| 2bl2 |
| ID: | 1499474456 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (149) | ||
| Sequences: | 1263 (702.4) | ||
| Seq/Len: | 8.477 | ||
| Nf(neff/√len): | 57.5 |
Jackhmmer Results: (2016_04)
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: 8.477).
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 | 3.548 | 1.00 |
| 102_T | 145_G | 2.809 | 1.00 |
| 21_T | 25_F | 2.464 | 1.00 |
| 20_A | 24_I | 2.461 | 1.00 |
| 96_S | 100_A | 2.359 | 1.00 |
| 85_S | 88_Q | 2.247 | 1.00 |
| 48_Q | 51_K | 2.065 | 1.00 |
| 36_M | 115_A | 2.006 | 1.00 |
| 65_Q | 103_G | 1.926 | 1.00 |
| 71_V | 147_V | 1.854 | 1.00 |
| 117_G | 135_A | 1.738 | 1.00 |
| 72_I | 149_S | 1.724 | 1.00 |
| 23_T | 73_A | 1.722 | 1.00 |
| 84_M | 92_F | 1.618 | 1.00 |
| 147_V | 150_F | 1.567 | 1.00 |
| 65_Q | 106_S | 1.544 | 1.00 |
| 29_G | 33_G | 1.527 | 1.00 |
| 71_V | 140_T | 1.516 | 1.00 |
| 18_A | 96_S | 1.484 | 1.00 |
| 136_A | 140_T | 1.467 | 0.99 |
| 104_L | 107_G | 1.466 | 0.99 |
| 68_Y | 139_E | 1.464 | 0.99 |
| 72_I | 150_F | 1.429 | 0.99 |
| 107_G | 136_A | 1.361 | 0.99 |
| 55_A | 121_L | 1.343 | 0.99 |
| 58_L | 63_G | 1.322 | 0.99 |
| 147_V | 151_L | 1.306 | 0.99 |
| 129_T | 132_I | 1.269 | 0.98 |
| 41_A | 57_I | 1.248 | 0.98 |
| 26_S | 69_G | 1.245 | 0.98 |
| 111_G | 115_A | 1.227 | 0.98 |
| 25_F | 100_A | 1.224 | 0.98 |
| 36_M | 108_I | 1.217 | 0.97 |
| 43_A | 62_P | 1.216 | 0.97 |
| 19_M | 95_A | 1.216 | 0.97 |
| 64_T | 71_V | 1.188 | 0.97 |
| 14_F | 90_L | 1.185 | 0.97 |
| 54_Q | 130_K | 1.179 | 0.97 |
| 89_G | 94_G | 1.175 | 0.97 |
| 23_T | 95_A | 1.175 | 0.97 |
| 29_G | 111_G | 1.144 | 0.96 |
| 74_F | 150_F | 1.143 | 0.96 |
| 113_V | 138_V | 1.141 | 0.96 |
| 141_Y | 144_L | 1.138 | 0.96 |
| 146_F | 150_F | 1.136 | 0.96 |
| 114_A | 135_A | 1.128 | 0.95 |
| 61_L | 64_T | 1.115 | 0.95 |
| 22_A | 35_G | 1.109 | 0.95 |
| 66_G | 141_Y | 1.106 | 0.95 |
| 107_G | 111_G | 1.101 | 0.95 |
| 120_I | 131_G | 1.098 | 0.94 |
| 26_S | 71_V | 1.081 | 0.94 |
| 75_L | 153_V | 1.073 | 0.94 |
| 26_S | 103_G | 1.069 | 0.93 |
| 94_G | 113_V | 1.057 | 0.93 |
| 62_P | 65_Q | 1.053 | 0.93 |
| 131_G | 135_A | 1.052 | 0.93 |
| 57_I | 132_I | 1.035 | 0.92 |
| 65_Q | 110_Q | 1.031 | 0.92 |
| 32_K | 36_M | 1.027 | 0.91 |
| 98_P | 149_S | 1.024 | 0.91 |
| 109_A | 138_V | 1.018 | 0.91 |
| 24_I | 36_M | 1.017 | 0.91 |
| 120_I | 127_H | 1.015 | 0.91 |
| 67_L | 144_L | 1.011 | 0.91 |
| 27_G | 66_G | 1.011 | 0.91 |
| 97_L | 104_L | 1.009 | 0.91 |
| 21_T | 24_I | 1.008 | 0.90 |
| 38_G | 42_A | 1.007 | 0.90 |
| 32_K | 109_A | 1.006 | 0.90 |
| 55_A | 134_F | 1.005 | 0.90 |
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 | 0.159 | Contact Map |
| 3j9tY | 10 | 0 | 100 | 0.21 | Contact Map |
| 4bemJ | 1 | 0.9872 | 99.9 | 0.359 | Contact Map |
| 2xquA | 5 | 0.4744 | 99.2 | 0.645 | Contact Map |
| 4v1gA | 3 | 0 | 99.2 | 0.646 | Contact Map |
| 1wu0A | 1 | 0.4359 | 99.1 | 0.654 | Contact Map |
| 1a91A | 1 | 0.4744 | 99.1 | 0.655 | Contact Map |
| 4cbkA | 13 | 0.4103 | 99.1 | 0.66 | Contact Map |
| 3zk1A | 22 | 0.5 | 99.1 | 0.661 | Contact Map |
| 4bemA | 9 | 0.4744 | 99.1 | 0.667 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)