| AlpB |
| ID: | 1456484038 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (121) | ||
| Sequences: | 154 (101.8) | ||
| Seq/Len: | 1.273 | ||
| Nf(neff/√len): | 9.3 |
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: 1.273).
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 |
| 1_M | 4_P | 1.765 | 0.93 |
| 44_F | 97_G | 1.763 | 0.93 |
| 28_G | 31_L | 1.726 | 0.92 |
| 39_I | 45_A | 1.593 | 0.87 |
| 59_V | 101_W | 1.519 | 0.84 |
| 27_D | 35_F | 1.464 | 0.81 |
| 21_M | 24_P | 1.445 | 0.79 |
| 42_V | 59_V | 1.429 | 0.78 |
| 6_S | 23_L | 1.408 | 0.77 |
| 8_A | 55_G | 1.396 | 0.76 |
| 109_S | 118_R | 1.368 | 0.74 |
| 67_A | 86_V | 1.351 | 0.73 |
| 43_V | 56_Y | 1.298 | 0.68 |
| 67_A | 88_A | 1.297 | 0.68 |
| 42_V | 52_T | 1.293 | 0.68 |
| 18_G | 60_S | 1.291 | 0.68 |
| 45_A | 56_Y | 1.286 | 0.67 |
| 41_F | 45_A | 1.284 | 0.67 |
| 36_G | 42_V | 1.275 | 0.66 |
| 18_G | 112_R | 1.273 | 0.66 |
| 47_D | 53_R | 1.261 | 0.65 |
| 18_G | 98_M | 1.219 | 0.61 |
| 50_A | 53_R | 1.203 | 0.60 |
| 118_R | 121_S | 1.201 | 0.59 |
| 43_V | 52_T | 1.192 | 0.59 |
| 16_G | 99_L | 1.190 | 0.58 |
| 14_M | 40_F | 1.181 | 0.57 |
| 13_A | 60_S | 1.177 | 0.57 |
| 12_S | 54_L | 1.171 | 0.56 |
| 13_A | 58_L | 1.158 | 0.55 |
| 12_S | 107_L | 1.157 | 0.55 |
| 17_V | 94_G | 1.153 | 0.55 |
| 25_G | 35_F | 1.145 | 0.54 |
| 1_M | 33_G | 1.141 | 0.54 |
| 7_A | 18_G | 1.136 | 0.53 |
| 51_L | 69_I | 1.111 | 0.51 |
| 117_R | 120_G | 1.107 | 0.50 |
| 24_P | 40_F | 1.102 | 0.50 |
| 35_F | 39_I | 1.100 | 0.49 |
| 60_S | 88_A | 1.097 | 0.49 |
| 3_E | 33_G | 1.097 | 0.49 |
| 117_R | 121_S | 1.094 | 0.49 |
| 35_F | 42_V | 1.093 | 0.49 |
| 52_T | 79_T | 1.085 | 0.48 |
| 85_F | 100_E | 1.083 | 0.48 |
| 38_A | 102_M | 1.080 | 0.48 |
| 28_G | 65_Y | 1.076 | 0.47 |
| 115_L | 120_G | 1.074 | 0.47 |
| 89_T | 99_L | 1.073 | 0.47 |
| 16_G | 49_N | 1.069 | 0.46 |
| 33_G | 66_Y | 1.069 | 0.46 |
| 41_F | 47_D | 1.066 | 0.46 |
| 4_P | 68_G | 1.063 | 0.46 |
| 7_A | 59_V | 1.059 | 0.45 |
| 1_M | 8_A | 1.058 | 0.45 |
| 83_A | 108_P | 1.055 | 0.45 |
| 85_F | 103_R | 1.054 | 0.45 |
| 7_A | 118_R | 1.052 | 0.45 |
| 69_I | 82_M | 1.052 | 0.45 |
| 8_A | 73_G | 1.051 | 0.45 |
| 28_G | 77_T | 1.049 | 0.44 |
| 115_L | 121_S | 1.048 | 0.44 |
| 15_A | 94_G | 1.047 | 0.44 |
| 9_S | 115_L | 1.045 | 0.44 |
| 40_F | 81_G | 1.044 | 0.44 |
| 98_M | 112_R | 1.028 | 0.42 |
| 56_Y | 100_E | 1.027 | 0.42 |
| 85_F | 99_L | 1.026 | 0.42 |
| 88_A | 96_I | 1.021 | 0.42 |
| 12_S | 50_A | 1.016 | 0.41 |
| 17_V | 22_Y | 1.011 | 0.41 |
| 67_A | 82_M | 1.011 | 0.41 |
| 59_V | 102_M | 1.006 | 0.40 |
| 13_A | 17_V | 1.003 | 0.40 |
| 32_L | 100_E | 1.003 | 0.40 |
| 3_E | 6_S | 1.002 | 0.40 |
| 79_T | 95_G | 1.000 | 0.40 |
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 | |
| 4hdrB | 2 | 0.9032 | 11.2 | 0.93 | Contact Map |
| 2nq2A | 2 | 0.75 | 6.4 | 0.937 | Contact Map |
| 4kqiA | 1 | 0.9274 | 5.2 | 0.939 | Contact Map |
| 3wu2X | 2 | 0.3065 | 3.9 | 0.943 | Contact Map |
| 3bz1X | 1 | 0.2903 | 3.9 | 0.943 | Contact Map |
| 1wx1A | 2 | 0.8871 | 3.5 | 0.945 | Contact Map |
| 4hdrA | 2 | 0.9274 | 3.1 | 0.946 | Contact Map |
| 2looA | 1 | 0.7258 | 3 | 0.946 | Contact Map |
| 2inyA | 1 | 0.3387 | 3 | 0.946 | Contact Map |
| 2qi9A | 2 | 0.9758 | 2.9 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)