| Tim17 Trunc Full Both |
| ID: | 1485176539 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (137) | ||
| Sequences: | 1233 (652.7) | ||
| Seq/Len: | 9.000 | ||
| Nf(neff/√len): | 55.8 |
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: 9.000).
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 |
| 96_F | 115_S | 4.341 | 1.00 |
| 83_R | 87_D | 2.919 | 1.00 |
| 83_R | 90_N | 2.521 | 1.00 |
| 75_F | 97_F | 2.351 | 1.00 |
| 10_C | 77_C | 2.133 | 1.00 |
| 79_V | 93_I | 1.891 | 1.00 |
| 100_G | 115_S | 1.761 | 1.00 |
| 19_G | 22_F | 1.759 | 1.00 |
| 57_R | 60_V | 1.742 | 1.00 |
| 96_F | 119_A | 1.657 | 1.00 |
| 118_C | 121_L | 1.606 | 1.00 |
| 2_S | 5_H | 1.510 | 1.00 |
| 42_P | 47_G | 1.498 | 1.00 |
| 31_V | 35_I | 1.497 | 1.00 |
| 108_W | 111_T | 1.496 | 1.00 |
| 74_T | 78_A | 1.491 | 1.00 |
| 75_F | 101_A | 1.480 | 1.00 |
| 3_A | 6_S | 1.453 | 1.00 |
| 131_M | 135_Y | 1.432 | 0.99 |
| 135_Y | 138_W | 1.415 | 0.99 |
| 23_A | 26_A | 1.400 | 0.99 |
| 95_G | 99_G | 1.385 | 0.99 |
| 58_A | 62_G | 1.327 | 0.99 |
| 92_I | 123_G | 1.319 | 0.99 |
| 101_A | 104_V | 1.318 | 0.99 |
| 80_K | 90_N | 1.302 | 0.99 |
| 133_Q | 136_A | 1.294 | 0.99 |
| 73_S | 76_D | 1.285 | 0.99 |
| 79_V | 94_A | 1.280 | 0.98 |
| 36_K | 57_R | 1.272 | 0.98 |
| 124_V | 127_G | 1.251 | 0.98 |
| 132_F | 136_A | 1.237 | 0.98 |
| 91_A | 126_E | 1.235 | 0.98 |
| 11_P | 14_I | 1.201 | 0.97 |
| 95_G | 102_L | 1.188 | 0.97 |
| 65_F | 90_N | 1.174 | 0.97 |
| 64_N | 71_L | 1.163 | 0.97 |
| 34_G | 54_I | 1.157 | 0.97 |
| 69_G | 73_S | 1.139 | 0.96 |
| 22_F | 59_P | 1.129 | 0.96 |
| 14_I | 17_D | 1.121 | 0.96 |
| 72_F | 76_D | 1.120 | 0.96 |
| 7_R | 10_C | 1.116 | 0.96 |
| 9_P | 12_I | 1.115 | 0.96 |
| 78_A | 81_A | 1.102 | 0.95 |
| 41_S | 49_G | 1.094 | 0.95 |
| 107_G | 111_T | 1.094 | 0.95 |
| 36_K | 61_L | 1.090 | 0.95 |
| 71_L | 75_F | 1.085 | 0.95 |
| 94_A | 98_T | 1.080 | 0.94 |
| 85_R | 90_N | 1.073 | 0.94 |
| 6_S | 138_W | 1.073 | 0.94 |
| 51_M | 55_K | 1.069 | 0.94 |
| 123_G | 127_G | 1.061 | 0.94 |
| 40_N | 49_G | 1.044 | 0.93 |
| 87_D | 90_N | 1.036 | 0.93 |
| 100_G | 111_T | 1.030 | 0.92 |
| 132_F | 135_Y | 1.026 | 0.92 |
| 66_G | 105_R | 1.020 | 0.92 |
| 26_A | 111_T | 1.019 | 0.92 |
| 86_E | 89_W | 1.017 | 0.92 |
| 33_H | 58_A | 1.015 | 0.92 |
| 10_C | 13_V | 1.010 | 0.91 |
| 90_N | 95_G | 1.006 | 0.91 |
| 132_F | 138_W | 1.006 | 0.91 |
| 93_I | 97_F | 1.005 | 0.91 |
| 118_C | 126_E | 1.004 | 0.91 |
| 30_V | 34_G | 1.002 | 0.91 |
| 72_F | 91_A | 1.000 | 0.91 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4c9gA | 1 | 0.9071 | 8.4 | 0.924 | Contact Map |
| 2lckA | 1 | 0.9071 | 2.9 | 0.939 | Contact Map |
| 2ls2A | 1 | 0.1786 | 2.7 | 0.94 | Contact Map |
| 4rqoA | 2 | 0.5071 | 2.6 | 0.94 | Contact Map |
| 2lonA | 1 | 0.5786 | 2.6 | 0.94 | Contact Map |
| 2wscL | 1 | 0.3143 | 2.5 | 0.941 | Contact Map |
| 2lomA | 1 | 0.5429 | 1.6 | 0.947 | Contact Map |
| 1okcA | 1 | 0.9429 | 1.6 | 0.947 | Contact Map |
| 2kegA | 1 | 0.2286 | 1.5 | 0.948 | Contact Map |
| 2k0mA | 1 | 0.2571 | 1.2 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)