| v2 |
| ID: | 1513314175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (90) | ||
| Sequences: | 245 (91) | ||
| Seq/Len: | 2.722 | ||
| Nf(neff/√len): | 9.6 |
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: 2.722).
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 |
| 48_I | 51_S | 2.242 | 1.00 |
| 29_S | 48_I | 1.922 | 0.99 |
| 41_L | 64_F | 1.818 | 0.99 |
| 101_A | 107_Q | 1.748 | 0.98 |
| 27_L | 30_Q | 1.623 | 0.97 |
| 96_G | 103_E | 1.622 | 0.97 |
| 32_Y | 38_G | 1.525 | 0.95 |
| 27_L | 37_L | 1.496 | 0.95 |
| 62_R | 97_M | 1.487 | 0.94 |
| 99_K | 105_E | 1.445 | 0.93 |
| 80_I | 85_C | 1.445 | 0.93 |
| 89_C | 92_H | 1.434 | 0.93 |
| 62_R | 65_N | 1.423 | 0.93 |
| 35_D | 71_T | 1.386 | 0.91 |
| 86_C | 89_C | 1.369 | 0.91 |
| 36_T | 44_D | 1.321 | 0.88 |
| 63_H | 69_E | 1.315 | 0.88 |
| 76_L | 86_C | 1.303 | 0.87 |
| 22_V | 26_Q | 1.281 | 0.86 |
| 31_D | 35_D | 1.250 | 0.84 |
| 98_D | 105_E | 1.242 | 0.84 |
| 78_Q | 90_P | 1.235 | 0.83 |
| 47_C | 51_S | 1.232 | 0.83 |
| 44_D | 91_R | 1.222 | 0.83 |
| 94_T | 103_E | 1.199 | 0.81 |
| 33_S | 39_Y | 1.175 | 0.79 |
| 28_L | 31_D | 1.161 | 0.78 |
| 88_H | 91_R | 1.156 | 0.77 |
| 29_S | 42_I | 1.150 | 0.77 |
| 26_Q | 97_M | 1.145 | 0.76 |
| 35_D | 39_Y | 1.143 | 0.76 |
| 81_H | 98_D | 1.113 | 0.74 |
| 82_Q | 93_K | 1.111 | 0.73 |
| 68_V | 106_A | 1.109 | 0.73 |
| 86_C | 92_H | 1.107 | 0.73 |
| 84_C | 87_P | 1.099 | 0.72 |
| 25_L | 29_S | 1.099 | 0.72 |
| 60_R | 67_R | 1.090 | 0.71 |
| 31_D | 71_T | 1.087 | 0.71 |
| 71_T | 75_E | 1.071 | 0.69 |
| 100_Q | 103_E | 1.070 | 0.69 |
| 53_N | 75_E | 1.069 | 0.69 |
| 51_S | 59_C | 1.058 | 0.68 |
| 59_C | 62_R | 1.049 | 0.67 |
| 36_T | 40_D | 1.046 | 0.67 |
| 44_D | 88_H | 1.024 | 0.64 |
| 68_V | 94_T | 1.021 | 0.64 |
| 72_S | 96_G | 1.008 | 0.63 |
| 21_S | 25_L | 1.001 | 0.62 |
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 | |
| 3qkyA | 1 | 0.9444 | 6.4 | 0.961 | Contact Map |
| 4oe9A | 2 | 0.3519 | 6 | 0.961 | Contact Map |
| 4w8yA | 2 | 0.6204 | 4.8 | 0.963 | Contact Map |
| 3x1lA | 1 | 0 | 4.5 | 0.964 | Contact Map |
| 4mbeH | 4 | 0.1204 | 4.3 | 0.964 | Contact Map |
| 2wnfA | 1 | 0.2037 | 4.1 | 0.964 | Contact Map |
| 1dl0A | 1 | 0.2593 | 3.8 | 0.965 | Contact Map |
| 2ashA | 4 | 0.9259 | 3.5 | 0.966 | Contact Map |
| 4p0gA | 1 | 0.5741 | 3.4 | 0.966 | Contact Map |
| 3pdeA | 4 | 0.5093 | 3.2 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)