| t cell receptor beta chain constant domain |
| ID: | 1486587778 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (112) | ||
| Sequences: | 382 (249.2) | ||
| Seq/Len: | 3.411 | ||
| Nf(neff/√len): | 23.5 |
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: 3.411).
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 |
| 31_A | 41_L | 2.345 | 1.00 |
| 110_D | 113_K | 2.056 | 1.00 |
| 34_F | 98_F | 1.954 | 1.00 |
| 14_P | 76_S | 1.831 | 0.99 |
| 43_W | 78_L | 1.771 | 0.99 |
| 36_P | 98_F | 1.745 | 0.99 |
| 33_G | 71_R | 1.652 | 0.98 |
| 24_K | 92_F | 1.633 | 0.98 |
| 19_I | 25_A | 1.613 | 0.98 |
| 43_W | 76_S | 1.539 | 0.97 |
| 31_A | 58_P | 1.412 | 0.95 |
| 27_L | 68_N | 1.397 | 0.94 |
| 46_N | 53_G | 1.385 | 0.94 |
| 11_V | 46_N | 1.379 | 0.94 |
| 87_D | 90_N | 1.308 | 0.91 |
| 18_E | 26_T | 1.298 | 0.91 |
| 19_I | 90_N | 1.269 | 0.90 |
| 107_W | 112_A | 1.266 | 0.90 |
| 14_P | 85_W | 1.251 | 0.89 |
| 8_E | 93_R | 1.248 | 0.89 |
| 100_G | 104_N | 1.244 | 0.88 |
| 15_S | 56_T | 1.239 | 0.88 |
| 26_T | 77_R | 1.237 | 0.88 |
| 14_P | 18_E | 1.233 | 0.88 |
| 41_L | 81_S | 1.222 | 0.87 |
| 16_E | 20_S | 1.221 | 0.87 |
| 13_E | 17_A | 1.210 | 0.87 |
| 9_V | 96_V | 1.185 | 0.85 |
| 42_S | 100_G | 1.173 | 0.84 |
| 108_T | 112_A | 1.172 | 0.84 |
| 111_R | 114_P | 1.170 | 0.84 |
| 12_F | 30_L | 1.156 | 0.83 |
| 11_V | 27_L | 1.156 | 0.83 |
| 37_D | 71_R | 1.154 | 0.83 |
| 57_D | 72_Y | 1.138 | 0.82 |
| 28_V | 75_S | 1.130 | 0.81 |
| 6_P | 71_R | 1.129 | 0.81 |
| 12_F | 25_A | 1.118 | 0.80 |
| 14_P | 26_T | 1.118 | 0.80 |
| 6_P | 33_G | 1.116 | 0.80 |
| 76_S | 85_W | 1.114 | 0.80 |
| 26_T | 76_S | 1.111 | 0.79 |
| 35_Y | 72_Y | 1.100 | 0.78 |
| 109_Q | 114_P | 1.095 | 0.78 |
| 98_F | 101_L | 1.082 | 0.77 |
| 106_E | 109_Q | 1.082 | 0.77 |
| 108_T | 111_R | 1.066 | 0.75 |
| 39_V | 80_V | 1.062 | 0.75 |
| 41_L | 96_V | 1.054 | 0.74 |
| 52_S | 83_T | 1.052 | 0.74 |
| 34_F | 41_L | 1.051 | 0.74 |
| 53_G | 78_L | 1.050 | 0.74 |
| 23_Q | 39_V | 1.046 | 0.73 |
| 40_E | 97_Q | 1.041 | 0.73 |
| 32_T | 87_D | 1.036 | 0.72 |
| 9_V | 48_K | 1.035 | 0.72 |
| 68_N | 93_R | 1.031 | 0.72 |
| 80_V | 96_V | 1.029 | 0.72 |
| 38_H | 98_F | 1.027 | 0.71 |
| 6_P | 100_G | 1.026 | 0.71 |
| 39_V | 72_Y | 1.014 | 0.70 |
| 45_V | 90_N | 1.013 | 0.70 |
| 61_L | 71_R | 1.012 | 0.70 |
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 | |
| 1iaoB | 1 | 0.7717 | 99.9 | 0.356 | Contact Map |
| 2p24B | 1 | 0.7323 | 99.9 | 0.36 | Contact Map |
| 4cvzA | 1 | 0 | 99.9 | 0.363 | Contact Map |
| 2qrtA | 2 | 0.7559 | 99.9 | 0.364 | Contact Map |
| 1iakA | 1 | 0.7795 | 99.9 | 0.364 | Contact Map |
| 4lldB | 1 | 0.7953 | 99.9 | 0.364 | Contact Map |
| 2bc4A | 2 | 0.8661 | 99.9 | 0.366 | Contact Map |
| 1uvqA | 1 | 0.7717 | 99.9 | 0.367 | Contact Map |
| 1k5nA | 1 | 0.7559 | 99.9 | 0.367 | Contact Map |
| 4p5mB | 4 | 0.7795 | 99.9 | 0.369 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)