sequences: | 500 (500) | ||
| Seq/Len: | 5.435 | ||
| Nf(neff/√len): | 52.1 |
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: 5.435).
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 |
| 28_Q | 48_L | 1.722 | 1.00 |
| 33_Q | 61_Y | 1.539 | 0.99 |
| 3_K | 53_S | 1.527 | 0.99 |
| 6_S | 86_V | 1.512 | 0.99 |
| 5_C | 53_S | 1.498 | 0.99 |
| 47_R | 71_E | 1.489 | 0.99 |
| 37_F | 70_F | 1.402 | 0.98 |
| 17_W | 89_G | 1.338 | 0.97 |
| 1_Q | 91_Q | 1.337 | 0.97 |
| 56_D | 81_A | 1.308 | 0.96 |
| 39_K | 77_M | 1.298 | 0.96 |
| 27_V | 76_D | 1.272 | 0.95 |
| 56_D | 85_T | 1.262 | 0.95 |
| 32_N | 60_N | 1.255 | 0.95 |
| 42_N | 81_A | 1.243 | 0.95 |
| 5_C | 60_N | 1.240 | 0.95 |
| 45_E | 59_E | 1.233 | 0.94 |
| 36_Q | 39_K | 1.211 | 0.94 |
| 40_D | 78_G | 1.210 | 0.94 |
| 45_E | 60_N | 1.202 | 0.93 |
| 27_V | 72_I | 1.189 | 0.93 |
| 16_C | 54_L | 1.145 | 0.91 |
| 2_I | 33_Q | 1.127 | 0.90 |
| 38_Y | 66_V | 1.120 | 0.90 |
| 27_V | 45_E | 1.118 | 0.90 |
| 69_A | 87_G | 1.118 | 0.90 |
| 57_F | 88_W | 1.117 | 0.89 |
| 34_L | 66_V | 1.115 | 0.89 |
| 35_W | 46_W | 1.111 | 0.89 |
| 46_W | 67_S | 1.105 | 0.89 |
| 2_I | 77_M | 1.100 | 0.89 |
| 14_Q | 67_S | 1.097 | 0.88 |
| 52_A | 71_E | 1.095 | 0.88 |
| 2_I | 79_C | 1.091 | 0.88 |
| 13_K | 49_R | 1.084 | 0.88 |
| 48_L | 54_L | 1.083 | 0.87 |
| 21_V | 34_L | 1.069 | 0.87 |
| 24_Y | 77_M | 1.065 | 0.86 |
| 6_S | 35_W | 1.055 | 0.86 |
| 61_Y | 76_D | 1.051 | 0.85 |
| 4_V | 68_W | 1.039 | 0.84 |
| 67_S | 73_E | 1.036 | 0.84 |
| 16_C | 63_P | 1.035 | 0.84 |
| 23_P | 50_I | 1.031 | 0.84 |
| 2_I | 92_L | 1.024 | 0.83 |
| 30_L | 73_E | 1.022 | 0.83 |
| 7_C | 32_N | 1.017 | 0.83 |
| 57_F | 75_G | 1.015 | 0.82 |
| 21_V | 49_R | 1.012 | 0.82 |
| 49_R | 58_S | 1.012 | 0.82 |
| 30_L | 72_I | 1.004 | 0.82 |
| 35_W | 48_L | 1.004 | 0.82 |
| 39_K | 60_N | 1.001 | 0.81 |
| 42_N | 47_R | 1.000 | 0.81 |
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 | |
| 1qysA | 1 | 1 | 99.7 | 0.488 | Contact Map |
| 4kyzA | 4 | 1 | 99.3 | 0.608 | Contact Map |
| 2gjhA | 2 | 0.5326 | 98.1 | 0.739 | Contact Map |
| 2mblA | 1 | 1 | 96.2 | 0.808 | Contact Map |
| 2jvfA | 1 | 1 | 33.3 | 0.904 | Contact Map |
| 2cy7A | 1 | 0.7717 | 9.5 | 0.926 | Contact Map |
| 1y5oA | 1 | 0.4565 | 8.4 | 0.928 | Contact Map |
| 3axyA | 4 | 0.6848 | 7.3 | 0.93 | Contact Map |
| 1q1uA | 1 | 0.6196 | 6.7 | 0.931 | Contact Map |
| 2p82A | 4 | 0.5978 | 5.8 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)