| vipA |
| ID: | 1396490331 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 168 (161) | ||
| Sequences: | 376 (224.2) | ||
| Seq/Len: | 2.335 | ||
| Nf(neff/√len): | 17.7 |
HHblits Results: (2013_03)
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: 2.335).
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 |
| 67_R | 96_K | 2.541 | 1.00 |
| 127_K | 131_G | 2.112 | 1.00 |
| 78_K | 88_E | 2.075 | 0.99 |
| 128_G | 131_G | 1.784 | 0.98 |
| 32_L | 137_R | 1.669 | 0.97 |
| 72_K | 92_E | 1.662 | 0.97 |
| 28_V | 136_F | 1.656 | 0.97 |
| 64_A | 107_A | 1.545 | 0.94 |
| 93_L | 109_Q | 1.516 | 0.94 |
| 76_T | 90_P | 1.481 | 0.93 |
| 23_D | 128_G | 1.442 | 0.91 |
| 119_L | 132_N | 1.396 | 0.89 |
| 62_F | 100_D | 1.392 | 0.89 |
| 84_D | 87_A | 1.380 | 0.89 |
| 111_P | 115_K | 1.378 | 0.89 |
| 74_T | 92_E | 1.372 | 0.88 |
| 66_M | 69_S | 1.311 | 0.85 |
| 6_S | 9_P | 1.299 | 0.84 |
| 133_I | 136_F | 1.296 | 0.84 |
| 72_K | 94_N | 1.287 | 0.83 |
| 36_V | 40_F | 1.280 | 0.83 |
| 22_G | 130_L | 1.273 | 0.83 |
| 86_N | 160_L | 1.262 | 0.82 |
| 129_P | 136_F | 1.232 | 0.80 |
| 22_G | 133_I | 1.214 | 0.78 |
| 129_P | 133_I | 1.208 | 0.78 |
| 152_K | 156_E | 1.206 | 0.78 |
| 63_E | 98_L | 1.202 | 0.77 |
| 107_A | 130_L | 1.199 | 0.77 |
| 21_T | 59_K | 1.186 | 0.76 |
| 63_E | 97_S | 1.183 | 0.76 |
| 44_A | 99_A | 1.179 | 0.75 |
| 22_G | 26_A | 1.179 | 0.75 |
| 108_S | 114_K | 1.178 | 0.75 |
| 55_V | 65_V | 1.177 | 0.75 |
| 99_A | 102_A | 1.172 | 0.75 |
| 78_K | 118_E | 1.172 | 0.75 |
| 14_N | 33_K | 1.167 | 0.74 |
| 55_V | 98_L | 1.164 | 0.74 |
| 23_D | 37_V | 1.157 | 0.73 |
| 7_V | 11_E | 1.154 | 0.73 |
| 148_E | 156_E | 1.149 | 0.73 |
| 20_A | 71_L | 1.139 | 0.72 |
| 22_G | 65_V | 1.123 | 0.70 |
| 132_N | 137_R | 1.118 | 0.70 |
| 139_R | 143_L | 1.117 | 0.70 |
| 107_A | 117_I | 1.110 | 0.69 |
| 8_A | 11_E | 1.101 | 0.68 |
| 80_K | 83_D | 1.090 | 0.67 |
| 13_I | 60_N | 1.087 | 0.67 |
| 40_F | 56_T | 1.083 | 0.66 |
| 58_D | 113_L | 1.083 | 0.66 |
| 10_K | 87_A | 1.082 | 0.66 |
| 43_H | 92_E | 1.077 | 0.65 |
| 146_S | 152_K | 1.076 | 0.65 |
| 10_K | 14_N | 1.075 | 0.65 |
| 32_L | 133_I | 1.072 | 0.65 |
| 27_E | 94_N | 1.072 | 0.65 |
| 122_A | 125_A | 1.070 | 0.65 |
| 45_E | 66_M | 1.064 | 0.64 |
| 44_A | 145_N | 1.063 | 0.64 |
| 79_N | 82_T | 1.062 | 0.64 |
| 49_L | 64_A | 1.061 | 0.64 |
| 57_V | 114_K | 1.060 | 0.64 |
| 22_G | 25_Q | 1.047 | 0.62 |
| 15_I | 56_T | 1.046 | 0.62 |
| 95_F | 101_F | 1.044 | 0.62 |
| 6_S | 10_K | 1.044 | 0.62 |
| 69_S | 110_V | 1.035 | 0.61 |
| 94_N | 106_V | 1.033 | 0.61 |
| 41_K | 64_A | 1.029 | 0.60 |
| 23_D | 98_L | 1.027 | 0.60 |
| 38_G | 42_G | 1.020 | 0.59 |
| 76_T | 88_E | 1.020 | 0.59 |
| 104_D | 143_L | 1.019 | 0.59 |
| 41_K | 45_E | 1.015 | 0.59 |
| 122_A | 144_L | 1.015 | 0.59 |
| 32_L | 102_A | 1.012 | 0.58 |
| 34_T | 107_A | 1.007 | 0.58 |
| 119_L | 131_G | 1.007 | 0.58 |
| 33_K | 40_F | 1.003 | 0.57 |
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 | |
| 1g6uA | 2 | 0.2619 | 10.1 | 0.959 | Contact Map |
| 1deqA | 4 | 0.6964 | 9.5 | 0.959 | Contact Map |
| 2llvA | 1 | 0.381 | 8.8 | 0.96 | Contact Map |
| 4n78F | 1 | 0.3393 | 7.5 | 0.961 | Contact Map |
| 3pcoA | 2 | 0.2798 | 5.9 | 0.963 | Contact Map |
| 1gqeA | 1 | 0.5 | 5 | 0.964 | Contact Map |
| 2rjzA | 2 | 0.3036 | 4.7 | 0.965 | Contact Map |
| 2lnmA | 1 | 0.2917 | 4.3 | 0.965 | Contact Map |
| 3gf6A | 2 | 0.3631 | 4.1 | 0.966 | Contact Map |
| 1sesA | 2 | 0.4881 | 3.9 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)