| d4lz2a_ |
| ID: | 1448374119 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (98) | ||
| Sequences: | 4916 (3351.1) | ||
| Seq/Len: | 50.163 | ||
| Nf(neff/√len): | 338.5 |
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: 50.163).
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 |
| 31_G | 74_F | 3.101 | 1.00 |
| 26_P | 33_R | 3.096 | 1.00 |
| 41_D | 44_T | 2.821 | 1.00 |
| 48_R | 53_G | 2.730 | 1.00 |
| 72_Q | 86_H | 2.474 | 1.00 |
| 54_Y | 63_D | 2.430 | 1.00 |
| 72_Q | 89_R | 2.265 | 1.00 |
| 12_E | 46_R | 2.161 | 1.00 |
| 76_E | 82_G | 2.110 | 1.00 |
| 64_A | 92_F | 2.096 | 1.00 |
| 45_M | 64_A | 1.983 | 1.00 |
| 65_L | 93_E | 1.968 | 1.00 |
| 12_E | 21_L | 1.950 | 1.00 |
| 95_R | 98_E | 1.622 | 1.00 |
| 38_N | 66_L | 1.604 | 1.00 |
| 65_L | 89_R | 1.601 | 1.00 |
| 40_M | 67_V | 1.590 | 1.00 |
| 38_N | 62_A | 1.547 | 1.00 |
| 61_A | 65_L | 1.526 | 1.00 |
| 61_A | 96_W | 1.492 | 1.00 |
| 55_T | 59_E | 1.483 | 1.00 |
| 45_M | 67_V | 1.481 | 1.00 |
| 36_I | 73_T | 1.468 | 1.00 |
| 8_L | 60_F | 1.467 | 1.00 |
| 25_N | 28_L | 1.445 | 1.00 |
| 61_A | 92_F | 1.428 | 1.00 |
| 71_C | 85_G | 1.423 | 1.00 |
| 48_R | 63_D | 1.383 | 0.99 |
| 82_G | 86_H | 1.379 | 0.99 |
| 72_Q | 82_G | 1.323 | 0.99 |
| 17_A | 21_L | 1.285 | 0.99 |
| 19_P | 84_A | 1.283 | 0.99 |
| 42_F | 67_V | 1.276 | 0.99 |
| 72_Q | 85_G | 1.268 | 0.99 |
| 79_S | 82_G | 1.228 | 0.98 |
| 69_D | 73_T | 1.214 | 0.98 |
| 23_P | 41_D | 1.213 | 0.98 |
| 22_E | 43_S | 1.164 | 0.97 |
| 78_D | 83_K | 1.157 | 0.97 |
| 89_R | 93_E | 1.142 | 0.97 |
| 76_E | 79_S | 1.137 | 0.97 |
| 91_F | 95_R | 1.114 | 0.96 |
| 71_C | 82_G | 1.112 | 0.96 |
| 32_Y | 36_I | 1.106 | 0.96 |
| 56_S | 59_E | 1.101 | 0.96 |
| 10_E | 95_R | 1.099 | 0.96 |
| 68_F | 88_M | 1.095 | 0.96 |
| 14_H | 91_F | 1.092 | 0.96 |
| 58_E | 62_A | 1.069 | 0.95 |
| 16_A | 87_I | 1.013 | 0.93 |
| 40_M | 63_D | 1.002 | 0.92 |
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 | |
| 4qc3A | 2 | 1 | 99.9 | -0.07 | Contact Map |
| 4qbmA | 2 | 1 | 99.9 | -0.068 | Contact Map |
| 4ir5A | 1 | 1 | 99.9 | -0.06 | Contact Map |
| 4uygA | 6 | 1 | 99.8 | -0.048 | Contact Map |
| 3mb3A | 1 | 1 | 99.8 | -0.031 | Contact Map |
| 1e6iA | 1 | 1 | 99.8 | -0.03 | Contact Map |
| 4bhwA | 2 | 1 | 99.8 | -0.028 | Contact Map |
| 3nxbA | 2 | 0.98 | 99.8 | -0.026 | Contact Map |
| 3q2eA | 1 | 1 | 99.8 | -0.026 | Contact Map |
| 4qnsA | 4 | 0.99 | 99.8 | -0.026 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)