| T0824 |
| ID: | 1423538743 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (107) | ||
| Sequences: | 415 (349.7) | ||
| Seq/Len: | 3.879 | ||
| Nf(neff/√len): | 33.8 |
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: 3.879).
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 |
| 24_D | 78_R | 3.864 | 1.00 |
| 59_D | 86_R | 3.675 | 1.00 |
| 45_R | 66_A | 2.094 | 1.00 |
| 18_T | 80_V | 2.023 | 1.00 |
| 63_W | 107_F | 1.974 | 1.00 |
| 49_L | 60_R | 1.906 | 1.00 |
| 67_M | 96_L | 1.892 | 1.00 |
| 21_H | 76_S | 1.861 | 1.00 |
| 15_Y | 87_G | 1.756 | 0.99 |
| 85_N | 88_A | 1.754 | 0.99 |
| 18_T | 84_D | 1.743 | 0.99 |
| 33_V | 70_E | 1.610 | 0.99 |
| 92_V | 96_L | 1.604 | 0.98 |
| 12_A | 19_G | 1.579 | 0.98 |
| 86_R | 90_S | 1.572 | 0.98 |
| 68_C | 105_I | 1.529 | 0.98 |
| 59_D | 85_N | 1.518 | 0.98 |
| 23_S | 79_Y | 1.472 | 0.97 |
| 12_A | 23_S | 1.472 | 0.97 |
| 34_C | 63_W | 1.460 | 0.97 |
| 72_G | 75_A | 1.417 | 0.96 |
| 17_E | 81_S | 1.413 | 0.96 |
| 18_T | 88_A | 1.378 | 0.95 |
| 92_V | 107_F | 1.352 | 0.94 |
| 100_A | 103_T | 1.351 | 0.94 |
| 67_M | 92_V | 1.325 | 0.94 |
| 49_L | 52_I | 1.285 | 0.92 |
| 58_F | 79_Y | 1.282 | 0.92 |
| 21_H | 25_A | 1.280 | 0.92 |
| 65_M | 68_C | 1.242 | 0.90 |
| 61_D | 85_N | 1.226 | 0.90 |
| 90_S | 94_N | 1.224 | 0.90 |
| 25_A | 63_W | 1.210 | 0.89 |
| 17_E | 84_D | 1.200 | 0.88 |
| 43_K | 46_Q | 1.193 | 0.88 |
| 59_D | 82_S | 1.190 | 0.88 |
| 18_T | 22_I | 1.165 | 0.86 |
| 80_V | 84_D | 1.146 | 0.85 |
| 33_V | 104_R | 1.137 | 0.84 |
| 37_E | 44_R | 1.118 | 0.83 |
| 61_D | 89_G | 1.101 | 0.82 |
| 59_D | 88_A | 1.048 | 0.77 |
| 22_I | 88_A | 1.040 | 0.76 |
| 31_A | 34_C | 1.033 | 0.76 |
| 25_A | 76_S | 1.031 | 0.75 |
| 42_D | 46_Q | 1.021 | 0.74 |
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 | |
| 2cmyB | 1 | 0.1909 | 5.3 | 0.935 | Contact Map |
| 1olgA | 4 | 0.1364 | 4.6 | 0.937 | Contact Map |
| 3bdlA | 1 | 0.2091 | 4 | 0.939 | Contact Map |
| 1q2fA | 1 | 0.2727 | 3 | 0.943 | Contact Map |
| 3zy0A | 4 | 0.0727 | 2.7 | 0.944 | Contact Map |
| 2plxB | 1 | 0.2364 | 2.3 | 0.946 | Contact Map |
| 1qgiA | 1 | 0.4818 | 2.3 | 0.946 | Contact Map |
| 1kvpA | 1 | 0.4 | 2.2 | 0.947 | Contact Map |
| 4m8nA | 4 | 0.9364 | 2.2 | 0.947 | Contact Map |
| 1gff1 | 1 | 0.3182 | 2.1 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)