| 1C7KA |
| ID: | 1411602047 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (129) | ||
| Sequences: | 1147 (869.7) | ||
| Seq/Len: | 8.891 | ||
| Nf(neff/√len): | 76.6 |
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: 8.891).
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 |
| 82_A | 102_L | 3.860 | 1.00 |
| 15_Q | 36_A | 2.999 | 1.00 |
| 25_W | 125_V | 2.997 | 1.00 |
| 19_A | 36_A | 2.959 | 1.00 |
| 23_Q | 28_S | 2.813 | 1.00 |
| 119_A | 123_S | 2.609 | 1.00 |
| 65_I | 88_V | 2.406 | 1.00 |
| 83_H | 87_H | 2.277 | 1.00 |
| 65_I | 85_T | 2.243 | 1.00 |
| 89_L | 125_V | 2.219 | 1.00 |
| 22_A | 85_T | 2.138 | 1.00 |
| 101_E | 124_R | 2.072 | 1.00 |
| 67_L | 81_T | 1.998 | 1.00 |
| 53_S | 58_D | 1.982 | 1.00 |
| 53_S | 56_Q | 1.966 | 1.00 |
| 24_I | 78_T | 1.899 | 1.00 |
| 25_W | 86_G | 1.735 | 1.00 |
| 21_A | 25_W | 1.704 | 1.00 |
| 126_N | 130_A | 1.694 | 1.00 |
| 54_Y | 58_D | 1.687 | 1.00 |
| 84_E | 87_H | 1.585 | 1.00 |
| 120_Q | 124_R | 1.528 | 1.00 |
| 94_H | 101_E | 1.502 | 1.00 |
| 44_Y | 85_T | 1.498 | 1.00 |
| 101_E | 120_Q | 1.492 | 1.00 |
| 87_H | 93_D | 1.399 | 0.99 |
| 55_A | 58_D | 1.385 | 0.99 |
| 83_H | 86_G | 1.254 | 0.98 |
| 24_I | 82_A | 1.242 | 0.98 |
| 47_G | 51_R | 1.210 | 0.98 |
| 22_A | 34_L | 1.208 | 0.98 |
| 40_A | 43_S | 1.207 | 0.97 |
| 83_H | 93_D | 1.179 | 0.97 |
| 18_I | 81_T | 1.178 | 0.97 |
| 25_W | 117_P | 1.160 | 0.97 |
| 46_E | 49_D | 1.156 | 0.97 |
| 48_N | 66_F | 1.143 | 0.96 |
| 42_F | 88_V | 1.127 | 0.96 |
| 64_Y | 88_V | 1.122 | 0.96 |
| 76_D | 79_R | 1.109 | 0.95 |
| 54_Y | 57_T | 1.107 | 0.95 |
| 20_N | 78_T | 1.092 | 0.95 |
| 91_L | 103_M | 1.083 | 0.94 |
| 53_S | 57_T | 1.065 | 0.94 |
| 25_W | 30_R | 1.056 | 0.93 |
| 23_Q | 29_V | 1.054 | 0.93 |
| 48_N | 54_Y | 1.052 | 0.93 |
| 86_G | 103_M | 1.051 | 0.93 |
| 3_T | 8_P | 1.041 | 0.93 |
| 122_R | 126_N | 1.038 | 0.93 |
| 64_Y | 74_Q | 1.029 | 0.92 |
| 87_H | 103_M | 1.025 | 0.92 |
| 42_F | 129_W | 1.014 | 0.91 |
| 17_E | 78_T | 1.002 | 0.91 |
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 | |
| 1c7kA | 1 | 1 | 100 | 0.129 | Contact Map |
| 1rm8A | 1 | 0.9697 | 99.9 | 0.279 | Contact Map |
| 1su3A | 2 | 0.9621 | 99.9 | 0.28 | Contact Map |
| 1slmA | 1 | 0.9773 | 99.9 | 0.282 | Contact Map |
| 4fvlA | 2 | 0.9773 | 99.9 | 0.284 | Contact Map |
| 3ma2D | 2 | 0.9697 | 99.9 | 0.293 | Contact Map |
| 2jsdA | 1 | 0.9697 | 99.9 | 0.301 | Contact Map |
| 3ba0A | 1 | 0.9773 | 99.9 | 0.302 | Contact Map |
| 1y93A | 1 | 0.9621 | 99.9 | 0.306 | Contact Map |
| 4h1qA | 2 | 0.947 | 99.9 | 0.306 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)