| 2bl2 |
| ID: | 1499447903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (147) | ||
| Sequences: | 1049 (594.4) | ||
| Seq/Len: | 7.136 | ||
| Nf(neff/√len): | 49.0 |
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: 7.136).
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 |
| 76_I | 96_S | 3.114 | 1.00 |
| 96_S | 100_A | 2.575 | 1.00 |
| 102_T | 145_G | 2.518 | 1.00 |
| 65_Q | 103_G | 2.032 | 1.00 |
| 36_M | 115_A | 1.967 | 1.00 |
| 29_G | 33_G | 1.817 | 1.00 |
| 26_S | 69_G | 1.759 | 1.00 |
| 136_A | 140_T | 1.718 | 1.00 |
| 71_V | 147_V | 1.714 | 1.00 |
| 48_Q | 51_K | 1.705 | 1.00 |
| 43_A | 62_P | 1.682 | 1.00 |
| 85_S | 88_Q | 1.677 | 1.00 |
| 107_G | 111_G | 1.588 | 1.00 |
| 135_A | 139_E | 1.552 | 1.00 |
| 65_Q | 106_S | 1.551 | 1.00 |
| 68_Y | 139_E | 1.544 | 1.00 |
| 23_T | 73_A | 1.536 | 0.99 |
| 147_V | 150_F | 1.523 | 0.99 |
| 11_G | 89_G | 1.516 | 0.99 |
| 71_V | 140_T | 1.503 | 0.99 |
| 20_A | 24_I | 1.479 | 0.99 |
| 21_T | 25_F | 1.385 | 0.99 |
| 117_G | 135_A | 1.383 | 0.99 |
| 104_L | 107_G | 1.364 | 0.98 |
| 19_M | 95_A | 1.338 | 0.98 |
| 57_I | 132_I | 1.333 | 0.98 |
| 146_F | 150_F | 1.301 | 0.98 |
| 15_A | 18_A | 1.285 | 0.98 |
| 22_A | 73_A | 1.274 | 0.97 |
| 24_I | 102_T | 1.265 | 0.97 |
| 72_I | 149_S | 1.247 | 0.97 |
| 28_I | 104_L | 1.228 | 0.97 |
| 67_L | 71_V | 1.224 | 0.96 |
| 36_M | 108_I | 1.222 | 0.96 |
| 141_Y | 144_L | 1.207 | 0.96 |
| 16_V | 19_M | 1.200 | 0.96 |
| 62_P | 65_Q | 1.199 | 0.96 |
| 72_I | 150_F | 1.185 | 0.96 |
| 75_L | 153_V | 1.160 | 0.95 |
| 109_A | 138_V | 1.147 | 0.94 |
| 34_V | 63_G | 1.146 | 0.94 |
| 58_L | 63_G | 1.139 | 0.94 |
| 59_Q | 102_T | 1.139 | 0.94 |
| 38_G | 43_A | 1.134 | 0.94 |
| 14_F | 89_G | 1.127 | 0.94 |
| 72_I | 99_I | 1.117 | 0.93 |
| 65_Q | 68_Y | 1.108 | 0.93 |
| 79_N | 154_L | 1.107 | 0.93 |
| 25_F | 100_A | 1.102 | 0.93 |
| 79_N | 92_F | 1.096 | 0.92 |
| 55_A | 134_F | 1.096 | 0.92 |
| 18_A | 96_S | 1.084 | 0.92 |
| 72_I | 148_I | 1.083 | 0.92 |
| 57_I | 155_N | 1.076 | 0.92 |
| 65_Q | 110_Q | 1.071 | 0.91 |
| 18_A | 93_L | 1.065 | 0.91 |
| 59_Q | 143_I | 1.063 | 0.91 |
| 23_T | 95_A | 1.055 | 0.90 |
| 55_A | 121_L | 1.055 | 0.90 |
| 40_A | 115_A | 1.053 | 0.90 |
| 32_K | 109_A | 1.053 | 0.90 |
| 16_V | 91_N | 1.049 | 0.90 |
| 111_G | 115_A | 1.042 | 0.90 |
| 74_F | 150_F | 1.039 | 0.90 |
| 22_A | 149_S | 1.032 | 0.89 |
| 63_G | 66_G | 1.032 | 0.89 |
| 76_I | 153_V | 1.028 | 0.89 |
| 41_A | 45_T | 1.026 | 0.89 |
| 60_L | 74_F | 1.022 | 0.88 |
| 109_A | 112_K | 1.019 | 0.88 |
| 143_I | 147_V | 1.019 | 0.88 |
| 32_K | 108_I | 1.015 | 0.88 |
| 76_I | 92_F | 1.014 | 0.88 |
| 17_L | 20_A | 1.012 | 0.88 |
| 91_N | 153_V | 1.011 | 0.88 |
| 28_I | 97_L | 1.009 | 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 | |
| 2bl2A | 10 | 1 | 100 | 0.171 | Contact Map |
| 3j9tY | 10 | 0 | 100 | 0.191 | Contact Map |
| 4bemJ | 1 | 0.9872 | 99.9 | 0.335 | Contact Map |
| 2xquA | 5 | 0.4744 | 99.2 | 0.648 | Contact Map |
| 4v1gA | 3 | 0 | 99.2 | 0.649 | Contact Map |
| 1wu0A | 1 | 0.4359 | 99.2 | 0.655 | Contact Map |
| 1a91A | 1 | 0.4744 | 99.2 | 0.657 | Contact Map |
| 3zk1A | 22 | 0.5449 | 99.2 | 0.661 | Contact Map |
| 4cbkA | 13 | 0.4103 | 99.1 | 0.668 | Contact Map |
| 4bemA | 9 | 0.4744 | 99.1 | 0.672 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)