| GLI1 100-270 |
| ID: | 1382082972 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 171 (150) | ||
| Sequences: | 16266 (13557.3) | ||
| Seq/Len: | 108.440 | ||
| Nf(neff/√len): | 1106.9 |
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: 108.440).
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 |
| 136_V | 145_R | 1.935 | 1.00 |
| 62_V | 122_A | 1.851 | 1.00 |
| 105_M | 114_A | 1.764 | 1.00 |
| 107_E | 138_K | 1.728 | 1.00 |
| 75_K | 84_S | 1.708 | 1.00 |
| 77_T | 107_E | 1.704 | 1.00 |
| 77_T | 138_K | 1.692 | 1.00 |
| 107_E | 125_Q | 1.676 | 1.00 |
| 138_K | 156_V | 1.668 | 1.00 |
| 42_V | 105_M | 1.612 | 1.00 |
| 77_T | 95_L | 1.598 | 1.00 |
| 92_K | 153_R | 1.565 | 1.00 |
| 75_K | 82_R | 1.519 | 1.00 |
| 105_M | 112_S | 1.497 | 1.00 |
| 15_C | 28_H | 1.488 | 1.00 |
| 90_N | 93_T | 1.483 | 1.00 |
| 92_K | 122_A | 1.471 | 1.00 |
| 43_C | 48_C | 1.447 | 1.00 |
| 75_K | 136_V | 1.440 | 1.00 |
| 105_M | 136_V | 1.439 | 1.00 |
| 44_H | 107_E | 1.437 | 1.00 |
| 26_V | 92_K | 1.415 | 1.00 |
| 42_V | 75_K | 1.413 | 1.00 |
| 120_D | 123_K | 1.391 | 0.99 |
| 75_K | 105_M | 1.386 | 0.99 |
| 57_A | 60_M | 1.364 | 0.99 |
| 21_S | 24_Q | 1.344 | 0.99 |
| 62_V | 153_R | 1.341 | 0.99 |
| 136_V | 143_T | 1.341 | 0.99 |
| 65_M | 125_Q | 1.329 | 0.99 |
| 122_A | 153_R | 1.328 | 0.99 |
| 26_V | 153_R | 1.327 | 0.99 |
| 62_V | 92_K | 1.317 | 0.99 |
| 26_V | 122_A | 1.312 | 0.99 |
| 87_R | 90_N | 1.310 | 0.99 |
| 95_L | 125_Q | 1.293 | 0.99 |
| 148_D | 151_S | 1.290 | 0.99 |
| 110_G | 125_Q | 1.272 | 0.99 |
| 80_G | 95_L | 1.271 | 0.99 |
| 117_N | 120_D | 1.268 | 0.99 |
| 44_H | 138_K | 1.268 | 0.99 |
| 149_P | 153_R | 1.264 | 0.99 |
| 63_V | 123_K | 1.263 | 0.99 |
| 42_V | 54_P | 1.261 | 0.99 |
| 44_H | 77_T | 1.250 | 0.99 |
| 151_S | 154_K | 1.249 | 0.99 |
| 51_E | 54_P | 1.237 | 0.98 |
| 88_L | 92_K | 1.229 | 0.98 |
| 27_H | 93_T | 1.225 | 0.98 |
| 106_C | 111_C | 1.222 | 0.98 |
| 65_M | 95_L | 1.219 | 0.98 |
| 95_L | 156_V | 1.217 | 0.98 |
| 42_V | 136_V | 1.211 | 0.98 |
| 137_C | 142_C | 1.208 | 0.98 |
| 125_Q | 156_V | 1.173 | 0.98 |
| 13_D | 77_T | 1.158 | 0.97 |
| 88_L | 149_P | 1.156 | 0.97 |
| 50_R | 65_M | 1.154 | 0.97 |
| 22_Q | 26_V | 1.151 | 0.97 |
| 58_Q | 62_V | 1.150 | 0.97 |
| 24_Q | 27_H | 1.145 | 0.97 |
| 26_V | 62_V | 1.143 | 0.97 |
| 58_Q | 88_L | 1.142 | 0.97 |
| 63_V | 93_T | 1.140 | 0.97 |
| 13_D | 29_I | 1.132 | 0.97 |
| 18_E | 84_S | 1.126 | 0.97 |
| 142_C | 155_H | 1.124 | 0.97 |
| 60_M | 63_V | 1.120 | 0.96 |
| 29_I | 95_L | 1.111 | 0.96 |
| 80_G | 110_G | 1.111 | 0.96 |
| 139_L | 143_T | 1.109 | 0.96 |
| 118_A | 122_A | 1.106 | 0.96 |
| 13_D | 44_H | 1.101 | 0.96 |
| 76_C | 81_C | 1.097 | 0.96 |
| 14_G | 29_I | 1.090 | 0.96 |
| 54_P | 114_A | 1.086 | 0.96 |
| 28_H | 35_H | 1.086 | 0.96 |
| 13_D | 138_K | 1.081 | 0.95 |
| 42_V | 52_L | 1.075 | 0.95 |
| 11_R | 16_S | 1.070 | 0.95 |
| 88_L | 118_A | 1.068 | 0.95 |
| 58_Q | 118_A | 1.066 | 0.95 |
| 64_H | 68_H | 1.057 | 0.95 |
| 80_G | 139_L | 1.056 | 0.95 |
| 27_H | 154_K | 1.047 | 0.94 |
| 22_Q | 88_L | 1.046 | 0.94 |
| 93_T | 123_K | 1.043 | 0.94 |
| 123_K | 154_K | 1.039 | 0.94 |
| 93_T | 154_K | 1.039 | 0.94 |
| 139_L | 156_V | 1.028 | 0.94 |
| 84_S | 114_A | 1.025 | 0.93 |
| 137_C | 155_H | 1.024 | 0.93 |
| 18_E | 145_R | 1.017 | 0.93 |
| 22_Q | 58_Q | 1.007 | 0.93 |
| 27_H | 63_V | 1.006 | 0.93 |
| 29_I | 65_M | 1.004 | 0.93 |
| 13_D | 107_E | 1.002 | 0.92 |
| 58_Q | 149_P | 1.001 | 0.92 |
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 | |
| 2i13A | 2 | 0.8713 | 100 | 0.237 | Contact Map |
| 3zmsC | 1 | 0 | 99.9 | 0.292 | Contact Map |
| 2gliA | 1 | 0.883 | 99.9 | 0.294 | Contact Map |
| 1tf6A | 2 | 0.9006 | 99.9 | 0.305 | Contact Map |
| 2jp9A | 1 | 0.6842 | 99.8 | 0.397 | Contact Map |
| 1ubdC | 1 | 0.655 | 99.8 | 0.399 | Contact Map |
| 2rpcA | 1 | 0.8363 | 99.8 | 0.41 | Contact Map |
| 2dlqA | 1 | 0.7018 | 99.8 | 0.417 | Contact Map |
| 2lt7A | 1 | 0.7427 | 99.8 | 0.453 | Contact Map |
| 2dmiA | 1 | 0.6374 | 99.7 | 0.501 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)