| rhod |
| ID: | 1431425881 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (119) | ||
| Sequences: | 382 (242) | ||
| Seq/Len: | 3.210 | ||
| Nf(neff/√len): | 22.2 |
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: 3.210).
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_D | 88_D | 2.908 | 1.00 |
| 82_D | 87_D | 2.681 | 1.00 |
| 8_L | 85_I | 2.317 | 1.00 |
| 3_F | 8_L | 2.270 | 1.00 |
| 33_T | 49_E | 2.016 | 1.00 |
| 37_D | 40_A | 1.925 | 1.00 |
| 50_Y | 81_L | 1.907 | 0.99 |
| 30_M | 52_L | 1.903 | 0.99 |
| 75_I | 80_F | 1.668 | 0.98 |
| 13_K | 20_G | 1.556 | 0.97 |
| 29_T | 107_H | 1.520 | 0.97 |
| 21_I | 101_I | 1.518 | 0.97 |
| 52_L | 57_N | 1.512 | 0.96 |
| 8_L | 27_I | 1.493 | 0.96 |
| 12_L | 53_F | 1.457 | 0.95 |
| 79_K | 82_D | 1.449 | 0.95 |
| 30_M | 36_Y | 1.443 | 0.95 |
| 96_L | 101_I | 1.434 | 0.95 |
| 4_T | 7_E | 1.385 | 0.93 |
| 25_E | 29_T | 1.380 | 0.93 |
| 2_Q | 37_D | 1.380 | 0.93 |
| 42_V | 46_E | 1.379 | 0.93 |
| 18_Y | 52_L | 1.371 | 0.93 |
| 50_Y | 57_N | 1.364 | 0.93 |
| 25_E | 107_H | 1.364 | 0.93 |
| 49_E | 56_S | 1.362 | 0.93 |
| 41_I | 81_L | 1.336 | 0.92 |
| 33_T | 56_S | 1.320 | 0.91 |
| 115_L | 118_W | 1.317 | 0.91 |
| 32_H | 110_L | 1.287 | 0.90 |
| 31_F | 35_G | 1.257 | 0.88 |
| 56_S | 107_H | 1.249 | 0.88 |
| 22_A | 96_L | 1.224 | 0.86 |
| 79_K | 88_D | 1.222 | 0.86 |
| 19_G | 22_A | 1.197 | 0.84 |
| 114_K | 118_W | 1.185 | 0.84 |
| 9_S | 30_M | 1.184 | 0.84 |
| 43_E | 46_E | 1.181 | 0.83 |
| 107_H | 113_E | 1.179 | 0.83 |
| 42_V | 45_N | 1.161 | 0.82 |
| 116_E | 119_L | 1.156 | 0.82 |
| 30_M | 85_I | 1.134 | 0.80 |
| 9_S | 13_K | 1.133 | 0.80 |
| 62_K | 69_S | 1.121 | 0.79 |
| 5_K | 31_F | 1.115 | 0.78 |
| 8_L | 30_M | 1.096 | 0.77 |
| 12_L | 27_I | 1.065 | 0.74 |
| 29_T | 101_I | 1.055 | 0.73 |
| 14_D | 84_D | 1.041 | 0.71 |
| 79_K | 87_D | 1.032 | 0.70 |
| 32_H | 36_Y | 1.027 | 0.70 |
| 60_W | 103_Y | 1.020 | 0.69 |
| 83_D | 86_T | 1.018 | 0.69 |
| 57_N | 64_S | 1.012 | 0.68 |
| 31_F | 84_D | 1.008 | 0.68 |
| 37_D | 112_T | 1.008 | 0.68 |
| 10_Q | 39_Q | 1.006 | 0.67 |
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 | |
| 3b72A | 1 | 1 | 100 | 0.102 | Contact Map |
| 2vb1A | 1 | 1 | 100 | 0.118 | Contact Map |
| 2z2fA | 1 | 1 | 100 | 0.126 | Contact Map |
| 1yroA | 2 | 0.9837 | 100 | 0.176 | Contact Map |
| 1b9oA | 1 | 0.9837 | 100 | 0.188 | Contact Map |
| 2goiA | 3 | 0.9919 | 100 | 0.2 | Contact Map |
| 2nwdX | 1 | 0.9919 | 100 | 0.201 | Contact Map |
| 1hmlA | 1 | 0.9837 | 100 | 0.204 | Contact Map |
| 1lmqA | 1 | 0.9919 | 100 | 0.21 | Contact Map |
| 2gv0A | 1 | 0.9919 | 100 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)