| d3c1nd3 |
| ID: | 1450773380 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 66 (66) | ||
| Sequences: | 3003 (1596) | ||
| Seq/Len: | 45.500 | ||
| Nf(neff/√len): | 196.5 |
HHblits Results: (2015_06)
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: 45.500).
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 |
| 52_D | 55_N | 3.664 | 1.00 |
| 20_K | 63_K | 3.628 | 1.00 |
| 2_C | 53_L | 2.487 | 1.00 |
| 21_I | 46_F | 2.312 | 1.00 |
| 23_T | 27_E | 2.145 | 1.00 |
| 28_S | 55_N | 2.035 | 1.00 |
| 27_E | 63_K | 2.028 | 1.00 |
| 21_I | 60_L | 1.894 | 1.00 |
| 5_S | 45_S | 1.891 | 1.00 |
| 11_M | 16_G | 1.684 | 1.00 |
| 49_D | 52_D | 1.632 | 1.00 |
| 55_N | 58_R | 1.550 | 1.00 |
| 4_I | 56_C | 1.469 | 1.00 |
| 23_T | 63_K | 1.460 | 1.00 |
| 18_A | 22_F | 1.441 | 1.00 |
| 4_I | 60_L | 1.424 | 1.00 |
| 28_S | 59_K | 1.399 | 0.99 |
| 3_V | 47_V | 1.392 | 0.99 |
| 24_A | 63_K | 1.310 | 0.99 |
| 47_V | 61_H | 1.264 | 0.99 |
| 54_L | 58_R | 1.246 | 0.98 |
| 30_A | 56_C | 1.225 | 0.98 |
| 2_C | 50_E | 1.212 | 0.98 |
| 31_N | 35_I | 1.197 | 0.98 |
| 6_V | 21_I | 1.181 | 0.98 |
| 33_K | 49_D | 1.173 | 0.98 |
| 9_A | 42_V | 1.170 | 0.97 |
| 24_A | 59_K | 1.169 | 0.97 |
| 25_V | 56_C | 1.154 | 0.97 |
| 34_M | 38_G | 1.149 | 0.97 |
| 19_G | 26_S | 1.123 | 0.97 |
| 62_E | 66_E | 1.075 | 0.95 |
| 24_A | 28_S | 1.069 | 0.95 |
| 3_V | 45_S | 1.058 | 0.95 |
| 25_V | 30_A | 1.032 | 0.94 |
| 5_S | 43_N | 1.023 | 0.93 |
| 53_L | 61_H | 1.017 | 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 | |
| 3tviA | 12 | 1 | 99.4 | -0.158 | Contact Map |
| 3c1mA | 4 | 1 | 99.4 | -0.146 | Contact Map |
| 2cdqA | 2 | 0.9848 | 99.3 | -0.124 | Contact Map |
| 3l76A | 2 | 0.9697 | 99.3 | -0.124 | Contact Map |
| 2j0wA | 1 | 0.9697 | 99.3 | -0.107 | Contact Map |
| 3ab4A | 8 | 0.9697 | 99.2 | -0.077 | Contact Map |
| 4go7X | 1 | 0.9697 | 99.1 | -0.032 | Contact Map |
| 3s1tA | 2 | 0.9697 | 99.1 | -0.029 | Contact Map |
| 2dt9A | 2 | 0.9545 | 99.1 | -0.027 | Contact Map |
| 3mahA | 1 | 0.8788 | 99.1 | -0.026 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)