| 2bl2 |
| ID: | 1499969598 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (143) | ||
| Sequences: | 1073 (613.5) | ||
| Seq/Len: | 7.503 | ||
| Nf(neff/√len): | 51.3 |
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: 7.503).
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 |
| 65_I | 85_S | 3.146 | 1.00 |
| 91_T | 134_G | 2.657 | 1.00 |
| 85_S | 89_A | 2.512 | 1.00 |
| 54_Q | 92_G | 2.230 | 1.00 |
| 18_G | 22_G | 2.040 | 1.00 |
| 25_M | 104_A | 1.915 | 1.00 |
| 124_A | 128_E | 1.753 | 1.00 |
| 60_V | 136_V | 1.749 | 1.00 |
| 125_A | 129_T | 1.744 | 1.00 |
| 32_A | 51_P | 1.726 | 1.00 |
| 37_Q | 40_K | 1.688 | 1.00 |
| 96_G | 100_G | 1.652 | 1.00 |
| 136_V | 139_F | 1.580 | 1.00 |
| 106_G | 124_A | 1.532 | 1.00 |
| 54_Q | 95_S | 1.515 | 0.99 |
| 60_V | 129_T | 1.500 | 0.99 |
| 93_L | 96_G | 1.483 | 0.99 |
| 12_T | 62_A | 1.460 | 0.99 |
| 9_A | 13_I | 1.426 | 0.99 |
| 51_P | 54_Q | 1.420 | 0.99 |
| 57_Y | 128_E | 1.411 | 0.99 |
| 135_F | 139_F | 1.409 | 0.99 |
| 74_S | 77_Q | 1.405 | 0.99 |
| 8_M | 84_A | 1.376 | 0.99 |
| 15_S | 58_G | 1.361 | 0.99 |
| 3_F | 78_G | 1.308 | 0.98 |
| 47_L | 52_G | 1.307 | 0.98 |
| 10_T | 14_F | 1.271 | 0.98 |
| 64_L | 142_V | 1.269 | 0.98 |
| 17_I | 93_L | 1.225 | 0.97 |
| 11_A | 62_A | 1.191 | 0.96 |
| 61_I | 88_I | 1.187 | 0.96 |
| 29_A | 47_L | 1.187 | 0.96 |
| 46_I | 144_N | 1.185 | 0.96 |
| 13_I | 25_M | 1.176 | 0.96 |
| 23_V | 52_G | 1.176 | 0.96 |
| 63_F | 139_F | 1.174 | 0.96 |
| 130_Y | 133_L | 1.174 | 0.96 |
| 56_L | 60_V | 1.163 | 0.95 |
| 4_A | 7_A | 1.162 | 0.95 |
| 46_I | 121_I | 1.145 | 0.95 |
| 21_K | 98_A | 1.141 | 0.95 |
| 111_A | 114_P | 1.137 | 0.95 |
| 14_F | 89_A | 1.132 | 0.94 |
| 61_I | 138_S | 1.125 | 0.94 |
| 48_Q | 91_T | 1.119 | 0.94 |
| 2_V | 6_L | 1.101 | 0.93 |
| 25_M | 97_I | 1.093 | 0.93 |
| 68_N | 81_F | 1.092 | 0.93 |
| 7_A | 85_S | 1.090 | 0.93 |
| 50_L | 53_T | 1.085 | 0.93 |
| 98_A | 127_V | 1.083 | 0.93 |
| 68_N | 143_L | 1.079 | 0.92 |
| 54_Q | 57_Y | 1.066 | 0.92 |
| 61_I | 139_F | 1.063 | 0.92 |
| 54_Q | 99_Q | 1.055 | 0.91 |
| 30_A | 46_I | 1.051 | 0.91 |
| 27_G | 32_A | 1.047 | 0.91 |
| 22_G | 100_G | 1.042 | 0.90 |
| 65_I | 142_V | 1.041 | 0.90 |
| 61_I | 137_I | 1.029 | 0.90 |
| 132_I | 136_V | 1.024 | 0.89 |
| 87_P | 138_S | 1.020 | 0.89 |
| 100_G | 104_A | 1.016 | 0.89 |
| 11_A | 138_S | 1.015 | 0.89 |
| 84_A | 141_L | 1.015 | 0.89 |
| 8_M | 65_I | 1.014 | 0.89 |
| 5_V | 8_M | 1.005 | 0.88 |
| 47_L | 50_L | 1.004 | 0.88 |
| 51_P | 99_Q | 1.001 | 0.88 |
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 | |
| 3j9tY | 10 | 0 | 100 | 0.116 | Contact Map |
| 2bl2A | 10 | 1 | 100 | 0.122 | Contact Map |
| 4bemJ | 1 | 0.9862 | 99.9 | 0.267 | Contact Map |
| 2xquA | 5 | 0.5103 | 99.1 | 0.602 | Contact Map |
| 4v1gA | 3 | 0 | 99.1 | 0.603 | Contact Map |
| 1a91A | 1 | 0.5103 | 99.1 | 0.606 | Contact Map |
| 1wu0A | 1 | 0.469 | 99 | 0.614 | Contact Map |
| 3zk1A | 22 | 0.5379 | 99 | 0.618 | Contact Map |
| 4bemA | 9 | 0.5103 | 98.9 | 0.63 | Contact Map |
| 4cbkA | 13 | 0.4414 | 98.9 | 0.633 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)