| 2BL2 |
| ID: | 1448019740 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (151) | ||
| Sequences: | 1056 (586.1) | ||
| Seq/Len: | 6.993 | ||
| Nf(neff/√len): | 47.7 |
HHblits Results: (2015_06)
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: 6.993).
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 | 2.787 | 1.00 |
| 96_S | 100_A | 2.332 | 1.00 |
| 102_T | 145_G | 2.182 | 1.00 |
| 136_A | 140_T | 1.951 | 1.00 |
| 21_T | 25_F | 1.911 | 1.00 |
| 20_A | 24_I | 1.797 | 1.00 |
| 99_I | 149_S | 1.791 | 1.00 |
| 71_V | 140_T | 1.764 | 1.00 |
| 147_V | 150_F | 1.751 | 1.00 |
| 146_F | 150_F | 1.734 | 1.00 |
| 65_Q | 103_G | 1.707 | 1.00 |
| 85_S | 88_Q | 1.701 | 1.00 |
| 26_S | 69_G | 1.690 | 1.00 |
| 36_M | 115_A | 1.673 | 1.00 |
| 43_A | 62_P | 1.519 | 0.99 |
| 135_A | 139_E | 1.503 | 0.99 |
| 89_G | 94_G | 1.488 | 0.99 |
| 107_G | 111_G | 1.483 | 0.99 |
| 65_Q | 106_S | 1.464 | 0.99 |
| 15_A | 18_A | 1.453 | 0.99 |
| 58_L | 63_G | 1.446 | 0.99 |
| 117_G | 135_A | 1.434 | 0.99 |
| 57_I | 132_I | 1.401 | 0.99 |
| 147_V | 151_L | 1.384 | 0.99 |
| 27_G | 66_G | 1.383 | 0.99 |
| 23_T | 73_A | 1.366 | 0.98 |
| 48_Q | 51_K | 1.355 | 0.98 |
| 104_L | 107_G | 1.315 | 0.98 |
| 109_A | 138_V | 1.289 | 0.98 |
| 98_P | 149_S | 1.263 | 0.97 |
| 79_N | 154_L | 1.250 | 0.97 |
| 71_V | 147_V | 1.243 | 0.97 |
| 18_A | 96_S | 1.238 | 0.97 |
| 68_Y | 139_E | 1.235 | 0.97 |
| 107_G | 145_G | 1.211 | 0.96 |
| 72_I | 149_S | 1.200 | 0.96 |
| 29_G | 33_G | 1.184 | 0.95 |
| 66_G | 99_I | 1.183 | 0.95 |
| 18_A | 29_G | 1.174 | 0.95 |
| 24_I | 36_M | 1.165 | 0.95 |
| 8_Q | 12_M | 1.156 | 0.94 |
| 9_N | 12_M | 1.151 | 0.94 |
| 134_F | 137_M | 1.149 | 0.94 |
| 89_G | 97_L | 1.146 | 0.94 |
| 101_F | 116_A | 1.121 | 0.93 |
| 13_V | 17_L | 1.117 | 0.93 |
| 16_V | 19_M | 1.117 | 0.93 |
| 79_N | 92_F | 1.111 | 0.93 |
| 137_M | 141_Y | 1.091 | 0.92 |
| 60_L | 74_F | 1.076 | 0.91 |
| 65_Q | 110_Q | 1.074 | 0.91 |
| 72_I | 148_I | 1.063 | 0.91 |
| 34_V | 63_G | 1.061 | 0.90 |
| 79_N | 152_L | 1.057 | 0.90 |
| 100_A | 128_A | 1.053 | 0.90 |
| 62_P | 65_Q | 1.051 | 0.90 |
| 16_V | 92_F | 1.049 | 0.90 |
| 41_A | 57_I | 1.047 | 0.90 |
| 72_I | 99_I | 1.046 | 0.90 |
| 17_L | 93_L | 1.045 | 0.90 |
| 23_T | 95_A | 1.044 | 0.89 |
| 36_M | 108_I | 1.034 | 0.89 |
| 72_I | 150_F | 1.031 | 0.89 |
| 26_S | 31_A | 1.027 | 0.88 |
| 111_G | 115_A | 1.026 | 0.88 |
| 22_A | 73_A | 1.026 | 0.88 |
| 17_L | 20_A | 1.024 | 0.88 |
| 59_Q | 102_T | 1.023 | 0.88 |
| 109_A | 112_K | 1.022 | 0.88 |
| 62_P | 110_Q | 1.015 | 0.88 |
| 36_M | 39_E | 1.012 | 0.87 |
| 88_Q | 91_N | 1.009 | 0.87 |
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 | 0.144 | Contact Map |
| 2bl2A | 10 | 1 | 100 | 0.145 | Contact Map |
| 4bemJ | 1 | 0.9872 | 99.9 | 0.301 | Contact Map |
| 2xquA | 5 | 0.4744 | 99.3 | 0.601 | Contact Map |
| 4v1gA | 3 | 0 | 99.3 | 0.602 | Contact Map |
| 1wu0A | 1 | 0.4359 | 99.3 | 0.607 | Contact Map |
| 1a91A | 1 | 0.4744 | 99.2 | 0.615 | Contact Map |
| 4cbkA | 13 | 0.4103 | 99.2 | 0.619 | Contact Map |
| 3zk1A | 22 | 0.5 | 99.2 | 0.622 | Contact Map |
| 4bemA | 9 | 0.4744 | 99.2 | 0.627 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)