| TssM_Cyto_CT |
| ID: | 1488992351 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 112 (110) | ||
| Sequences: | 257 (194.2) | ||
| Seq/Len: | 2.336 | ||
| Nf(neff/√len): | 18.5 |
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: 2.336).
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 |
| 62_A | 93_T | 2.143 | 1.00 |
| 29_Y | 33_S | 1.905 | 0.99 |
| 63_G | 66_F | 1.847 | 0.99 |
| 12_P | 35_A | 1.637 | 0.96 |
| 45_V | 49_L | 1.589 | 0.95 |
| 28_Y | 38_F | 1.563 | 0.95 |
| 32_L | 79_H | 1.539 | 0.94 |
| 11_L | 60_L | 1.482 | 0.93 |
| 94_V | 102_Q | 1.433 | 0.91 |
| 67_S | 79_H | 1.401 | 0.90 |
| 32_L | 67_S | 1.361 | 0.88 |
| 63_G | 87_W | 1.334 | 0.86 |
| 103_P | 106_T | 1.332 | 0.86 |
| 19_I | 54_R | 1.330 | 0.86 |
| 33_S | 68_P | 1.308 | 0.85 |
| 14_L | 32_L | 1.306 | 0.85 |
| 57_R | 60_L | 1.283 | 0.83 |
| 42_I | 49_L | 1.270 | 0.82 |
| 30_F | 81_W | 1.269 | 0.82 |
| 14_L | 34_L | 1.255 | 0.81 |
| 22_I | 50_S | 1.240 | 0.80 |
| 12_P | 32_L | 1.201 | 0.77 |
| 20_Q | 54_R | 1.200 | 0.77 |
| 2_K | 5_A | 1.196 | 0.77 |
| 87_W | 105_R | 1.194 | 0.77 |
| 31_L | 79_H | 1.184 | 0.76 |
| 45_V | 112_R | 1.175 | 0.75 |
| 81_W | 91_P | 1.171 | 0.75 |
| 56_Y | 96_Q | 1.167 | 0.74 |
| 12_P | 17_Q | 1.158 | 0.73 |
| 64_I | 111_R | 1.153 | 0.73 |
| 15_V | 62_A | 1.151 | 0.73 |
| 68_P | 108_H | 1.151 | 0.73 |
| 45_V | 52_L | 1.143 | 0.72 |
| 45_V | 64_I | 1.120 | 0.70 |
| 27_R | 46_V | 1.118 | 0.70 |
| 3_L | 36_E | 1.116 | 0.69 |
| 2_K | 76_S | 1.115 | 0.69 |
| 66_F | 107_G | 1.112 | 0.69 |
| 7_L | 22_I | 1.111 | 0.69 |
| 29_Y | 49_L | 1.096 | 0.67 |
| 95_Q | 103_P | 1.092 | 0.67 |
| 11_L | 39_R | 1.088 | 0.67 |
| 43_D | 49_L | 1.085 | 0.66 |
| 6_Q | 108_H | 1.081 | 0.66 |
| 3_L | 94_V | 1.070 | 0.65 |
| 44_A | 64_I | 1.064 | 0.64 |
| 41_N | 49_L | 1.060 | 0.64 |
| 30_F | 107_G | 1.050 | 0.63 |
| 20_Q | 81_W | 1.048 | 0.62 |
| 29_Y | 61_L | 1.046 | 0.62 |
| 67_S | 107_G | 1.044 | 0.62 |
| 35_A | 70_T | 1.038 | 0.61 |
| 28_Y | 31_L | 1.037 | 0.61 |
| 10_M | 87_W | 1.030 | 0.60 |
| 41_N | 60_L | 1.029 | 0.60 |
| 16_A | 19_I | 1.025 | 0.60 |
| 21_Q | 53_L | 1.024 | 0.60 |
| 4_K | 35_A | 1.012 | 0.58 |
| 100_R | 106_T | 1.005 | 0.58 |
| 77_V | 83_M | 1.002 | 0.57 |
| 75_R | 100_R | 1.001 | 0.57 |
| 58_Q | 83_M | 1.001 | 0.57 |
| 75_R | 92_E | 1.000 | 0.57 |
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 | |
| 2li6A | 1 | 0.8036 | 21.3 | 0.897 | Contact Map |
| 1ig6A | 1 | 0.7054 | 9.2 | 0.912 | Contact Map |
| 2zshB | 1 | 0.3482 | 8.3 | 0.914 | Contact Map |
| 2lm1A | 1 | 0.7768 | 6.9 | 0.917 | Contact Map |
| 4z9nA | 6 | 0 | 6.9 | 0.917 | Contact Map |
| 2eqyA | 1 | 0.7768 | 6.5 | 0.918 | Contact Map |
| 2jxjA | 1 | 0.7232 | 6.5 | 0.918 | Contact Map |
| 2rq5A | 1 | 0.7679 | 5.6 | 0.921 | Contact Map |
| 2nlyA | 1 | 0.4732 | 5.5 | 0.921 | Contact Map |
| 2jrzA | 1 | 0.7589 | 4.8 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)