| NTF2_3t8n |
| ID: | 1433799041 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (123) | ||
| Sequences: | 3901 (3060.5) | ||
| Seq/Len: | 31.715 | ||
| Nf(neff/√len): | 276.0 |
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: 31.715).
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 |
| 106_R | 115_T | 2.991 | 1.00 |
| 34_D | 50_R | 2.965 | 1.00 |
| 33_A | 114_Q | 2.780 | 1.00 |
| 29_V | 54_A | 2.587 | 1.00 |
| 86_F | 101_V | 2.535 | 1.00 |
| 24_D | 27_A | 2.402 | 1.00 |
| 14_A | 18_E | 2.112 | 1.00 |
| 108_D | 114_Q | 2.090 | 1.00 |
| 36_A | 53_I | 2.063 | 1.00 |
| 71_T | 87_R | 1.961 | 1.00 |
| 26_E | 54_A | 1.864 | 1.00 |
| 10_Q | 14_A | 1.779 | 1.00 |
| 12_L | 107_F | 1.704 | 1.00 |
| 87_R | 98_A | 1.688 | 1.00 |
| 83_A | 104_V | 1.665 | 1.00 |
| 18_E | 22_V | 1.592 | 1.00 |
| 29_V | 50_R | 1.584 | 1.00 |
| 89_E | 98_A | 1.563 | 1.00 |
| 103_A | 118_A | 1.554 | 1.00 |
| 86_F | 103_A | 1.549 | 1.00 |
| 32_Y | 36_A | 1.533 | 1.00 |
| 37_T | 115_T | 1.533 | 1.00 |
| 39_E | 117_Q | 1.533 | 1.00 |
| 19_L | 27_A | 1.508 | 1.00 |
| 81_C | 106_R | 1.491 | 1.00 |
| 25_I | 29_V | 1.487 | 1.00 |
| 8_E | 11_G | 1.461 | 1.00 |
| 85_P | 117_Q | 1.438 | 1.00 |
| 23_G | 61_L | 1.432 | 1.00 |
| 15_R | 31_M | 1.429 | 1.00 |
| 27_A | 30_Q | 1.413 | 1.00 |
| 51_E | 55_A | 1.407 | 0.99 |
| 11_G | 15_R | 1.383 | 0.99 |
| 73_P | 85_P | 1.367 | 0.99 |
| 40_D | 118_A | 1.366 | 0.99 |
| 39_E | 115_T | 1.357 | 0.99 |
| 10_Q | 78_H | 1.342 | 0.99 |
| 9_V | 107_F | 1.339 | 0.99 |
| 32_Y | 53_I | 1.332 | 0.99 |
| 80_G | 106_R | 1.320 | 0.99 |
| 106_R | 114_Q | 1.301 | 0.99 |
| 15_R | 19_L | 1.277 | 0.99 |
| 51_E | 54_A | 1.274 | 0.99 |
| 37_T | 48_H | 1.263 | 0.99 |
| 33_A | 108_D | 1.255 | 0.99 |
| 75_R | 83_A | 1.238 | 0.98 |
| 33_A | 110_H | 1.235 | 0.98 |
| 54_A | 58_R | 1.225 | 0.98 |
| 19_L | 24_D | 1.193 | 0.98 |
| 39_E | 46_P | 1.191 | 0.98 |
| 85_P | 119_Y | 1.177 | 0.98 |
| 49_G | 52_Q | 1.173 | 0.98 |
| 69_C | 87_R | 1.171 | 0.98 |
| 74_V | 84_M | 1.136 | 0.97 |
| 26_E | 29_V | 1.134 | 0.97 |
| 50_R | 112_R | 1.133 | 0.97 |
| 80_G | 108_D | 1.129 | 0.97 |
| 73_P | 81_C | 1.127 | 0.97 |
| 34_D | 112_R | 1.125 | 0.97 |
| 25_I | 58_R | 1.123 | 0.97 |
| 87_R | 100_D | 1.119 | 0.96 |
| 35_D | 114_Q | 1.118 | 0.96 |
| 7_Q | 11_G | 1.110 | 0.96 |
| 89_E | 96_P | 1.103 | 0.96 |
| 123_V | 127_V | 1.080 | 0.95 |
| 26_E | 30_Q | 1.077 | 0.95 |
| 75_R | 78_H | 1.070 | 0.95 |
| 108_D | 112_R | 1.056 | 0.95 |
| 88_V | 99_L | 1.036 | 0.94 |
| 35_D | 49_G | 1.030 | 0.94 |
| 15_R | 30_Q | 1.029 | 0.94 |
| 32_Y | 116_M | 1.005 | 0.93 |
| 55_A | 58_R | 1.003 | 0.93 |
| 13_M | 105_M | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1oh0A | 2 | 0.9695 | 99.8 | 0.218 | Contact Map |
| 3i0yA | 4 | 0.9695 | 99.8 | 0.233 | Contact Map |
| 3wmdA | 2 | 0.9542 | 99.8 | 0.238 | Contact Map |
| 1s5aA | 4 | 0.9847 | 99.8 | 0.245 | Contact Map |
| 3k0zA | 2 | 0.9695 | 99.8 | 0.254 | Contact Map |
| 3rgaA | 1 | 0.9695 | 99.8 | 0.257 | Contact Map |
| 3msoA | 2 | 0.9389 | 99.8 | 0.261 | Contact Map |
| 3f9sA | 2 | 0.9695 | 99.8 | 0.264 | Contact Map |
| 4lgqA | 4 | 0.9313 | 99.8 | 0.265 | Contact Map |
| 2geyA | 4 | 0.9237 | 99.8 | 0.266 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)