| 2kqf |
| ID: | 1468855554 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (95) | ||
| Sequences: | 102 (58.9) | ||
| Seq/Len: | 1.074 | ||
| Nf(neff/√len): | 6.0 |
HHblits Results: (2016_02)
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: 1.074).
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 |
| 3_S | 45_D | 1.713 | 0.89 |
| 58_D | 63_V | 1.549 | 0.82 |
| 23_A | 37_H | 1.488 | 0.78 |
| 23_A | 38_H | 1.450 | 0.75 |
| 67_P | 89_I | 1.445 | 0.75 |
| 52_A | 64_N | 1.437 | 0.74 |
| 57_G | 95_E | 1.424 | 0.73 |
| 10_I | 48_P | 1.415 | 0.73 |
| 44_E | 75_E | 1.395 | 0.71 |
| 23_A | 36_V | 1.374 | 0.69 |
| 16_K | 75_E | 1.338 | 0.67 |
| 3_S | 9_I | 1.331 | 0.66 |
| 70_G | 76_V | 1.298 | 0.63 |
| 20_T | 75_E | 1.289 | 0.62 |
| 73_H | 77_V | 1.276 | 0.61 |
| 42_H | 83_S | 1.273 | 0.61 |
| 8_I | 40_V | 1.267 | 0.60 |
| 20_T | 27_Y | 1.266 | 0.60 |
| 34_Y | 40_V | 1.265 | 0.60 |
| 77_V | 80_I | 1.251 | 0.59 |
| 66_E | 76_V | 1.244 | 0.58 |
| 45_D | 65_G | 1.242 | 0.58 |
| 72_V | 91_T | 1.242 | 0.58 |
| 29_G | 34_Y | 1.239 | 0.58 |
| 91_T | 96_N | 1.223 | 0.56 |
| 26_V | 38_H | 1.215 | 0.56 |
| 31_S | 60_I | 1.207 | 0.55 |
| 16_K | 44_E | 1.206 | 0.55 |
| 66_E | 79_L | 1.203 | 0.54 |
| 37_H | 70_G | 1.147 | 0.49 |
| 24_I | 38_H | 1.146 | 0.49 |
| 68_V | 80_I | 1.137 | 0.48 |
| 12_R | 16_K | 1.135 | 0.48 |
| 31_S | 48_P | 1.126 | 0.47 |
| 41_W | 48_P | 1.125 | 0.47 |
| 82_K | 89_I | 1.107 | 0.45 |
| 6_P | 51_E | 1.101 | 0.45 |
| 34_Y | 60_I | 1.092 | 0.44 |
| 5_R | 42_H | 1.089 | 0.44 |
| 50_S | 55_R | 1.073 | 0.42 |
| 13_A | 16_K | 1.066 | 0.42 |
| 69_H | 94_L | 1.063 | 0.41 |
| 19_F | 40_V | 1.059 | 0.41 |
| 27_Y | 34_Y | 1.057 | 0.41 |
| 25_R | 31_S | 1.053 | 0.40 |
| 12_R | 65_G | 1.050 | 0.40 |
| 45_D | 87_V | 1.040 | 0.39 |
| 40_V | 76_V | 1.040 | 0.39 |
| 18_G | 58_D | 1.037 | 0.39 |
| 12_R | 80_I | 1.035 | 0.39 |
| 48_P | 60_I | 1.022 | 0.38 |
| 7_P | 62_H | 1.000 | 0.36 |
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 | |
| 3khfA | 2 | 0.9583 | 99.7 | 0.543 | Contact Map |
| 2yuyA | 1 | 1 | 99.7 | 0.547 | Contact Map |
| 2z17A | 1 | 0.9583 | 99.6 | 0.575 | Contact Map |
| 2egoA | 2 | 0.9271 | 99.6 | 0.579 | Contact Map |
| 2xkxA | 2 | 0.9792 | 99.5 | 0.583 | Contact Map |
| 1z87A | 1 | 0.9271 | 99.5 | 0.594 | Contact Map |
| 3qe1A | 1 | 0.9583 | 99.5 | 0.595 | Contact Map |
| 1uewA | 1 | 1 | 99.5 | 0.595 | Contact Map |
| 3l4fD | 1 | 1 | 99.5 | 0.596 | Contact Map |
| 1q3oA | 2 | 1 | 99.5 | 0.596 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)