| Tim2317 |
| ID: | 1487008053 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (74) | ||
| Sequences: | 680 (355.6) | ||
| Seq/Len: | 9.189 | ||
| Nf(neff/√len): | 41.3 |
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: 9.189).
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 |
| 70_R | 74_D | 2.773 | 1.00 |
| 1_I | 4_D | 2.076 | 1.00 |
| 44_R | 47_A | 2.039 | 1.00 |
| 45_A | 49_G | 1.782 | 1.00 |
| 61_I | 65_A | 1.572 | 1.00 |
| 65_A | 68_G | 1.479 | 1.00 |
| 55_W | 64_C | 1.433 | 0.99 |
| 56_G | 60_S | 1.411 | 0.99 |
| 21_G | 41_I | 1.396 | 0.99 |
| 35_I | 39_T | 1.386 | 0.99 |
| 21_G | 37_A | 1.344 | 0.99 |
| 47_A | 51_N | 1.333 | 0.99 |
| 5_F | 10_A | 1.308 | 0.99 |
| 17_T | 39_T | 1.297 | 0.99 |
| 25_F | 33_R | 1.254 | 0.98 |
| 18_I | 22_V | 1.246 | 0.98 |
| 16_G | 20_H | 1.243 | 0.98 |
| 38_V | 42_K | 1.233 | 0.98 |
| 60_S | 63_D | 1.202 | 0.98 |
| 10_A | 45_A | 1.192 | 0.97 |
| 34_R | 38_V | 1.190 | 0.97 |
| 4_D | 63_D | 1.189 | 0.97 |
| 39_T | 43_L | 1.183 | 0.97 |
| 32_E | 39_T | 1.126 | 0.96 |
| 35_I | 38_V | 1.116 | 0.96 |
| 42_K | 47_A | 1.109 | 0.96 |
| 4_D | 73_D | 1.083 | 0.95 |
| 36_G | 40_A | 1.083 | 0.95 |
| 54_A | 58_L | 1.080 | 0.95 |
| 45_A | 50_G | 1.072 | 0.94 |
| 57_G | 61_I | 1.069 | 0.94 |
| 34_R | 53_G | 1.065 | 0.94 |
| 31_G | 71_R | 1.058 | 0.94 |
| 8_A | 56_G | 1.054 | 0.94 |
| 27_N | 36_G | 1.037 | 0.93 |
| 19_W | 44_R | 1.030 | 0.93 |
| 1_I | 53_G | 1.019 | 0.92 |
| 31_G | 36_G | 1.013 | 0.92 |
| 3_T | 53_G | 1.009 | 0.92 |
| 19_W | 23_K | 1.009 | 0.92 |
| 27_N | 31_G | 1.008 | 0.92 |
| 43_L | 66_I | 1.002 | 0.91 |
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 | |
| 3egaA | 1 | 0.1892 | 3.8 | 0.897 | Contact Map |
| 4ryoA | 1 | 0 | 2.7 | 0.904 | Contact Map |
| 3t5oA | 1 | 0.9595 | 2.7 | 0.904 | Contact Map |
| 4cwuU | 2 | 0.9054 | 2.2 | 0.909 | Contact Map |
| 3lloA | 1 | 0.9865 | 2.1 | 0.91 | Contact Map |
| 4yarA | 1 | 0.5405 | 1.9 | 0.912 | Contact Map |
| 4xatA | 1 | 0 | 1.9 | 0.912 | Contact Map |
| 2fozA | 1 | 0.7568 | 1.7 | 0.914 | Contact Map |
| 2whxA | 1 | 0.9595 | 1.6 | 0.915 | Contact Map |
| 4wxsA | 1 | 0.9595 | 1.6 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)