| xc0362N |
| ID: | 1450200132 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (133) | ||
| Sequences: | 682 (544.9) | ||
| Seq/Len: | 5.128 | ||
| Nf(neff/√len): | 47.2 |
HHblits Results: (2015_06)
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: 5.128).
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 |
| 12_P | 40_V | 2.904 | 1.00 |
| 28_F | 33_F | 2.585 | 1.00 |
| 37_A | 41_G | 2.324 | 1.00 |
| 19_L | 43_I | 2.142 | 1.00 |
| 54_D | 57_R | 2.093 | 1.00 |
| 23_W | 26_H | 2.021 | 1.00 |
| 53_I | 58_G | 1.864 | 1.00 |
| 8_D | 44_H | 1.838 | 1.00 |
| 26_H | 33_F | 1.794 | 1.00 |
| 23_W | 28_F | 1.784 | 1.00 |
| 15_Y | 54_D | 1.781 | 1.00 |
| 23_W | 33_F | 1.757 | 1.00 |
| 23_W | 27_P | 1.705 | 1.00 |
| 4_T | 50_Q | 1.692 | 1.00 |
| 6_D | 9_Q | 1.690 | 1.00 |
| 21_G | 26_H | 1.594 | 0.99 |
| 7_S | 35_V | 1.513 | 0.99 |
| 12_P | 35_V | 1.471 | 0.98 |
| 26_H | 31_T | 1.442 | 0.98 |
| 34_L | 58_G | 1.414 | 0.98 |
| 40_V | 51_L | 1.408 | 0.98 |
| 20_L | 26_H | 1.403 | 0.98 |
| 23_W | 39_D | 1.367 | 0.97 |
| 20_L | 50_Q | 1.365 | 0.97 |
| 7_S | 10_L | 1.305 | 0.96 |
| 4_T | 52_V | 1.299 | 0.96 |
| 15_Y | 57_R | 1.260 | 0.95 |
| 40_V | 47_R | 1.254 | 0.94 |
| 53_I | 127_F | 1.245 | 0.94 |
| 10_L | 13_G | 1.219 | 0.93 |
| 3_R | 60_D | 1.198 | 0.92 |
| 16_V | 36_D | 1.196 | 0.92 |
| 33_F | 39_D | 1.194 | 0.92 |
| 29_W | 127_F | 1.190 | 0.92 |
| 26_H | 46_S | 1.190 | 0.92 |
| 17_Y | 54_D | 1.184 | 0.92 |
| 44_H | 106_E | 1.168 | 0.91 |
| 34_L | 59_L | 1.163 | 0.91 |
| 5_I | 43_I | 1.150 | 0.90 |
| 16_V | 123_V | 1.146 | 0.90 |
| 122_V | 126_M | 1.143 | 0.90 |
| 10_L | 52_V | 1.127 | 0.89 |
| 26_H | 32_S | 1.120 | 0.89 |
| 41_G | 44_H | 1.119 | 0.89 |
| 28_F | 32_S | 1.118 | 0.89 |
| 115_I | 137_D | 1.118 | 0.89 |
| 31_T | 48_I | 1.107 | 0.88 |
| 105_I | 108_E | 1.104 | 0.88 |
| 32_S | 48_I | 1.100 | 0.87 |
| 20_L | 31_T | 1.087 | 0.87 |
| 27_P | 46_S | 1.086 | 0.87 |
| 95_R | 99_V | 1.067 | 0.85 |
| 19_L | 52_V | 1.054 | 0.84 |
| 88_A | 96_A | 1.053 | 0.84 |
| 91_E | 95_R | 1.051 | 0.84 |
| 17_Y | 57_R | 1.044 | 0.84 |
| 107_A | 110_V | 1.037 | 0.83 |
| 16_V | 51_L | 1.023 | 0.82 |
| 15_Y | 58_G | 1.019 | 0.81 |
| 20_L | 23_W | 1.017 | 0.81 |
| 34_L | 113_R | 1.012 | 0.81 |
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 | |
| 3tm8A | 2 | 0.7786 | 98.4 | 0.668 | Contact Map |
| 2rjgA | 4 | 0.3786 | 23.1 | 0.898 | Contact Map |
| 4dyjA | 2 | 0.3786 | 18.5 | 0.903 | Contact Map |
| 2i32A | 2 | 0.5286 | 13.1 | 0.909 | Contact Map |
| 4dzaA | 1 | 0.3786 | 12.2 | 0.91 | Contact Map |
| 4bhyA | 4 | 0.3714 | 10.5 | 0.913 | Contact Map |
| 3kw3A | 2 | 0.3714 | 9.8 | 0.914 | Contact Map |
| 1xfcA | 2 | 0.3857 | 9.6 | 0.914 | Contact Map |
| 1rcqA | 1 | 0.3786 | 9.3 | 0.915 | Contact Map |
| 3s46A | 2 | 0.3643 | 8.3 | 0.917 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)