| sh3_2 |
| ID: | 1513268967 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 71 (63) | ||
| Sequences: | 8847 (4938.4) | ||
| Seq/Len: | 140.429 | ||
| Nf(neff/√len): | 622.2 |
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: 140.429).
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 |
| 13_A | 20_S | 3.354 | 1.00 |
| 43_C | 52_V | 2.910 | 1.00 |
| 42_L | 49_Q | 2.817 | 1.00 |
| 10_D | 22_R | 2.771 | 1.00 |
| 7_A | 21_F | 2.740 | 1.00 |
| 28_T | 44_S | 2.388 | 1.00 |
| 31_E | 42_L | 2.380 | 1.00 |
| 3_V | 32_R | 2.351 | 1.00 |
| 52_V | 57_L | 2.234 | 1.00 |
| 25_D | 45_L | 2.111 | 1.00 |
| 44_S | 49_Q | 2.084 | 1.00 |
| 4_L | 26_I | 2.059 | 1.00 |
| 4_L | 28_T | 1.901 | 1.00 |
| 5_A | 59_I | 1.856 | 1.00 |
| 6_K | 58_K | 1.784 | 1.00 |
| 41_W | 54_G | 1.652 | 1.00 |
| 21_F | 27_M | 1.641 | 1.00 |
| 22_R | 25_D | 1.597 | 1.00 |
| 3_V | 59_I | 1.582 | 1.00 |
| 6_K | 60_L | 1.504 | 1.00 |
| 8_L | 58_K | 1.484 | 1.00 |
| 27_M | 43_C | 1.436 | 1.00 |
| 10_D | 23_K | 1.418 | 1.00 |
| 26_I | 60_L | 1.380 | 0.99 |
| 5_A | 57_L | 1.367 | 0.99 |
| 5_A | 29_V | 1.316 | 0.99 |
| 6_K | 26_I | 1.314 | 0.99 |
| 50_G | 53_P | 1.280 | 0.99 |
| 45_L | 48_R | 1.143 | 0.97 |
| 53_P | 56_R | 1.083 | 0.96 |
| 32_R | 59_I | 1.067 | 0.95 |
| 30_L | 44_S | 1.060 | 0.95 |
| 39_G | 54_G | 1.052 | 0.95 |
| 12_V | 20_S | 1.023 | 0.93 |
| 19_L | 43_C | 1.006 | 0.93 |
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 | |
| 4n78F | 1 | 0 | 99.3 | 0 | Contact Map |
| 4mt7A | 1 | 0 | 99.2 | 0.009 | Contact Map |
| 2pz1A | 1 | 0.8451 | 99.2 | 0.019 | Contact Map |
| 2dvjA | 1 | 0.9577 | 99.2 | 0.029 | Contact Map |
| 4igzA | 1 | 0.9577 | 99.2 | 0.04 | Contact Map |
| 2dybA | 2 | 0.9577 | 99.2 | 0.042 | Contact Map |
| 4bneA | 2 | 0 | 99.2 | 0.048 | Contact Map |
| 3jv3A | 2 | 0.9577 | 99.2 | 0.049 | Contact Map |
| 1ug1A | 1 | 0.9859 | 99.2 | 0.05 | Contact Map |
| 3pvlA | 1 | 0.9014 | 99.2 | 0.052 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)