| Precursor-HVR-1 |
| ID: | 1495170273 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (141) | ||
| Sequences: | 715 (583.7) | ||
| Seq/Len: | 5.071 | ||
| Nf(neff/√len): | 49.2 |
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: 5.071).
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 |
| 13_Y | 16_P | 4.152 | 1.00 |
| 22_G | 28_T | 2.438 | 1.00 |
| 21_M | 27_V | 2.020 | 1.00 |
| 34_W | 38_N | 1.902 | 1.00 |
| 13_Y | 22_G | 1.816 | 1.00 |
| 37_E | 44_R | 1.737 | 1.00 |
| 39_D | 42_C | 1.727 | 1.00 |
| 24_F | 28_T | 1.698 | 1.00 |
| 13_Y | 24_F | 1.697 | 1.00 |
| 20_E | 26_E | 1.672 | 0.99 |
| 13_Y | 28_T | 1.608 | 0.99 |
| 37_E | 41_S | 1.546 | 0.99 |
| 23_A | 28_T | 1.524 | 0.99 |
| 61_G | 64_A | 1.424 | 0.98 |
| 37_E | 40_W | 1.417 | 0.98 |
| 25_S | 39_D | 1.416 | 0.98 |
| 120_A | 123_A | 1.402 | 0.97 |
| 4_E | 7_G | 1.366 | 0.97 |
| 37_E | 46_C | 1.363 | 0.97 |
| 1_M | 5_K | 1.339 | 0.96 |
| 126_A | 131_L | 1.329 | 0.96 |
| 38_N | 44_R | 1.324 | 0.96 |
| 22_G | 27_V | 1.313 | 0.96 |
| 134_D | 138_S | 1.305 | 0.96 |
| 37_E | 43_V | 1.292 | 0.95 |
| 41_S | 45_V | 1.286 | 0.95 |
| 29_L | 38_N | 1.253 | 0.94 |
| 2_D | 5_K | 1.248 | 0.94 |
| 21_M | 24_F | 1.246 | 0.94 |
| 10_I | 16_P | 1.226 | 0.93 |
| 1_M | 4_E | 1.224 | 0.93 |
| 36_F | 44_R | 1.216 | 0.93 |
| 40_W | 44_R | 1.211 | 0.93 |
| 120_A | 124_V | 1.206 | 0.93 |
| 35_G | 38_N | 1.192 | 0.92 |
| 3_E | 6_I | 1.159 | 0.91 |
| 1_M | 6_I | 1.147 | 0.90 |
| 5_K | 8_N | 1.146 | 0.90 |
| 31_R | 36_F | 1.140 | 0.90 |
| 30_G | 37_E | 1.138 | 0.90 |
| 130_A | 134_D | 1.136 | 0.89 |
| 47_L | 52_P | 1.127 | 0.89 |
| 134_D | 137_L | 1.114 | 0.88 |
| 31_R | 40_W | 1.112 | 0.88 |
| 3_E | 7_G | 1.111 | 0.88 |
| 13_Y | 23_A | 1.111 | 0.88 |
| 112_S | 131_L | 1.110 | 0.88 |
| 41_S | 44_R | 1.090 | 0.87 |
| 38_N | 41_S | 1.081 | 0.86 |
| 24_F | 29_L | 1.081 | 0.86 |
| 76_G | 105_P | 1.078 | 0.86 |
| 7_G | 10_I | 1.073 | 0.85 |
| 18_V | 28_T | 1.049 | 0.84 |
| 4_E | 8_N | 1.047 | 0.84 |
| 68_W | 76_G | 1.047 | 0.84 |
| 37_E | 45_V | 1.045 | 0.83 |
| 31_R | 44_R | 1.042 | 0.83 |
| 23_A | 26_E | 1.035 | 0.83 |
| 40_W | 43_V | 1.024 | 0.82 |
| 83_F | 88_G | 1.021 | 0.81 |
| 10_I | 13_Y | 1.019 | 0.81 |
| 57_A | 61_G | 1.015 | 0.81 |
| 39_D | 43_V | 1.011 | 0.80 |
| 135_D | 138_S | 1.009 | 0.80 |
| 34_W | 37_E | 1.007 | 0.80 |
| 54_K | 58_H | 1.006 | 0.80 |
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 | |
| 3iylA | 20 | 0.5141 | 0.7 | 0.894 | Contact Map |
| 2pstX | 1 | 0.4296 | 0.6 | 0.901 | Contact Map |
| 1tz7A | 2 | 0.9296 | 0.6 | 0.902 | Contact Map |
| 3j2vC | 4 | 0.669 | 0.5 | 0.904 | Contact Map |
| 1x1nA | 1 | 0.9296 | 0.5 | 0.906 | Contact Map |
| 1eswA | 1 | 0.9296 | 0.5 | 0.908 | Contact Map |
| 3kxsF | 6 | 0.669 | 0.4 | 0.91 | Contact Map |
| 3hheA | 2 | 0.338 | 0.4 | 0.912 | Contact Map |
| 2ra1A | 1 | 0.3873 | 0.4 | 0.912 | Contact Map |
| 2f8mA | 2 | 0.331 | 0.4 | 0.916 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)