| 4nn2A |
| ID: | 1491921418 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (123) | ||
| Sequences: | 1134 (696.8) | ||
| Seq/Len: | 9.220 | ||
| Nf(neff/√len): | 62.8 |
HHblits Results: (2016_02)
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: 9.220).
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 |
| 68_G | 82_T | 3.124 | 1.00 |
| 119_C | 122_H | 2.988 | 1.00 |
| 71_M | 84_G | 2.729 | 1.00 |
| 5_C | 8_C | 2.586 | 1.00 |
| 94_Y | 117_L | 2.572 | 1.00 |
| 32_H | 35_C | 2.245 | 1.00 |
| 67_R | 84_G | 2.073 | 1.00 |
| 64_E | 67_R | 1.887 | 1.00 |
| 95_H | 98_C | 1.722 | 1.00 |
| 84_G | 93_T | 1.674 | 1.00 |
| 73_C | 76_C | 1.619 | 1.00 |
| 90_C | 95_H | 1.602 | 1.00 |
| 90_C | 98_C | 1.581 | 1.00 |
| 33_Y | 44_Q | 1.536 | 1.00 |
| 38_F | 99_G | 1.523 | 1.00 |
| 75_L | 104_A | 1.476 | 1.00 |
| 19_G | 22_H | 1.470 | 1.00 |
| 41_G | 64_E | 1.460 | 1.00 |
| 71_M | 93_T | 1.458 | 1.00 |
| 7_F | 31_A | 1.424 | 0.99 |
| 57_D | 60_T | 1.400 | 0.99 |
| 39_S | 82_T | 1.370 | 0.99 |
| 76_C | 80_G | 1.364 | 0.99 |
| 5_C | 35_C | 1.302 | 0.99 |
| 5_C | 32_H | 1.294 | 0.99 |
| 14_E | 17_A | 1.285 | 0.99 |
| 76_C | 90_C | 1.259 | 0.98 |
| 65_I | 68_G | 1.256 | 0.98 |
| 12_E | 19_G | 1.238 | 0.98 |
| 85_C | 95_H | 1.223 | 0.98 |
| 85_C | 98_C | 1.211 | 0.98 |
| 39_S | 68_G | 1.206 | 0.98 |
| 40_S | 84_G | 1.197 | 0.98 |
| 63_Q | 88_K | 1.194 | 0.97 |
| 64_E | 69_K | 1.185 | 0.97 |
| 10_V | 97_H | 1.170 | 0.97 |
| 94_Y | 102_D | 1.147 | 0.97 |
| 34_K | 44_Q | 1.144 | 0.96 |
| 6_G | 29_A | 1.141 | 0.96 |
| 76_C | 95_H | 1.139 | 0.96 |
| 76_C | 85_C | 1.134 | 0.96 |
| 105_K | 123_S | 1.107 | 0.96 |
| 4_K | 9_H | 1.062 | 0.94 |
| 26_A | 89_A | 1.061 | 0.94 |
| 120_K | 123_S | 1.061 | 0.94 |
| 22_H | 30_A | 1.057 | 0.94 |
| 74_T | 120_K | 1.049 | 0.94 |
| 68_G | 71_M | 1.043 | 0.93 |
| 37_L | 56_F | 1.035 | 0.93 |
| 85_C | 90_C | 1.029 | 0.93 |
| 62_L | 66_K | 1.017 | 0.92 |
| 111_S | 114_I | 1.014 | 0.92 |
| 61_V | 67_R | 1.012 | 0.92 |
| 73_C | 85_C | 1.010 | 0.92 |
| 82_T | 96_Y | 1.002 | 0.91 |
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 | |
| 4nn2A | 2 | 0.9919 | 100 | 0.126 | Contact Map |
| 2lq6A | 1 | 0.5081 | 99.4 | 0.565 | Contact Map |
| 4lk9A | 1 | 0.8145 | 90.3 | 0.841 | Contact Map |
| 4gneA | 1 | 0.7177 | 89.3 | 0.844 | Contact Map |
| 2kwjA | 1 | 0.8065 | 83 | 0.858 | Contact Map |
| 3v43A | 1 | 0.8145 | 79.6 | 0.862 | Contact Map |
| 1wewA | 1 | 0.5484 | 72 | 0.871 | Contact Map |
| 2ro1A | 1 | 0.3871 | 70.9 | 0.872 | Contact Map |
| 3u5nA | 2 | 0.4113 | 67.1 | 0.875 | Contact Map |
| 2g6qA | 1 | 0.371 | 65.8 | 0.876 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)