| d4aiva_ |
| ID: | 1450282011 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (105) | ||
| Sequences: | 9970 (6590.9) | ||
| Seq/Len: | 94.952 | ||
| Nf(neff/√len): | 643.2 |
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: 94.952).
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 |
| 7_T | 105_R | 3.183 | 1.00 |
| 79_A | 82_D | 3.080 | 1.00 |
| 11_Y | 100_V | 2.941 | 1.00 |
| 48_P | 78_F | 2.611 | 1.00 |
| 68_M | 77_A | 2.146 | 1.00 |
| 44_G | 94_P | 2.069 | 1.00 |
| 42_A | 98_A | 2.014 | 1.00 |
| 5_W | 99_R | 1.984 | 1.00 |
| 7_T | 107_Q | 1.904 | 1.00 |
| 52_A | 73_I | 1.904 | 1.00 |
| 10_A | 105_R | 1.846 | 1.00 |
| 11_Y | 40_V | 1.831 | 1.00 |
| 32_L | 42_A | 1.787 | 1.00 |
| 99_R | 107_Q | 1.778 | 1.00 |
| 97_P | 109_A | 1.775 | 1.00 |
| 42_A | 108_V | 1.772 | 1.00 |
| 43_V | 93_V | 1.767 | 1.00 |
| 23_L | 29_Q | 1.760 | 1.00 |
| 45_N | 56_S | 1.720 | 1.00 |
| 101_T | 107_Q | 1.692 | 1.00 |
| 28_S | 44_G | 1.682 | 1.00 |
| 41_H | 95_V | 1.638 | 1.00 |
| 77_A | 87_D | 1.600 | 1.00 |
| 45_N | 53_A | 1.571 | 1.00 |
| 70_Q | 77_A | 1.518 | 1.00 |
| 76_Q | 90_R | 1.517 | 1.00 |
| 10_A | 13_H | 1.455 | 1.00 |
| 68_M | 86_L | 1.450 | 1.00 |
| 79_A | 86_L | 1.441 | 1.00 |
| 44_G | 96_Y | 1.428 | 1.00 |
| 30_V | 42_A | 1.424 | 1.00 |
| 8_A | 108_V | 1.410 | 1.00 |
| 100_V | 106_I | 1.403 | 0.99 |
| 35_L | 41_H | 1.335 | 0.99 |
| 35_L | 39_S | 1.264 | 0.99 |
| 79_A | 84_S | 1.263 | 0.99 |
| 84_S | 92_S | 1.195 | 0.98 |
| 11_Y | 34_R | 1.185 | 0.98 |
| 40_V | 98_A | 1.182 | 0.98 |
| 19_G | 31_A | 1.168 | 0.97 |
| 9_C | 13_H | 1.144 | 0.97 |
| 7_T | 10_A | 1.104 | 0.96 |
| 34_R | 40_V | 1.096 | 0.96 |
| 40_V | 106_I | 1.096 | 0.96 |
| 43_V | 95_V | 1.092 | 0.96 |
| 9_C | 14_L | 1.091 | 0.96 |
| 50_S | 73_I | 1.087 | 0.96 |
| 33_F | 43_V | 1.082 | 0.96 |
| 52_A | 72_P | 1.080 | 0.95 |
| 48_P | 93_V | 1.061 | 0.95 |
| 19_G | 33_F | 1.060 | 0.95 |
| 76_Q | 88_D | 1.056 | 0.95 |
| 3_Q | 111_V | 1.049 | 0.94 |
| 19_G | 69_V | 1.031 | 0.94 |
| 21_G | 56_S | 1.024 | 0.93 |
| 33_F | 69_V | 1.019 | 0.93 |
| 39_S | 81_D | 1.019 | 0.93 |
| 16_P | 34_R | 1.017 | 0.93 |
| 13_H | 20_V | 1.016 | 0.93 |
| 34_R | 38_G | 1.006 | 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 | |
| 2jzaA | 1 | 0.9735 | 99.9 | 0.05 | Contact Map |
| 2jo6A | 1 | 0.9558 | 99.9 | 0.055 | Contact Map |
| 3c0dA | 8 | 0.9646 | 99.9 | 0.067 | Contact Map |
| 1vm9A | 1 | 0.9115 | 99.9 | 0.078 | Contact Map |
| 2i7fA | 2 | 0.885 | 99.9 | 0.087 | Contact Map |
| 4aivA | 1 | 0.9735 | 99.9 | 0.089 | Contact Map |
| 3gceA | 1 | 0.8938 | 99.9 | 0.09 | Contact Map |
| 2qpzA | 1 | 0.9027 | 99.9 | 0.096 | Contact Map |
| 1fqtA | 2 | 0.9115 | 99.9 | 0.096 | Contact Map |
| 2de6D | 3 | 0.9115 | 99.9 | 0.099 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)