| NRH |
| ID: | 1490993420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 101 (92) | ||
| Sequences: | 349 (209.6) | ||
| Seq/Len: | 3.793 | ||
| Nf(neff/√len): | 21.9 |
Jackhmmer Results: (2016_04)
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: 3.793).
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 |
| 24_D | 27_L | 2.243 | 1.00 |
| 5_L | 17_F | 2.093 | 1.00 |
| 29_Y | 32_K | 2.066 | 1.00 |
| 17_F | 72_F | 1.676 | 0.99 |
| 17_F | 26_E | 1.617 | 0.99 |
| 13_E | 21_F | 1.563 | 0.98 |
| 12_A | 62_E | 1.510 | 0.97 |
| 16_S | 89_Q | 1.438 | 0.96 |
| 10_R | 13_E | 1.377 | 0.95 |
| 19_I | 25_V | 1.300 | 0.93 |
| 75_N | 85_Y | 1.294 | 0.92 |
| 44_S | 50_P | 1.249 | 0.90 |
| 6_L | 94_Y | 1.243 | 0.90 |
| 5_L | 10_R | 1.232 | 0.90 |
| 7_H | 31_V | 1.222 | 0.89 |
| 53_W | 91_M | 1.195 | 0.88 |
| 6_L | 16_S | 1.180 | 0.87 |
| 17_F | 29_Y | 1.178 | 0.87 |
| 12_A | 16_S | 1.168 | 0.86 |
| 62_E | 86_E | 1.168 | 0.86 |
| 67_I | 86_E | 1.166 | 0.86 |
| 11_F | 26_E | 1.152 | 0.85 |
| 14_A | 18_A | 1.146 | 0.85 |
| 21_F | 69_D | 1.139 | 0.84 |
| 6_L | 64_L | 1.134 | 0.84 |
| 44_S | 52_E | 1.134 | 0.84 |
| 73_V | 78_L | 1.117 | 0.82 |
| 5_L | 72_F | 1.095 | 0.81 |
| 82_W | 88_T | 1.094 | 0.81 |
| 75_N | 78_L | 1.085 | 0.80 |
| 69_D | 73_V | 1.080 | 0.79 |
| 18_A | 24_D | 1.077 | 0.79 |
| 30_K | 69_D | 1.065 | 0.78 |
| 5_L | 8_K | 1.064 | 0.78 |
| 6_L | 15_E | 1.058 | 0.77 |
| 13_E | 92_L | 1.054 | 0.77 |
| 26_E | 57_V | 1.051 | 0.77 |
| 15_E | 25_V | 1.048 | 0.76 |
| 4_R | 94_Y | 1.043 | 0.76 |
| 42_L | 51_T | 1.039 | 0.76 |
| 59_E | 72_F | 1.033 | 0.75 |
| 6_L | 11_F | 1.033 | 0.75 |
| 50_P | 53_W | 1.029 | 0.75 |
| 11_F | 82_W | 1.028 | 0.75 |
| 75_N | 79_E | 1.025 | 0.74 |
| 33_S | 36_I | 1.021 | 0.74 |
| 29_Y | 68_Q | 1.017 | 0.73 |
| 21_F | 27_L | 1.013 | 0.73 |
| 8_K | 36_I | 1.011 | 0.73 |
| 8_K | 17_F | 1.011 | 0.73 |
| 17_F | 23_L | 1.005 | 0.72 |
| 69_D | 82_W | 1.005 | 0.72 |
| 5_L | 23_L | 1.003 | 0.72 |
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 | |
| 5a1uD | 1 | 0 | 69.8 | 0.853 | Contact Map |
| 3mkqA | 3 | 0.5545 | 37.3 | 0.879 | Contact Map |
| 1xi4A | 9 | 0.8218 | 26.6 | 0.888 | Contact Map |
| 5a1uC | 1 | 0 | 26.5 | 0.889 | Contact Map |
| 4kmoB | 1 | 0.8218 | 19.3 | 0.896 | Contact Map |
| 1bpoA | 3 | 0.8218 | 17.6 | 0.897 | Contact Map |
| 4bx9C | 1 | 0.3762 | 15.9 | 0.899 | Contact Map |
| 2p58C | 1 | 0.6337 | 15.8 | 0.899 | Contact Map |
| 2uwjG | 1 | 0.6337 | 15.4 | 0.9 | Contact Map |
| 4rr2B | 2 | 0.9901 | 14.5 | 0.901 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)