| vipA jackhmmer test |
| ID: | 1396507434 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 168 (159) | ||
| Sequences: | 553 (320.8) | ||
| Seq/Len: | 3.478 | ||
| Nf(neff/√len): | 25.4 |
Jackhmmer Results: (2014_03_19)
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: 3.478).
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 | 3.078 | 1.00 |
| 78_K | 88_E | 2.511 | 1.00 |
| 84_D | 87_A | 2.506 | 1.00 |
| 36_V | 40_F | 1.879 | 1.00 |
| 114_K | 118_E | 1.804 | 0.99 |
| 127_K | 131_G | 1.802 | 0.99 |
| 10_K | 14_N | 1.729 | 0.99 |
| 108_S | 114_K | 1.710 | 0.99 |
| 64_A | 107_A | 1.644 | 0.98 |
| 128_G | 131_G | 1.558 | 0.98 |
| 63_E | 97_S | 1.519 | 0.97 |
| 80_K | 83_D | 1.517 | 0.97 |
| 76_T | 90_P | 1.468 | 0.96 |
| 9_P | 14_N | 1.467 | 0.96 |
| 106_V | 110_V | 1.465 | 0.96 |
| 139_R | 143_L | 1.440 | 0.96 |
| 93_L | 109_Q | 1.422 | 0.95 |
| 28_V | 136_F | 1.414 | 0.95 |
| 74_T | 92_E | 1.414 | 0.95 |
| 11_E | 14_N | 1.379 | 0.94 |
| 23_D | 128_G | 1.357 | 0.93 |
| 72_K | 92_E | 1.345 | 0.93 |
| 78_K | 152_K | 1.335 | 0.93 |
| 62_F | 100_D | 1.320 | 0.92 |
| 32_L | 137_R | 1.320 | 0.92 |
| 107_A | 117_I | 1.303 | 0.91 |
| 5_G | 11_E | 1.300 | 0.91 |
| 55_V | 65_V | 1.292 | 0.91 |
| 34_T | 107_A | 1.280 | 0.90 |
| 115_K | 118_E | 1.275 | 0.90 |
| 133_I | 136_F | 1.272 | 0.90 |
| 40_F | 56_T | 1.265 | 0.90 |
| 143_L | 147_E | 1.264 | 0.90 |
| 58_D | 105_A | 1.244 | 0.89 |
| 28_V | 133_I | 1.209 | 0.87 |
| 5_G | 9_P | 1.205 | 0.87 |
| 91_V | 116_L | 1.191 | 0.86 |
| 43_H | 92_E | 1.190 | 0.86 |
| 14_N | 33_K | 1.185 | 0.85 |
| 11_E | 19_P | 1.184 | 0.85 |
| 115_K | 149_S | 1.177 | 0.85 |
| 129_P | 136_F | 1.174 | 0.85 |
| 41_K | 64_A | 1.158 | 0.84 |
| 41_K | 69_S | 1.155 | 0.83 |
| 75_A | 95_F | 1.148 | 0.83 |
| 66_M | 97_S | 1.143 | 0.82 |
| 152_K | 156_E | 1.140 | 0.82 |
| 111_P | 115_K | 1.137 | 0.82 |
| 130_L | 137_R | 1.137 | 0.82 |
| 71_L | 95_F | 1.129 | 0.81 |
| 111_P | 114_K | 1.127 | 0.81 |
| 107_A | 144_L | 1.118 | 0.80 |
| 105_A | 108_S | 1.101 | 0.79 |
| 78_K | 92_E | 1.098 | 0.79 |
| 50_E | 134_P | 1.095 | 0.79 |
| 7_V | 11_E | 1.094 | 0.78 |
| 51_E | 160_L | 1.093 | 0.78 |
| 13_I | 18_I | 1.092 | 0.78 |
| 121_E | 153_L | 1.081 | 0.77 |
| 106_V | 138_E | 1.077 | 0.77 |
| 24_A | 53_A | 1.075 | 0.77 |
| 64_A | 160_L | 1.073 | 0.77 |
| 104_D | 117_I | 1.073 | 0.77 |
| 22_G | 26_A | 1.071 | 0.76 |
| 15_I | 48_P | 1.069 | 0.76 |
| 48_P | 63_E | 1.068 | 0.76 |
| 60_N | 64_A | 1.065 | 0.76 |
| 28_V | 146_S | 1.064 | 0.76 |
| 9_P | 35_L | 1.061 | 0.75 |
| 8_A | 122_A | 1.060 | 0.75 |
| 44_A | 47_T | 1.056 | 0.75 |
| 32_L | 98_L | 1.055 | 0.75 |
| 76_T | 88_E | 1.054 | 0.75 |
| 105_A | 146_S | 1.052 | 0.75 |
| 22_G | 130_L | 1.049 | 0.74 |
| 129_P | 133_I | 1.046 | 0.74 |
| 99_A | 102_A | 1.044 | 0.74 |
| 7_V | 15_I | 1.043 | 0.74 |
| 5_G | 8_A | 1.027 | 0.72 |
| 3_K | 6_S | 1.024 | 0.72 |
| 75_A | 106_V | 1.023 | 0.72 |
| 130_L | 133_I | 1.022 | 0.71 |
| 72_K | 94_N | 1.009 | 0.70 |
| 9_P | 33_K | 1.008 | 0.70 |
| 25_Q | 98_L | 1.005 | 0.70 |
| 66_M | 116_L | 1.003 | 0.69 |
| 6_S | 14_N | 1.003 | 0.69 |
| 49_L | 57_V | 1.002 | 0.69 |
| 36_V | 144_L | 1.000 | 0.69 |
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 | |
| 1deqA | 4 | 0.6964 | 18.6 | 0.953 | Contact Map |
| 1g6uA | 2 | 0.2619 | 8.4 | 0.959 | Contact Map |
| 1sesA | 2 | 0.4524 | 6.8 | 0.961 | Contact Map |
| 2fu2A | 1 | 0.2262 | 5.7 | 0.962 | Contact Map |
| 2rjzA | 2 | 0.3036 | 5.3 | 0.963 | Contact Map |
| 1vtze | 30 | 0.3333 | 4.8 | 0.964 | Contact Map |
| 2xn6A | 1 | 0.4345 | 3.8 | 0.965 | Contact Map |
| 2dq0A | 2 | 0.4524 | 3.8 | 0.966 | Contact Map |
| 1vq8X | 1 | 0.1726 | 3.6 | 0.966 | Contact Map |
| 1gqeA | 1 | 0.4762 | 3.6 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)