| av1 25-210 15-170 1-110 1-90 |
| ID: | 1513195801 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (90) | ||
| Sequences: | 164 (50) | ||
| Seq/Len: | 1.822 | ||
| Nf(neff/√len): | 5.3 |
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: 1.822).
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 |
| 61_V | 83_F | 1.733 | 0.96 |
| 13_C | 16_P | 1.609 | 0.93 |
| 71_I | 80_V | 1.570 | 0.92 |
| 64_K | 77_T | 1.537 | 0.91 |
| 48_H | 52_K | 1.531 | 0.91 |
| 11_R | 14_E | 1.403 | 0.85 |
| 47_T | 52_K | 1.390 | 0.84 |
| 13_C | 20_Q | 1.377 | 0.84 |
| 56_V | 62_L | 1.358 | 0.82 |
| 24_S | 31_I | 1.355 | 0.82 |
| 42_R | 76_H | 1.347 | 0.82 |
| 45_G | 58_S | 1.306 | 0.79 |
| 75_N | 78_N | 1.291 | 0.78 |
| 86_R | 89_R | 1.291 | 0.78 |
| 33_K | 36_C | 1.284 | 0.77 |
| 17_C | 20_Q | 1.277 | 0.77 |
| 16_P | 20_Q | 1.263 | 0.76 |
| 86_R | 90_P | 1.217 | 0.72 |
| 6_S | 9_V | 1.213 | 0.71 |
| 49_R | 57_K | 1.192 | 0.69 |
| 14_E | 17_C | 1.191 | 0.69 |
| 26_H | 33_K | 1.165 | 0.67 |
| 1_Y | 8_D | 1.160 | 0.66 |
| 14_E | 18_K | 1.158 | 0.66 |
| 70_N | 76_H | 1.148 | 0.65 |
| 44_T | 83_F | 1.141 | 0.64 |
| 71_I | 75_N | 1.139 | 0.64 |
| 10_P | 13_C | 1.138 | 0.64 |
| 66_W | 78_N | 1.133 | 0.64 |
| 50_V | 54_F | 1.129 | 0.63 |
| 23_E | 30_H | 1.129 | 0.63 |
| 60_Y | 63_G | 1.123 | 0.63 |
| 68_D | 88_R | 1.108 | 0.61 |
| 72_K | 76_H | 1.106 | 0.61 |
| 10_P | 16_P | 1.105 | 0.61 |
| 14_E | 21_S | 1.101 | 0.60 |
| 48_H | 53_R | 1.089 | 0.59 |
| 39_D | 43_G | 1.089 | 0.59 |
| 37_V | 83_F | 1.079 | 0.58 |
| 10_P | 15_G | 1.067 | 0.57 |
| 85_V | 88_R | 1.064 | 0.56 |
| 12_G | 42_R | 1.051 | 0.55 |
| 15_G | 18_K | 1.035 | 0.53 |
| 27_D | 32_G | 1.035 | 0.53 |
| 79_S | 83_F | 1.031 | 0.53 |
| 27_D | 34_V | 1.025 | 0.52 |
| 2_R | 5_R | 1.019 | 0.52 |
| 26_H | 35_M | 1.018 | 0.52 |
| 54_F | 72_K | 1.010 | 0.51 |
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 | |
| 1ansA | 1 | 0.2 | 4 | 0.959 | Contact Map |
| 1d2pA | 1 | 0.3778 | 2.7 | 0.962 | Contact Map |
| 2plxB | 1 | 0.2889 | 2.1 | 0.964 | Contact Map |
| 2lisA | 1 | 0.4444 | 2 | 0.965 | Contact Map |
| 2l1uA | 1 | 0.7556 | 1.9 | 0.965 | Contact Map |
| 1d2oA | 2 | 0.3889 | 1.6 | 0.967 | Contact Map |
| 2k8dA | 1 | 0.7444 | 1.5 | 0.967 | Contact Map |
| 4u4hA | 1 | 0.3889 | 1.5 | 0.967 | Contact Map |
| 2knpA | 1 | 0.3556 | 1.5 | 0.967 | Contact Map |
| 3ojoA | 2 | 0.3667 | 1.2 | 0.969 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)