| VP1 -force run |
| ID: | 1502232372 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (119) | ||
| Sequences: | 69 (42.6) | ||
| Seq/Len: | 0.580 | ||
| Nf(neff/√len): | 3.9 |
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: 0.580).
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 |
| 5_V | 112_S | 1.958 | 0.87 |
| 101_V | 106_G | 1.744 | 0.77 |
| 35_S | 38_G | 1.716 | 0.76 |
| 86_G | 120_I | 1.632 | 0.70 |
| 98_A | 114_W | 1.620 | 0.69 |
| 108_W | 119_V | 1.617 | 0.69 |
| 47_A | 50_R | 1.599 | 0.68 |
| 111_D | 114_W | 1.553 | 0.65 |
| 46_P | 50_R | 1.494 | 0.60 |
| 95_N | 117_D | 1.491 | 0.60 |
| 102_G | 106_G | 1.450 | 0.57 |
| 63_P | 120_I | 1.424 | 0.55 |
| 47_A | 52_N | 1.388 | 0.52 |
| 47_A | 51_L | 1.352 | 0.49 |
| 34_D | 38_G | 1.335 | 0.48 |
| 99_D | 112_S | 1.329 | 0.47 |
| 110_C | 114_W | 1.314 | 0.46 |
| 109_H | 114_W | 1.313 | 0.46 |
| 46_P | 49_K | 1.297 | 0.45 |
| 97_G | 101_V | 1.280 | 0.43 |
| 15_P | 21_G | 1.264 | 0.42 |
| 100_G | 106_G | 1.248 | 0.41 |
| 10_G | 13_E | 1.225 | 0.39 |
| 58_D | 119_V | 1.217 | 0.38 |
| 19_A | 25_P | 1.214 | 0.38 |
| 105_S | 111_D | 1.208 | 0.38 |
| 98_A | 111_D | 1.195 | 0.37 |
| 46_P | 51_L | 1.195 | 0.37 |
| 35_S | 39_T | 1.189 | 0.36 |
| 101_V | 104_S | 1.188 | 0.36 |
| 73_A | 79_G | 1.165 | 0.35 |
| 107_N | 111_D | 1.151 | 0.34 |
| 29_S | 64_D | 1.143 | 0.33 |
| 48_R | 51_L | 1.139 | 0.33 |
| 15_P | 117_D | 1.130 | 0.32 |
| 16_V | 30_P | 1.128 | 0.32 |
| 76_S | 95_N | 1.106 | 0.30 |
| 33_P | 36_S | 1.103 | 0.30 |
| 7_E | 105_S | 1.094 | 0.30 |
| 97_G | 100_G | 1.086 | 0.29 |
| 34_D | 39_T | 1.084 | 0.29 |
| 40_G | 43_G | 1.080 | 0.29 |
| 100_G | 103_N | 1.080 | 0.29 |
| 72_P | 75_P | 1.079 | 0.29 |
| 33_P | 38_G | 1.078 | 0.29 |
| 35_S | 40_G | 1.075 | 0.28 |
| 34_D | 41_K | 1.074 | 0.28 |
| 32_E | 98_A | 1.067 | 0.28 |
| 97_G | 102_G | 1.058 | 0.27 |
| 9_L | 21_G | 1.051 | 0.27 |
| 91_M | 117_D | 1.046 | 0.27 |
| 98_A | 105_S | 1.043 | 0.26 |
| 31_V | 116_G | 1.040 | 0.26 |
| 95_N | 120_I | 1.036 | 0.26 |
| 4_R | 12_V | 1.035 | 0.26 |
| 60_D | 84_A | 1.035 | 0.26 |
| 4_R | 17_K | 1.033 | 0.26 |
| 105_S | 114_W | 1.033 | 0.26 |
| 97_G | 106_G | 1.033 | 0.26 |
| 62_V | 104_S | 1.031 | 0.26 |
| 33_P | 39_T | 1.024 | 0.25 |
| 101_V | 105_S | 1.024 | 0.25 |
| 14_E | 59_A | 1.024 | 0.25 |
| 3_K | 32_E | 1.015 | 0.25 |
| 16_V | 19_A | 1.015 | 0.25 |
| 10_G | 114_W | 1.012 | 0.24 |
| 6_L | 12_V | 1.007 | 0.24 |
| 10_G | 109_H | 1.006 | 0.24 |
| 19_A | 112_S | 1.005 | 0.24 |
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 | |
| 3ng9A | 10 | 0.2 | 99.9 | 0.396 | Contact Map |
| 4iovA | 1 | 0.175 | 99.9 | 0.445 | Contact Map |
| 3nttA | 1 | 0.1833 | 99.9 | 0.456 | Contact Map |
| 4g0rA | 1 | 0.175 | 99.8 | 0.509 | Contact Map |
| 4qc8A | 1 | 0.175 | 99.5 | 0.609 | Contact Map |
| 1k3vA | 1 | 0.175 | 99.3 | 0.644 | Contact Map |
| 4dpvZ | 1 | 0.3 | 99.1 | 0.681 | Contact Map |
| 2pk2A | 4 | 0.25 | 81 | 0.883 | Contact Map |
| 4kblA | 2 | 0.1 | 10.9 | 0.932 | Contact Map |
| 1s58A | 1 | 0.1667 | 5.2 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)