| VP4 |
| ID: | 1414277159 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 68 (68) | ||
| Sequences: | 163 (64.3) | ||
| Seq/Len: | 2.397 | ||
| Nf(neff/√len): | 7.8 |
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: 2.397).
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 |
| 51_K | 58_D | 2.213 | 1.00 |
| 14_N | 28_T | 2.060 | 0.99 |
| 1_G | 5_S | 2.026 | 0.99 |
| 18_A | 24_I | 1.869 | 0.99 |
| 27_T | 39_A | 1.524 | 0.94 |
| 49_P | 55_P | 1.511 | 0.94 |
| 51_K | 55_P | 1.494 | 0.93 |
| 52_F | 55_P | 1.444 | 0.92 |
| 6_S | 9_V | 1.379 | 0.89 |
| 52_F | 58_D | 1.370 | 0.89 |
| 14_N | 56_I | 1.352 | 0.88 |
| 4_V | 10_G | 1.348 | 0.87 |
| 48_D | 55_P | 1.332 | 0.87 |
| 54_E | 61_I | 1.330 | 0.87 |
| 49_P | 53_T | 1.306 | 0.85 |
| 57_K | 62_K | 1.282 | 0.84 |
| 9_V | 37_S | 1.223 | 0.80 |
| 4_V | 7_Q | 1.208 | 0.78 |
| 50_S | 53_T | 1.194 | 0.77 |
| 24_I | 35_S | 1.193 | 0.77 |
| 42_K | 47_Q | 1.167 | 0.75 |
| 2_A | 5_S | 1.167 | 0.75 |
| 15_S | 28_T | 1.153 | 0.74 |
| 48_D | 53_T | 1.116 | 0.70 |
| 33_R | 45_F | 1.097 | 0.68 |
| 7_Q | 10_G | 1.083 | 0.67 |
| 3_Q | 10_G | 1.071 | 0.66 |
| 41_S | 45_F | 1.059 | 0.64 |
| 62_K | 68_N | 1.051 | 0.63 |
| 64_A | 68_N | 1.046 | 0.63 |
| 14_N | 46_S | 1.043 | 0.63 |
| 11_A | 21_G | 1.042 | 0.62 |
| 18_A | 26_Y | 1.042 | 0.62 |
| 7_Q | 13_E | 1.032 | 0.61 |
| 10_G | 18_A | 1.029 | 0.61 |
| 33_R | 39_A | 1.016 | 0.60 |
| 12_H | 44_D | 1.009 | 0.59 |
| 43_Q | 64_A | 1.008 | 0.59 |
| 8_K | 37_S | 1.006 | 0.58 |
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 | |
| 1ncqD | 1 | 0.5882 | 100 | 0.007 | Contact Map |
| 4cdqD | 1 | 0.8529 | 100 | 0.009 | Contact Map |
| 1hxs4 | 1 | 1 | 100 | 0.009 | Contact Map |
| 4gb34 | 1 | 0.8088 | 100 | 0.009 | Contact Map |
| 1bev4 | 1 | 0.5882 | 100 | 0.009 | Contact Map |
| 1aym4 | 1 | 0.4265 | 100 | 0.01 | Contact Map |
| 1c8m4 | 1 | 0.4265 | 100 | 0.012 | Contact Map |
| 1pov0 | 1 | 0.6618 | 100 | 0.106 | Contact Map |
| 4gmp0 | 1 | 0 | 100 | 0.112 | Contact Map |
| 3vbhD | 1 | 0.8529 | 99.9 | 0.16 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)