| 53_t2_hh |
| ID: | 1432713285 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 196 (100) | ||
| Sequences: | 21155 (16826.5) | ||
| Seq/Len: | 211.550 | ||
| Nf(neff/√len): | 1682.7 |
Jackhmmer Results: (2015_01_07)
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: 211.550).
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 |
| 47_T | 90_Q | 3.734 | 1.00 |
| 76_C | 94_Y | 3.719 | 1.00 |
| 49_Y | 90_Q | 3.080 | 1.00 |
| 55_R | 58_E | 2.760 | 1.00 |
| 69_L | 72_V | 2.511 | 1.00 |
| 70_Y | 74_L | 2.420 | 1.00 |
| 48_Y | 63_I | 2.345 | 1.00 |
| 47_T | 92_A | 2.310 | 1.00 |
| 86_W | 89_S | 2.290 | 1.00 |
| 74_L | 82_P | 2.223 | 1.00 |
| 48_Y | 54_P | 2.159 | 1.00 |
| 72_V | 76_C | 2.072 | 1.00 |
| 45_L | 92_A | 2.029 | 1.00 |
| 57_E | 61_N | 2.025 | 1.00 |
| 56_P | 79_N | 1.773 | 1.00 |
| 74_L | 83_Y | 1.691 | 1.00 |
| 58_E | 62_A | 1.610 | 1.00 |
| 56_P | 74_L | 1.583 | 1.00 |
| 56_P | 70_Y | 1.511 | 1.00 |
| 68_Q | 72_V | 1.467 | 1.00 |
| 68_Q | 76_C | 1.460 | 1.00 |
| 79_N | 89_S | 1.416 | 1.00 |
| 74_L | 79_N | 1.412 | 1.00 |
| 63_I | 93_A | 1.409 | 1.00 |
| 71_W | 74_L | 1.385 | 0.99 |
| 50_I | 89_S | 1.364 | 0.99 |
| 72_V | 75_M | 1.354 | 0.99 |
| 60_A | 70_Y | 1.332 | 0.99 |
| 71_W | 75_M | 1.329 | 0.99 |
| 56_P | 73_L | 1.304 | 0.99 |
| 81_D | 84_Y | 1.299 | 0.99 |
| 64_Y | 69_L | 1.297 | 0.99 |
| 74_L | 81_D | 1.294 | 0.99 |
| 48_Y | 51_K | 1.252 | 0.99 |
| 52_G | 87_I | 1.224 | 0.98 |
| 73_L | 91_E | 1.221 | 0.98 |
| 57_E | 70_Y | 1.215 | 0.98 |
| 48_Y | 59_L | 1.199 | 0.98 |
| 76_C | 92_A | 1.183 | 0.98 |
| 74_L | 78_D | 1.144 | 0.97 |
| 56_P | 85_G | 1.144 | 0.97 |
| 60_A | 73_L | 1.113 | 0.96 |
| 58_E | 61_N | 1.100 | 0.96 |
| 50_I | 59_L | 1.094 | 0.96 |
| 66_N | 69_L | 1.090 | 0.96 |
| 45_L | 94_Y | 1.087 | 0.96 |
| 79_N | 82_P | 1.058 | 0.95 |
| 68_Q | 73_L | 1.042 | 0.94 |
| 51_K | 54_P | 1.013 | 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 | |
| 2djpA | 1 | 0.3929 | 99.2 | 0.65 | Contact Map |
| 2mkxA | 1 | 0.2602 | 99.2 | 0.658 | Contact Map |
| 4b8vA | 1 | 0.4847 | 99 | 0.68 | Contact Map |
| 1e0gA | 1 | 0.2449 | 99 | 0.681 | Contact Map |
| 4uz3A | 3 | 0.4439 | 98.8 | 0.707 | Contact Map |
| 2ltfA | 1 | 0.3469 | 98.8 | 0.71 | Contact Map |
| 4xcmA | 2 | 0.5204 | 98.7 | 0.711 | Contact Map |
| 4ebyA | 1 | 0.5051 | 98.7 | 0.715 | Contact Map |
| 2l9yA | 1 | 0.7347 | 98.7 | 0.719 | Contact Map |
| 4a1kA | 1 | 0.5663 | 98.6 | 0.726 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)