| 1wdn_gln_id95_min100 |
| ID: | 1394220284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (99) | ||
| Sequences: | 4121 (2786.7) | ||
| Seq/Len: | 41.626 | ||
| Nf(neff/√len): | 280.1 |
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: 41.626).
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 |
| 35_D | 38_K | 4.036 | 1.00 |
| 75_N | 78_N | 3.520 | 1.00 |
| 63_V | 72_Q | 3.324 | 1.00 |
| 63_V | 67_K | 2.927 | 1.00 |
| 83_H | 88_I | 2.708 | 1.00 |
| 23_I | 40_I | 2.331 | 1.00 |
| 4_T | 16_P | 2.296 | 1.00 |
| 33_I | 38_K | 2.213 | 1.00 |
| 50_L | 62_S | 2.159 | 1.00 |
| 27_A | 31_I | 2.137 | 1.00 |
| 74_P | 78_N | 2.044 | 1.00 |
| 23_I | 31_I | 1.912 | 1.00 |
| 57_K | 60_T | 1.892 | 1.00 |
| 55_A | 73_F | 1.853 | 1.00 |
| 12_F | 16_P | 1.828 | 1.00 |
| 17_M | 25_L | 1.803 | 1.00 |
| 9_F | 46_Y | 1.757 | 1.00 |
| 58_S | 74_P | 1.734 | 1.00 |
| 67_K | 72_Q | 1.665 | 1.00 |
| 56_V | 63_V | 1.655 | 1.00 |
| 55_A | 79_A | 1.631 | 1.00 |
| 33_I | 44_G | 1.574 | 1.00 |
| 33_I | 99_G | 1.527 | 1.00 |
| 2_T | 29_A | 1.518 | 1.00 |
| 64_D | 68_A | 1.505 | 1.00 |
| 85_T | 89_L | 1.421 | 1.00 |
| 52_V | 82_L | 1.380 | 0.99 |
| 22_I | 27_A | 1.354 | 0.99 |
| 19_F | 22_I | 1.337 | 0.99 |
| 38_K | 41_D | 1.283 | 0.99 |
| 53_M | 88_I | 1.246 | 0.98 |
| 4_T | 10_E | 1.236 | 0.98 |
| 96_Q | 99_G | 1.233 | 0.98 |
| 6_F | 30_G | 1.223 | 0.98 |
| 48_S | 85_T | 1.212 | 0.98 |
| 4_T | 12_F | 1.200 | 0.98 |
| 31_I | 40_I | 1.197 | 0.98 |
| 51_L | 85_T | 1.197 | 0.98 |
| 18_D | 21_G | 1.178 | 0.98 |
| 64_D | 67_K | 1.171 | 0.98 |
| 22_I | 25_L | 1.168 | 0.97 |
| 66_A | 82_L | 1.162 | 0.97 |
| 21_G | 25_L | 1.159 | 0.97 |
| 53_M | 92_S | 1.119 | 0.96 |
| 76_I | 83_H | 1.102 | 0.96 |
| 19_F | 31_I | 1.081 | 0.95 |
| 1_A | 22_I | 1.065 | 0.95 |
| 10_E | 16_P | 1.059 | 0.95 |
| 28_L | 45_Y | 1.053 | 0.95 |
| 90_Y | 93_L | 1.023 | 0.93 |
| 56_V | 72_Q | 1.001 | 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 | |
| 1wdnA | 1 | 1 | 97.8 | 0.646 | Contact Map |
| 4oenA | 2 | 1 | 97.4 | 0.673 | Contact Map |
| 2rc8A | 2 | 1 | 94.9 | 0.743 | Contact Map |
| 1pb7A | 1 | 0.9223 | 94.6 | 0.747 | Contact Map |
| 3i6vA | 1 | 0.9903 | 93.3 | 0.76 | Contact Map |
| 3vv5A | 2 | 1 | 92.6 | 0.766 | Contact Map |
| 2v3uA | 1 | 0.9903 | 90.6 | 0.778 | Contact Map |
| 4jwxA | 1 | 1 | 90.2 | 0.78 | Contact Map |
| 4dz1A | 1 | 0.9903 | 89.2 | 0.784 | Contact Map |
| 3kbrA | 1 | 1 | 87.8 | 0.79 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)