| 3LDC |
| ID: | 1448275534 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (75) | ||
| Sequences: | 4574 (2977.6) | ||
| Seq/Len: | 60.987 | ||
| Nf(neff/√len): | 343.8 |
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: 60.987).
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 |
| 28_S | 31_V | 2.529 | 1.00 |
| 52_T | 55_G | 2.452 | 1.00 |
| 39_T | 45_Y | 2.251 | 1.00 |
| 38_V | 63_I | 2.218 | 1.00 |
| 34_Y | 47_D | 2.002 | 1.00 |
| 20_G | 58_F | 2.001 | 1.00 |
| 22_H | 29_W | 1.958 | 1.00 |
| 31_V | 56_M | 1.946 | 1.00 |
| 41_A | 63_I | 1.837 | 1.00 |
| 43_V | 63_I | 1.787 | 1.00 |
| 30_T | 60_C | 1.768 | 1.00 |
| 24_I | 54_L | 1.703 | 1.00 |
| 25_E | 55_G | 1.600 | 1.00 |
| 19_A | 23_F | 1.484 | 1.00 |
| 73_A | 76_R | 1.426 | 1.00 |
| 18_T | 29_W | 1.384 | 0.99 |
| 24_I | 58_F | 1.316 | 0.99 |
| 70_F | 74_V | 1.288 | 0.99 |
| 31_V | 48_Y | 1.261 | 0.99 |
| 76_R | 80_F | 1.260 | 0.99 |
| 63_I | 67_I | 1.258 | 0.99 |
| 35_W | 59_T | 1.212 | 0.98 |
| 74_V | 79_E | 1.200 | 0.98 |
| 75_E | 78_L | 1.185 | 0.98 |
| 18_T | 22_H | 1.178 | 0.98 |
| 35_W | 47_D | 1.175 | 0.98 |
| 57_Y | 61_T | 1.157 | 0.97 |
| 17_G | 58_F | 1.145 | 0.97 |
| 34_Y | 59_T | 1.145 | 0.97 |
| 28_S | 53_P | 1.144 | 0.97 |
| 17_G | 62_L | 1.144 | 0.97 |
| 52_T | 56_M | 1.085 | 0.96 |
| 27_E | 48_Y | 1.063 | 0.95 |
| 24_I | 55_G | 1.046 | 0.94 |
| 14_I | 18_T | 1.040 | 0.94 |
| 76_R | 79_E | 1.039 | 0.94 |
| 21_F | 35_W | 1.013 | 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 | |
| 3ldcA | 1 | 1 | 99.5 | 0.041 | Contact Map |
| 4bw5A | 4 | 1 | 99.4 | 0.072 | Contact Map |
| 3pjsK | 4 | 1 | 99.4 | 0.073 | Contact Map |
| 4twkA | 2 | 0.9878 | 99.4 | 0.082 | Contact Map |
| 1lnqA | 8 | 0.9756 | 99.4 | 0.083 | Contact Map |
| 4wfeA | 2 | 1 | 99.4 | 0.1 | Contact Map |
| 3effK | 4 | 1 | 99.4 | 0.1 | Contact Map |
| 3ukmA | 4 | 1 | 99.3 | 0.113 | Contact Map |
| 2q67A | 2 | 1 | 99.3 | 0.116 | Contact Map |
| 4h33A | 1 | 1 | 99.3 | 0.119 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)