| T0824 |
| ID: | 1403209699 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (106) | ||
| Sequences: | 197 (166.9) | ||
| Seq/Len: | 1.858 | ||
| Nf(neff/√len): | 16.2 |
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: 1.858).
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 | 4.736 | 1.00 |
| 59_D | 86_R | 2.388 | 1.00 |
| 34_C | 63_W | 2.112 | 0.99 |
| 68_C | 105_I | 1.961 | 0.99 |
| 92_V | 107_F | 1.916 | 0.98 |
| 21_H | 76_S | 1.831 | 0.97 |
| 67_M | 96_L | 1.795 | 0.97 |
| 63_W | 107_F | 1.767 | 0.97 |
| 80_V | 84_D | 1.568 | 0.92 |
| 18_T | 80_V | 1.563 | 0.92 |
| 72_G | 75_A | 1.559 | 0.92 |
| 12_A | 23_S | 1.527 | 0.91 |
| 67_M | 92_V | 1.521 | 0.91 |
| 15_Y | 87_G | 1.475 | 0.89 |
| 34_C | 65_M | 1.470 | 0.89 |
| 45_R | 66_A | 1.390 | 0.85 |
| 49_L | 60_R | 1.380 | 0.84 |
| 11_P | 34_C | 1.324 | 0.81 |
| 21_H | 88_A | 1.277 | 0.77 |
| 18_T | 88_A | 1.246 | 0.75 |
| 18_T | 84_D | 1.234 | 0.74 |
| 34_C | 68_C | 1.233 | 0.74 |
| 21_H | 85_N | 1.233 | 0.74 |
| 94_N | 109_V | 1.215 | 0.72 |
| 59_D | 90_S | 1.208 | 0.71 |
| 7_V | 42_D | 1.207 | 0.71 |
| 25_A | 63_W | 1.176 | 0.68 |
| 10_F | 91_W | 1.125 | 0.63 |
| 25_A | 85_N | 1.121 | 0.63 |
| 19_G | 25_A | 1.111 | 0.62 |
| 47_E | 50_K | 1.111 | 0.62 |
| 12_A | 19_G | 1.110 | 0.62 |
| 60_R | 65_M | 1.108 | 0.62 |
| 10_F | 68_C | 1.099 | 0.61 |
| 48_S | 103_T | 1.097 | 0.61 |
| 98_G | 109_V | 1.097 | 0.61 |
| 8_L | 20_A | 1.096 | 0.60 |
| 49_L | 52_I | 1.096 | 0.60 |
| 82_S | 99_Y | 1.094 | 0.60 |
| 34_C | 91_W | 1.084 | 0.59 |
| 106_L | 109_V | 1.079 | 0.59 |
| 76_S | 80_V | 1.071 | 0.58 |
| 49_L | 59_D | 1.070 | 0.58 |
| 58_F | 79_Y | 1.051 | 0.56 |
| 85_N | 88_A | 1.051 | 0.56 |
| 16_P | 55_K | 1.049 | 0.55 |
| 25_A | 29_G | 1.048 | 0.55 |
| 16_P | 84_D | 1.045 | 0.55 |
| 60_R | 79_Y | 1.044 | 0.55 |
| 19_G | 23_S | 1.028 | 0.53 |
| 65_M | 96_L | 1.016 | 0.52 |
| 18_T | 65_M | 1.010 | 0.51 |
| 59_D | 85_N | 1.007 | 0.51 |
| 26_I | 106_L | 1.002 | 0.50 |
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 | 12.6 | 0.93 | Contact Map |
| 3cb4D | 6 | 0.9909 | 5.2 | 0.942 | Contact Map |
| 2plxB | 1 | 0.2364 | 5 | 0.942 | Contact Map |
| 3bdlA | 1 | 0.2091 | 4.6 | 0.943 | Contact Map |
| 3j3bT | 1 | 0.3909 | 4.4 | 0.943 | Contact Map |
| 4a17P | 1 | 0.3909 | 4.3 | 0.944 | Contact Map |
| 3u5eT | 1 | 0.3909 | 4.3 | 0.944 | Contact Map |
| 3iz5U | 1 | 0.4 | 4.2 | 0.944 | Contact Map |
| 3zf7U | 1 | 0.3909 | 4 | 0.945 | Contact Map |
| 1vq8Q | 1 | 0.3909 | 3.4 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)