| T0848 172-354 Tp848 |
| ID: | 1407216776 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 183 (179) | ||
| Sequences: | 291 (263) | ||
| Seq/Len: | 1.626 | ||
| Nf(neff/√len): | 19.7 |
Jackhmmer Results: (2014_04_16)
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: 1.626).
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 |
| 96_T | 149_E | 2.221 | 0.99 |
| 159_N | 163_Q | 2.144 | 0.99 |
| 124_S | 127_E | 2.072 | 0.99 |
| 80_Q | 96_T | 2.009 | 0.98 |
| 98_K | 149_E | 1.989 | 0.98 |
| 86_I | 89_D | 1.828 | 0.97 |
| 82_K | 94_E | 1.807 | 0.96 |
| 5_K | 8_S | 1.775 | 0.96 |
| 96_T | 151_T | 1.761 | 0.96 |
| 94_E | 151_T | 1.721 | 0.95 |
| 99_P | 179_A | 1.689 | 0.94 |
| 69_I | 140_F | 1.591 | 0.91 |
| 85_S | 93_V | 1.588 | 0.91 |
| 157_K | 167_D | 1.579 | 0.91 |
| 102_A | 136_Y | 1.570 | 0.91 |
| 32_N | 36_N | 1.562 | 0.90 |
| 131_Y | 134_Q | 1.554 | 0.90 |
| 89_D | 158_K | 1.530 | 0.89 |
| 23_F | 30_N | 1.495 | 0.87 |
| 97_V | 152_V | 1.480 | 0.87 |
| 27_T | 93_V | 1.452 | 0.85 |
| 138_E | 141_K | 1.447 | 0.85 |
| 98_K | 147_S | 1.403 | 0.83 |
| 28_G | 32_N | 1.384 | 0.81 |
| 123_A | 127_E | 1.375 | 0.81 |
| 5_K | 9_A | 1.341 | 0.78 |
| 77_S | 93_V | 1.337 | 0.78 |
| 6_A | 18_K | 1.313 | 0.76 |
| 79_I | 153_E | 1.305 | 0.76 |
| 84_T | 91_A | 1.299 | 0.75 |
| 117_Y | 151_T | 1.293 | 0.75 |
| 23_F | 93_V | 1.289 | 0.75 |
| 108_R | 112_K | 1.286 | 0.74 |
| 150_K | 175_E | 1.261 | 0.72 |
| 4_A | 7_L | 1.260 | 0.72 |
| 95_A | 162_D | 1.250 | 0.71 |
| 112_K | 138_E | 1.248 | 0.71 |
| 85_S | 144_G | 1.241 | 0.70 |
| 23_F | 31_K | 1.231 | 0.70 |
| 80_Q | 114_K | 1.219 | 0.69 |
| 159_N | 165_Q | 1.217 | 0.68 |
| 155_K | 167_D | 1.210 | 0.68 |
| 4_A | 9_A | 1.204 | 0.67 |
| 6_A | 23_F | 1.203 | 0.67 |
| 7_L | 156_M | 1.200 | 0.67 |
| 156_M | 166_L | 1.200 | 0.67 |
| 4_A | 8_S | 1.196 | 0.66 |
| 110_E | 114_K | 1.188 | 0.66 |
| 39_N | 169_D | 1.187 | 0.66 |
| 84_T | 93_V | 1.175 | 0.64 |
| 160_D | 163_Q | 1.172 | 0.64 |
| 33_E | 102_A | 1.166 | 0.63 |
| 4_A | 10_Y | 1.157 | 0.63 |
| 42_A | 67_N | 1.155 | 0.62 |
| 154_V | 166_L | 1.152 | 0.62 |
| 56_Y | 155_K | 1.142 | 0.61 |
| 34_I | 135_V | 1.139 | 0.61 |
| 175_E | 179_A | 1.138 | 0.61 |
| 41_S | 162_D | 1.119 | 0.59 |
| 59_S | 76_N | 1.111 | 0.58 |
| 99_P | 150_K | 1.110 | 0.58 |
| 78_S | 98_K | 1.106 | 0.57 |
| 91_A | 98_K | 1.104 | 0.57 |
| 74_S | 140_F | 1.102 | 0.57 |
| 95_A | 165_Q | 1.097 | 0.56 |
| 113_V | 119_K | 1.089 | 0.56 |
| 108_R | 138_E | 1.080 | 0.55 |
| 172_R | 175_E | 1.072 | 0.54 |
| 35_V | 78_S | 1.069 | 0.54 |
| 52_L | 55_T | 1.066 | 0.53 |
| 102_A | 143_L | 1.061 | 0.53 |
| 31_K | 97_V | 1.057 | 0.52 |
| 114_K | 118_S | 1.055 | 0.52 |
| 44_D | 139_E | 1.053 | 0.52 |
| 93_V | 149_E | 1.052 | 0.52 |
| 67_N | 71_E | 1.047 | 0.51 |
| 86_I | 142_K | 1.046 | 0.51 |
| 141_K | 144_G | 1.045 | 0.51 |
| 79_I | 125_Y | 1.034 | 0.50 |
| 6_A | 9_A | 1.031 | 0.50 |
| 117_Y | 128_A | 1.031 | 0.50 |
| 71_E | 132_A | 1.030 | 0.49 |
| 59_S | 154_V | 1.024 | 0.49 |
| 53_S | 149_E | 1.020 | 0.48 |
| 116_Y | 119_K | 1.017 | 0.48 |
| 6_A | 16_F | 1.008 | 0.47 |
| 94_E | 153_E | 1.006 | 0.47 |
| 27_T | 35_V | 1.004 | 0.47 |
| 34_I | 38_F | 1.002 | 0.47 |
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 | |
| 3k7cA | 4 | 0.5519 | 95.9 | 0.816 | Contact Map |
| 4hz9B | 2 | 0.6557 | 58.1 | 0.891 | Contact Map |
| 1vqqA | 2 | 0.623 | 37.1 | 0.904 | Contact Map |
| 3robA | 4 | 0.694 | 18.8 | 0.917 | Contact Map |
| 2gxfA | 4 | 0.6175 | 16 | 0.919 | Contact Map |
| 3fkaA | 4 | 0.612 | 12.6 | 0.923 | Contact Map |
| 3hx8A | 4 | 0.6721 | 9.6 | 0.927 | Contact Map |
| 3blzA | 12 | 0.6393 | 7.2 | 0.931 | Contact Map |
| 3dukA | 6 | 0.6503 | 6.9 | 0.932 | Contact Map |
| 3ehcA | 4 | 0.612 | 4.2 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)