| TV-40-120 |
| ID: | 1508089229 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (81) | ||
| Sequences: | 96 (52.3) | ||
| Seq/Len: | 1.185 | ||
| Nf(neff/√len): | 5.8 |
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: 1.185).
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 |
| 17_F | 72_L | 1.707 | 0.91 |
| 42_T | 56_F | 1.610 | 0.87 |
| 60_L | 74_A | 1.585 | 0.86 |
| 41_Y | 44_H | 1.488 | 0.80 |
| 27_S | 42_T | 1.470 | 0.79 |
| 4_W | 77_I | 1.420 | 0.76 |
| 60_L | 76_I | 1.420 | 0.76 |
| 40_L | 56_F | 1.373 | 0.72 |
| 19_V | 66_A | 1.369 | 0.72 |
| 61_L | 72_L | 1.344 | 0.70 |
| 26_G | 35_S | 1.317 | 0.68 |
| 17_F | 26_G | 1.298 | 0.66 |
| 47_R | 53_S | 1.295 | 0.66 |
| 37_E | 75_A | 1.286 | 0.65 |
| 21_S | 60_L | 1.281 | 0.65 |
| 38_L | 77_I | 1.274 | 0.64 |
| 65_N | 68_S | 1.252 | 0.62 |
| 1_L | 5_V | 1.234 | 0.60 |
| 49_Y | 53_S | 1.221 | 0.59 |
| 34_I | 40_L | 1.210 | 0.58 |
| 38_L | 49_Y | 1.189 | 0.56 |
| 30_L | 71_K | 1.152 | 0.52 |
| 63_A | 68_S | 1.149 | 0.52 |
| 44_H | 69_A | 1.127 | 0.50 |
| 59_K | 80_N | 1.119 | 0.49 |
| 31_E | 68_S | 1.115 | 0.49 |
| 59_K | 66_A | 1.115 | 0.49 |
| 35_S | 80_N | 1.109 | 0.48 |
| 22_A | 41_Y | 1.108 | 0.48 |
| 55_G | 62_V | 1.107 | 0.48 |
| 24_Q | 55_G | 1.103 | 0.48 |
| 21_S | 45_L | 1.088 | 0.46 |
| 15_G | 25_P | 1.078 | 0.45 |
| 33_E | 45_L | 1.077 | 0.45 |
| 44_H | 48_M | 1.076 | 0.45 |
| 20_S | 60_L | 1.060 | 0.44 |
| 59_K | 65_N | 1.057 | 0.43 |
| 35_S | 44_H | 1.042 | 0.42 |
| 48_M | 51_G | 1.027 | 0.40 |
| 20_S | 56_F | 1.023 | 0.40 |
| 7_L | 28_V | 1.022 | 0.40 |
| 59_K | 68_S | 1.022 | 0.40 |
| 17_F | 37_E | 1.021 | 0.40 |
| 29_L | 61_L | 1.015 | 0.39 |
| 18_T | 48_M | 1.012 | 0.39 |
| 20_S | 72_L | 1.009 | 0.39 |
| 55_G | 63_A | 1.007 | 0.39 |
| 35_S | 75_A | 1.003 | 0.38 |
| 3_P | 9_Q | 1.003 | 0.38 |
| 22_A | 69_A | 1.000 | 0.38 |
| 37_E | 57_S | 1.000 | 0.38 |
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 | |
| 1ihmA | 3 | 1 | 99.9 | 0.288 | Contact Map |
| 2gh8A | 3 | 0.963 | 99.9 | 0.356 | Contact Map |
| 3j1pA | 3 | 0.963 | 99.9 | 0.365 | Contact Map |
| 3m8lA | 2 | 0.963 | 99.9 | 0.372 | Contact Map |
| 4ejrA | 2 | 0.9383 | 99.9 | 0.407 | Contact Map |
| 3vbhC | 1 | 1 | 99.9 | 0.42 | Contact Map |
| 1aym3 | 1 | 1 | 99.9 | 0.422 | Contact Map |
| 4gb33 | 1 | 1 | 99.8 | 0.43 | Contact Map |
| 1bev3 | 1 | 1 | 99.8 | 0.435 | Contact Map |
| 4wm8C | 1 | 1 | 99.8 | 0.438 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)