| hat |
| ID: | 1430231621 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 65 (65) | ||
| Sequences: | 142 (79.1) | ||
| Seq/Len: | 2.185 | ||
| Nf(neff/√len): | 9.8 |
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: 2.185).
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 |
| 15_I | 31_C | 2.190 | 1.00 |
| 25_F | 63_L | 1.827 | 0.98 |
| 34_T | 37_E | 1.773 | 0.98 |
| 29_V | 52_D | 1.692 | 0.97 |
| 44_T | 48_N | 1.691 | 0.97 |
| 40_K | 61_H | 1.632 | 0.96 |
| 1_N | 26_V | 1.354 | 0.86 |
| 3_V | 29_V | 1.343 | 0.85 |
| 6_K | 12_I | 1.337 | 0.85 |
| 26_V | 65_Y | 1.336 | 0.85 |
| 47_M | 51_K | 1.335 | 0.85 |
| 49_H | 63_L | 1.324 | 0.84 |
| 29_V | 45_H | 1.322 | 0.84 |
| 20_F | 29_V | 1.288 | 0.82 |
| 43_G | 64_T | 1.286 | 0.82 |
| 43_G | 51_K | 1.224 | 0.77 |
| 41_G | 51_K | 1.223 | 0.77 |
| 33_I | 39_V | 1.194 | 0.75 |
| 41_G | 47_M | 1.194 | 0.75 |
| 1_N | 4_I | 1.189 | 0.74 |
| 43_G | 47_M | 1.126 | 0.68 |
| 9_M | 29_V | 1.094 | 0.65 |
| 4_I | 22_S | 1.091 | 0.65 |
| 16_C | 59_I | 1.085 | 0.64 |
| 6_K | 61_H | 1.072 | 0.63 |
| 33_I | 63_L | 1.072 | 0.63 |
| 19_T | 33_I | 1.051 | 0.61 |
| 3_V | 20_F | 1.041 | 0.60 |
| 3_V | 7_R | 1.040 | 0.59 |
| 8_D | 46_L | 1.033 | 0.59 |
| 9_M | 33_I | 1.030 | 0.58 |
| 12_I | 22_S | 1.012 | 0.56 |
| 14_G | 25_F | 1.003 | 0.55 |
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 | |
| 1yghA | 2 | 1 | 97.9 | 0.734 | Contact Map |
| 2r7hA | 2 | 1 | 97.7 | 0.746 | Contact Map |
| 4nsqA | 4 | 0.9846 | 97.7 | 0.747 | Contact Map |
| 1qstA | 1 | 1 | 97.3 | 0.764 | Contact Map |
| 1z4rA | 1 | 1 | 97.3 | 0.766 | Contact Map |
| 3d2mA | 1 | 1 | 97 | 0.774 | Contact Map |
| 3e0kA | 1 | 1 | 96.9 | 0.779 | Contact Map |
| 1n71A | 4 | 0.9846 | 96.8 | 0.781 | Contact Map |
| 2aj6A | 1 | 1 | 96.7 | 0.784 | Contact Map |
| 2fiaA | 2 | 1 | 96.7 | 0.785 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)