| 1LOP |
| ID: | 1429459369 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 164 (153) | ||
| Sequences: | 5794 (3422.7) | ||
| Seq/Len: | 37.869 | ||
| Nf(neff/√len): | 276.7 |
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: 37.869).
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 |
| 80_R | 134_D | 3.600 | 1.00 |
| 12_V | 128_E | 3.059 | 1.00 |
| 81_G | 130_M | 2.922 | 1.00 |
| 5_H | 10_D | 2.741 | 1.00 |
| 102_V | 137_K | 2.737 | 1.00 |
| 79_T | 125_E | 2.666 | 1.00 |
| 37_N | 159_S | 2.410 | 1.00 |
| 14_K | 125_E | 2.269 | 1.00 |
| 39_T | 52_G | 2.223 | 1.00 |
| 11_I | 133_V | 2.206 | 1.00 |
| 84_A | 99_F | 2.189 | 1.00 |
| 4_F | 11_I | 2.015 | 1.00 |
| 25_K | 29_D | 2.012 | 1.00 |
| 3_T | 10_D | 1.917 | 1.00 |
| 22_E | 69_K | 1.893 | 1.00 |
| 11_I | 126_V | 1.845 | 1.00 |
| 4_F | 160_V | 1.834 | 1.00 |
| 13_I | 83_L | 1.796 | 1.00 |
| 4_F | 13_I | 1.762 | 1.00 |
| 29_D | 33_E | 1.736 | 1.00 |
| 5_H | 161_T | 1.725 | 1.00 |
| 15_T | 24_V | 1.713 | 1.00 |
| 14_K | 127_V | 1.699 | 1.00 |
| 3_T | 163_S | 1.696 | 1.00 |
| 40_I | 154_D | 1.582 | 1.00 |
| 68_I | 94_A | 1.570 | 1.00 |
| 50_I | 102_V | 1.527 | 1.00 |
| 17_D | 24_V | 1.526 | 1.00 |
| 14_K | 17_D | 1.509 | 1.00 |
| 46_N | 137_K | 1.503 | 1.00 |
| 82_T | 125_E | 1.484 | 1.00 |
| 8_H | 135_K | 1.483 | 1.00 |
| 77_K | 84_A | 1.480 | 1.00 |
| 101_N | 105_N | 1.474 | 1.00 |
| 31_C | 160_V | 1.467 | 1.00 |
| 82_T | 101_N | 1.462 | 1.00 |
| 19_K | 75_G | 1.450 | 1.00 |
| 28_L | 32_R | 1.440 | 1.00 |
| 46_N | 141_T | 1.420 | 1.00 |
| 16_F | 125_E | 1.401 | 0.99 |
| 140_A | 152_K | 1.400 | 0.99 |
| 5_H | 158_E | 1.397 | 0.99 |
| 69_K | 92_H | 1.373 | 0.99 |
| 79_T | 82_T | 1.371 | 0.99 |
| 139_V | 155_V | 1.358 | 0.99 |
| 3_T | 12_V | 1.347 | 0.99 |
| 5_H | 159_S | 1.335 | 0.99 |
| 45_I | 49_M | 1.315 | 0.99 |
| 157_I | 160_V | 1.302 | 0.99 |
| 44_V | 136_I | 1.301 | 0.99 |
| 16_F | 19_K | 1.299 | 0.99 |
| 20_A | 24_V | 1.293 | 0.99 |
| 50_I | 136_I | 1.270 | 0.99 |
| 23_T | 85_M | 1.255 | 0.99 |
| 78_N | 82_T | 1.249 | 0.99 |
| 46_N | 138_G | 1.249 | 0.99 |
| 32_R | 162_V | 1.239 | 0.98 |
| 2_V | 28_L | 1.237 | 0.98 |
| 134_D | 137_K | 1.232 | 0.98 |
| 81_G | 134_D | 1.219 | 0.98 |
| 126_V | 133_V | 1.212 | 0.98 |
| 82_T | 122_V | 1.209 | 0.98 |
| 3_T | 161_T | 1.182 | 0.98 |
| 84_A | 109_N | 1.176 | 0.98 |
| 23_T | 123_F | 1.151 | 0.97 |
| 41_F | 52_G | 1.140 | 0.97 |
| 130_M | 133_V | 1.129 | 0.97 |
| 77_K | 109_N | 1.110 | 0.96 |
| 57_P | 61_Q | 1.107 | 0.96 |
| 84_A | 122_V | 1.103 | 0.96 |
| 100_I | 133_V | 1.094 | 0.96 |
| 4_F | 157_I | 1.092 | 0.96 |
| 141_T | 149_D | 1.054 | 0.95 |
| 79_T | 104_D | 1.049 | 0.94 |
| 39_T | 54_G | 1.048 | 0.94 |
| 145_G | 149_D | 1.038 | 0.94 |
| 22_E | 25_K | 1.033 | 0.94 |
| 130_M | 134_D | 1.027 | 0.94 |
| 87_R | 93_S | 1.023 | 0.93 |
| 90_A | 93_S | 1.019 | 0.93 |
| 43_R | 51_Q | 1.010 | 0.93 |
| 25_K | 28_L | 1.008 | 0.93 |
| 72_A | 118_W | 1.003 | 0.93 |
| 136_I | 155_V | 1.002 | 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 | |
| 1lopA | 1 | 1 | 100 | 0.046 | Contact Map |
| 3s6mA | 1 | 0.9756 | 100 | 0.053 | Contact Map |
| 1v9tA | 2 | 0.9512 | 100 | 0.056 | Contact Map |
| 1w74A | 2 | 0.9085 | 100 | 0.067 | Contact Map |
| 2poeA | 1 | 0.9207 | 100 | 0.07 | Contact Map |
| 2fu0A | 1 | 0.9085 | 100 | 0.074 | Contact Map |
| 2k7nA | 1 | 0.9146 | 100 | 0.074 | Contact Map |
| 2b71A | 1 | 0.9024 | 100 | 0.075 | Contact Map |
| 1zkcA | 2 | 0.9207 | 100 | 0.078 | Contact Map |
| 2oseA | 1 | 0.8963 | 100 | 0.081 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)