| iggdomainJHfuerte |
| ID: | 1477166836 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (52) | ||
| Sequences: | 4091 (3071.1) | ||
| Seq/Len: | 78.673 | ||
| Nf(neff/√len): | 425.9 |
Jackhmmer Results: (2016_04)
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: 78.673).
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 |
| 46_D | 51_T | 3.972 | 1.00 |
| 46_D | 49_T | 3.754 | 1.00 |
| 40_D | 54_V | 2.780 | 1.00 |
| 43_W | 52_F | 2.296 | 1.00 |
| 20_A | 29_V | 1.772 | 1.00 |
| 9_G | 12_L | 1.753 | 1.00 |
| 17_T | 51_T | 1.740 | 1.00 |
| 33_Y | 36_D | 1.716 | 1.00 |
| 7_I | 10_K | 1.682 | 1.00 |
| 20_A | 31_K | 1.568 | 1.00 |
| 3_Y | 7_I | 1.396 | 0.99 |
| 5_L | 16_T | 1.392 | 0.99 |
| 40_D | 52_F | 1.352 | 0.99 |
| 25_T | 28_K | 1.306 | 0.99 |
| 17_T | 20_A | 1.286 | 0.99 |
| 26_A | 29_V | 1.271 | 0.99 |
| 42_E | 55_T | 1.178 | 0.98 |
| 37_N | 42_E | 1.171 | 0.98 |
| 45_Y | 50_K | 1.167 | 0.97 |
| 16_T | 20_A | 1.150 | 0.97 |
| 20_A | 27_E | 1.103 | 0.96 |
| 8_N | 12_L | 1.094 | 0.96 |
| 7_I | 11_T | 1.073 | 0.95 |
| 34_A | 37_N | 1.057 | 0.95 |
| 36_D | 39_V | 1.010 | 0.93 |
| 41_G | 54_V | 1.000 | 0.92 |
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 | |
| 1pgxA | 1 | 1 | 86.1 | 0.647 | Contact Map |
| 1igdA | 1 | 1 | 82.5 | 0.663 | Contact Map |
| 1pn5A | 1 | 0 | 80.7 | 0.668 | Contact Map |
| 1l3wA | 1 | 0.9643 | 78.6 | 0.676 | Contact Map |
| 2rpvA | 1 | 1 | 78.3 | 0.676 | Contact Map |
| 1q55A | 4 | 0.9643 | 77.8 | 0.678 | Contact Map |
| 2khuA | 1 | 0 | 77 | 0.68 | Contact Map |
| 3q2vA | 2 | 0.9643 | 76.5 | 0.682 | Contact Map |
| 3q2wA | 1 | 0.9643 | 76.4 | 0.682 | Contact Map |
| 3ui3A | 2 | 0.8214 | 73.9 | 0.688 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)