| 4J8T_A |
| ID: | 1415824321 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (126) | ||
| Sequences: | 282 (245.4) | ||
| Seq/Len: | 2.238 | ||
| Nf(neff/√len): | 21.9 |
Jackhmmer Results: (2014_04_16)
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: 2.238).
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 |
| 30_G | 51_I | 2.356 | 1.00 |
| 83_E | 116_R | 2.160 | 1.00 |
| 26_F | 30_G | 2.065 | 0.99 |
| 6_I | 107_T | 1.981 | 0.99 |
| 46_E | 50_T | 1.815 | 0.98 |
| 27_H | 36_Y | 1.799 | 0.98 |
| 36_Y | 99_A | 1.761 | 0.98 |
| 18_D | 21_G | 1.748 | 0.98 |
| 31_V | 44_R | 1.728 | 0.97 |
| 28_P | 111_Q | 1.724 | 0.97 |
| 74_T | 77_P | 1.692 | 0.97 |
| 33_E | 44_R | 1.690 | 0.97 |
| 20_R | 52_W | 1.657 | 0.96 |
| 78_D | 108_R | 1.646 | 0.96 |
| 34_Y | 119_F | 1.611 | 0.95 |
| 108_R | 113_L | 1.521 | 0.93 |
| 48_R | 56_R | 1.494 | 0.92 |
| 104_V | 117_L | 1.489 | 0.92 |
| 7_V | 80_A | 1.471 | 0.92 |
| 26_F | 115_Y | 1.455 | 0.91 |
| 63_T | 89_V | 1.414 | 0.89 |
| 88_G | 97_L | 1.386 | 0.88 |
| 27_H | 113_L | 1.384 | 0.88 |
| 72_Y | 104_V | 1.381 | 0.88 |
| 7_V | 82_G | 1.377 | 0.88 |
| 7_V | 105_L | 1.339 | 0.86 |
| 87_D | 98_A | 1.335 | 0.85 |
| 101_Y | 119_F | 1.325 | 0.85 |
| 76_D | 108_R | 1.307 | 0.84 |
| 84_F | 103_S | 1.293 | 0.83 |
| 33_E | 114_L | 1.274 | 0.82 |
| 37_P | 119_F | 1.244 | 0.79 |
| 84_F | 115_Y | 1.213 | 0.77 |
| 68_D | 85_H | 1.210 | 0.77 |
| 18_D | 51_I | 1.209 | 0.77 |
| 106_R | 114_L | 1.198 | 0.76 |
| 81_I | 104_V | 1.196 | 0.76 |
| 79_L | 106_R | 1.190 | 0.75 |
| 30_G | 114_L | 1.185 | 0.75 |
| 27_H | 32_L | 1.174 | 0.74 |
| 28_P | 113_L | 1.173 | 0.74 |
| 31_V | 114_L | 1.158 | 0.72 |
| 44_R | 47_G | 1.155 | 0.72 |
| 84_F | 101_Y | 1.143 | 0.71 |
| 74_T | 79_L | 1.137 | 0.70 |
| 85_H | 100_D | 1.135 | 0.70 |
| 28_P | 49_E | 1.134 | 0.70 |
| 48_R | 74_T | 1.105 | 0.67 |
| 76_D | 106_R | 1.093 | 0.66 |
| 120_N | 123_R | 1.087 | 0.65 |
| 34_Y | 115_Y | 1.078 | 0.64 |
| 10_A | 22_W | 1.062 | 0.63 |
| 38_P | 120_N | 1.046 | 0.61 |
| 106_R | 113_L | 1.044 | 0.61 |
| 84_F | 102_I | 1.039 | 0.60 |
| 31_V | 47_G | 1.039 | 0.60 |
| 22_W | 100_D | 1.025 | 0.58 |
| 78_D | 107_T | 1.014 | 0.57 |
| 4_K | 73_E | 1.013 | 0.57 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1s5aA | 4 | 1 | 99.9 | 0.495 | Contact Map |
| 1z1sA | 1 | 0.9847 | 99.9 | 0.499 | Contact Map |
| 3jumA | 2 | 0.9924 | 99.9 | 0.526 | Contact Map |
| 3ff0A | 2 | 0.9924 | 99.9 | 0.531 | Contact Map |
| 3grdA | 2 | 0.9847 | 99.8 | 0.554 | Contact Map |
| 3dm8A | 1 | 0.9847 | 99.8 | 0.557 | Contact Map |
| 2a15A | 1 | 0.9695 | 99.8 | 0.572 | Contact Map |
| 3fgyA | 2 | 0.9771 | 99.8 | 0.572 | Contact Map |
| 3dmcA | 2 | 0.9237 | 99.8 | 0.576 | Contact Map |
| 3i0yA | 4 | 0.9542 | 99.8 | 0.579 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)