| NTF2_3t8n |
| ID: | 1436406365 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (125) | ||
| Sequences: | 19718 (15901) | ||
| Seq/Len: | 157.744 | ||
| Nf(neff/√len): | 1422.2 |
Jackhmmer Results: (2015_01_07)
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: 157.744).
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 |
| 29_V | 54_A | 3.249 | 1.00 |
| 24_D | 27_A | 3.196 | 1.00 |
| 33_A | 114_Q | 2.231 | 1.00 |
| 39_E | 117_Q | 2.042 | 1.00 |
| 86_F | 101_V | 2.036 | 1.00 |
| 36_A | 53_I | 2.035 | 1.00 |
| 18_E | 22_V | 2.023 | 1.00 |
| 32_Y | 36_A | 1.955 | 1.00 |
| 19_L | 27_A | 1.919 | 1.00 |
| 34_D | 50_R | 1.871 | 1.00 |
| 26_E | 54_A | 1.869 | 1.00 |
| 106_R | 115_T | 1.864 | 1.00 |
| 37_T | 115_T | 1.822 | 1.00 |
| 29_V | 50_R | 1.812 | 1.00 |
| 54_A | 58_R | 1.789 | 1.00 |
| 109_E | 114_Q | 1.767 | 1.00 |
| 49_G | 52_Q | 1.765 | 1.00 |
| 27_A | 30_Q | 1.734 | 1.00 |
| 10_Q | 14_A | 1.680 | 1.00 |
| 15_R | 31_M | 1.666 | 1.00 |
| 72_G | 87_R | 1.649 | 1.00 |
| 39_E | 115_T | 1.603 | 1.00 |
| 37_T | 48_H | 1.586 | 1.00 |
| 6_A | 10_Q | 1.569 | 1.00 |
| 106_R | 114_Q | 1.554 | 1.00 |
| 25_I | 29_V | 1.554 | 1.00 |
| 7_Q | 10_Q | 1.485 | 1.00 |
| 11_G | 15_R | 1.444 | 1.00 |
| 25_I | 58_R | 1.417 | 1.00 |
| 39_E | 46_P | 1.406 | 0.99 |
| 81_C | 106_R | 1.398 | 0.99 |
| 89_E | 98_A | 1.391 | 0.99 |
| 103_A | 116_M | 1.387 | 0.99 |
| 51_E | 55_A | 1.360 | 0.99 |
| 6_A | 11_G | 1.315 | 0.99 |
| 55_A | 58_R | 1.291 | 0.99 |
| 19_L | 31_M | 1.287 | 0.99 |
| 88_V | 99_L | 1.283 | 0.99 |
| 15_R | 27_A | 1.262 | 0.99 |
| 70_L | 89_E | 1.254 | 0.99 |
| 32_Y | 116_M | 1.248 | 0.99 |
| 107_F | 113_I | 1.240 | 0.98 |
| 26_E | 29_V | 1.239 | 0.98 |
| 16_A | 31_M | 1.230 | 0.98 |
| 14_A | 18_E | 1.221 | 0.98 |
| 51_E | 54_A | 1.220 | 0.98 |
| 83_A | 104_V | 1.211 | 0.98 |
| 15_R | 19_L | 1.210 | 0.98 |
| 55_A | 59_Q | 1.205 | 0.98 |
| 7_Q | 11_G | 1.174 | 0.98 |
| 32_Y | 53_I | 1.161 | 0.97 |
| 58_R | 62_G | 1.158 | 0.97 |
| 103_A | 118_A | 1.154 | 0.97 |
| 50_R | 54_A | 1.144 | 0.97 |
| 17_I | 21_D | 1.119 | 0.96 |
| 86_F | 103_A | 1.113 | 0.96 |
| 87_R | 98_A | 1.099 | 0.96 |
| 47_I | 52_Q | 1.080 | 0.95 |
| 23_G | 61_L | 1.072 | 0.95 |
| 15_R | 18_E | 1.071 | 0.95 |
| 81_C | 104_V | 1.061 | 0.95 |
| 87_R | 100_D | 1.059 | 0.95 |
| 33_A | 108_D | 1.049 | 0.94 |
| 33_A | 112_R | 1.049 | 0.94 |
| 29_V | 51_E | 1.041 | 0.94 |
| 108_D | 112_R | 1.038 | 0.94 |
| 19_L | 24_D | 1.036 | 0.94 |
| 37_T | 46_P | 1.032 | 0.94 |
| 18_E | 21_D | 1.024 | 0.93 |
| 22_V | 27_A | 1.004 | 0.93 |
| 59_Q | 63_G | 1.002 | 0.92 |
| 16_A | 28_I | 1.001 | 0.92 |
| 12_L | 31_M | 1.000 | 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 | |
| 3k0zA | 2 | 0.9771 | 99.7 | 0.205 | Contact Map |
| 1oh0A | 2 | 0.9695 | 99.7 | 0.206 | Contact Map |
| 1s5aA | 4 | 0.9924 | 99.7 | 0.228 | Contact Map |
| 3wmdA | 2 | 0.9695 | 99.7 | 0.23 | Contact Map |
| 3i0yA | 4 | 0.9771 | 99.7 | 0.232 | Contact Map |
| 2a15A | 1 | 0.9466 | 99.7 | 0.232 | Contact Map |
| 3rgaA | 1 | 0.9847 | 99.7 | 0.233 | Contact Map |
| 4lgqA | 4 | 0.9389 | 99.7 | 0.238 | Contact Map |
| 2f99A | 4 | 0.9389 | 99.7 | 0.238 | Contact Map |
| 2gexA | 2 | 0.9466 | 99.7 | 0.238 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)