| 1DJTA |
| ID: | 1411752223 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 64 (64) | ||
| Sequences: | 225 (148.8) | ||
| Seq/Len: | 3.516 | ||
| Nf(neff/√len): | 18.6 |
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: 3.516).
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 |
| 23_N | 27_T | 2.426 | 1.00 |
| 33_S | 49_I | 2.251 | 1.00 |
| 42_Y | 60_P | 2.101 | 1.00 |
| 32_K | 50_E | 2.068 | 1.00 |
| 30_G | 33_S | 1.631 | 0.98 |
| 12_C | 52_P | 1.621 | 0.98 |
| 11_N | 58_R | 1.572 | 0.98 |
| 20_E | 24_D | 1.524 | 0.97 |
| 14_Y | 47_W | 1.519 | 0.97 |
| 30_G | 49_I | 1.454 | 0.96 |
| 4_A | 12_C | 1.401 | 0.95 |
| 2_R | 7_A | 1.396 | 0.95 |
| 6_I | 25_L | 1.381 | 0.94 |
| 7_A | 57_I | 1.365 | 0.94 |
| 11_N | 25_L | 1.300 | 0.92 |
| 42_Y | 61_G | 1.279 | 0.91 |
| 11_N | 61_G | 1.277 | 0.91 |
| 7_A | 58_R | 1.229 | 0.88 |
| 38_W | 44_N | 1.222 | 0.88 |
| 6_I | 47_W | 1.209 | 0.87 |
| 6_I | 43_G | 1.181 | 0.85 |
| 2_R | 30_G | 1.170 | 0.85 |
| 61_G | 64_H | 1.168 | 0.84 |
| 45_G | 52_P | 1.104 | 0.80 |
| 32_K | 55_V | 1.102 | 0.79 |
| 2_R | 12_C | 1.083 | 0.78 |
| 30_G | 55_V | 1.056 | 0.75 |
| 10_H | 54_N | 1.050 | 0.75 |
| 31_A | 55_V | 1.050 | 0.75 |
| 9_P | 19_N | 1.045 | 0.74 |
| 19_N | 35_Y | 1.030 | 0.73 |
| 23_N | 33_S | 1.027 | 0.72 |
| 2_R | 57_I | 1.019 | 0.71 |
| 4_A | 40_G | 1.012 | 0.71 |
| 3_D | 52_P | 1.007 | 0.70 |
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 | |
| 2yeoA | 1 | 1 | 99.9 | 0.041 | Contact Map |
| 1dq7A | 2 | 1 | 99.9 | 0.041 | Contact Map |
| 1kv0A | 2 | 1 | 99.9 | 0.041 | Contact Map |
| 1ahoA | 1 | 1 | 99.9 | 0.044 | Contact Map |
| 1snbA | 1 | 1 | 99.9 | 0.045 | Contact Map |
| 1bmrA | 1 | 1 | 99.9 | 0.051 | Contact Map |
| 1nraA | 1 | 0.9531 | 99.9 | 0.092 | Contact Map |
| 1t1tA | 1 | 0.9531 | 99.8 | 0.113 | Contact Map |
| 1i6fA | 1 | 0.9062 | 99.8 | 0.174 | Contact Map |
| 2i61A | 1 | 0.9219 | 99.8 | 0.183 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)