| Q5SHP3 |
| ID: | 1377397301 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (111) | ||
| Sequences: | 1834 (985.3) | ||
| Seq/Len: | 16.523 | ||
| Nf(neff/√len): | 93.5 |
HHblits Results: (2013_03)
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: 16.523).
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 |
| 9_Y | 80_P | 2.862 | 1.00 |
| 7_A | 50_V | 2.860 | 1.00 |
| 21_V | 76_V | 2.749 | 1.00 |
| 72_K | 108_G | 2.596 | 1.00 |
| 7_A | 10_V | 2.204 | 1.00 |
| 48_A | 52_E | 2.154 | 1.00 |
| 29_L | 55_A | 2.084 | 1.00 |
| 78_E | 81_A | 2.065 | 1.00 |
| 85_V | 93_A | 2.015 | 1.00 |
| 37_R | 48_A | 1.961 | 1.00 |
| 27_K | 31_E | 1.958 | 1.00 |
| 27_K | 35_I | 1.956 | 1.00 |
| 78_E | 99_R | 1.759 | 1.00 |
| 24_I | 51_L | 1.758 | 1.00 |
| 22_D | 25_R | 1.725 | 1.00 |
| 68_R | 109_E | 1.659 | 1.00 |
| 88_R | 94_D | 1.639 | 1.00 |
| 21_V | 74_A | 1.606 | 1.00 |
| 21_V | 47_V | 1.592 | 1.00 |
| 33_R | 48_A | 1.585 | 1.00 |
| 54_A | 107_L | 1.578 | 1.00 |
| 10_V | 46_F | 1.572 | 1.00 |
| 12_I | 17_V | 1.571 | 1.00 |
| 85_V | 95_I | 1.566 | 1.00 |
| 86_L | 94_D | 1.564 | 1.00 |
| 42_R | 46_F | 1.556 | 1.00 |
| 59_V | 66_E | 1.532 | 1.00 |
| 81_A | 99_R | 1.511 | 1.00 |
| 3_A | 62_H | 1.492 | 1.00 |
| 28_S | 31_E | 1.450 | 1.00 |
| 51_L | 55_A | 1.449 | 1.00 |
| 77_D | 104_T | 1.403 | 0.99 |
| 51_L | 105_V | 1.383 | 0.99 |
| 87_P | 93_A | 1.357 | 0.99 |
| 17_V | 47_V | 1.344 | 0.99 |
| 33_R | 55_A | 1.319 | 0.99 |
| 51_L | 71_V | 1.305 | 0.99 |
| 79_G | 100_T | 1.286 | 0.99 |
| 12_I | 43_G | 1.273 | 0.99 |
| 47_V | 74_A | 1.251 | 0.99 |
| 85_V | 94_D | 1.241 | 0.98 |
| 70_Y | 110_K | 1.240 | 0.98 |
| 81_A | 97_K | 1.209 | 0.98 |
| 87_P | 94_D | 1.206 | 0.98 |
| 73_A | 106_I | 1.197 | 0.98 |
| 50_V | 103_I | 1.174 | 0.98 |
| 74_A | 105_V | 1.171 | 0.98 |
| 61_N | 64_M | 1.165 | 0.97 |
| 53_S | 57_N | 1.163 | 0.97 |
| 65_L | 68_R | 1.157 | 0.97 |
| 75_Y | 104_T | 1.153 | 0.97 |
| 3_A | 107_L | 1.120 | 0.96 |
| 72_K | 106_I | 1.112 | 0.96 |
| 58_A | 69_L | 1.107 | 0.96 |
| 19_L | 41_K | 1.098 | 0.96 |
| 2_E | 108_G | 1.089 | 0.96 |
| 23_L | 39_T | 1.072 | 0.95 |
| 23_L | 35_I | 1.070 | 0.95 |
| 2_E | 73_A | 1.067 | 0.95 |
| 17_V | 103_I | 1.036 | 0.94 |
| 18_R | 77_D | 1.015 | 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 | |
| 2zjrP | 1 | 1 | 100 | 0.002 | Contact Map |
| 3j3wS | 1 | 0.9912 | 100 | 0.01 | Contact Map |
| 4kixS | 1 | 0.9735 | 100 | 0.01 | Contact Map |
| 3bboU | 1 | 1 | 100 | 0.024 | Contact Map |
| 1i4jA | 2 | 0.9735 | 100 | 0.041 | Contact Map |
| 4ce4W | 1 | 0.9646 | 100 | 0.047 | Contact Map |
| 3j21S | 1 | 0.9823 | 100 | 0.088 | Contact Map |
| 1vq8R | 1 | 0.9646 | 100 | 0.088 | Contact Map |
| 3u5eP | 1 | 0.9912 | 100 | 0.09 | Contact Map |
| 3zf7R | 1 | 0.9823 | 100 | 0.09 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)