| T4_Jack |
| ID: | 1500497499 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 164 (148) | ||
| Sequences: | 1167 (906.5) | ||
| Seq/Len: | 7.885 | ||
| Nf(neff/√len): | 74.5 |
Jackhmmer Results: (2016_04)
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: 7.885).
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 |
| 125_R | 128_E | 3.484 | 1.00 |
| 31_H | 70_D | 3.480 | 1.00 |
| 93_A | 97_A | 3.444 | 1.00 |
| 142_T | 146_A | 2.963 | 1.00 |
| 146_A | 149_V | 2.582 | 1.00 |
| 92_D | 95_R | 2.413 | 1.00 |
| 13_L | 63_A | 2.369 | 1.00 |
| 10_D | 148_R | 2.109 | 1.00 |
| 8_R | 64_E | 2.088 | 1.00 |
| 117_S | 132_N | 2.039 | 1.00 |
| 77_G | 108_E | 2.004 | 1.00 |
| 105_Q | 142_T | 1.966 | 1.00 |
| 19_K | 25_Y | 1.911 | 1.00 |
| 24_Y | 32_L | 1.897 | 1.00 |
| 120_M | 132_N | 1.872 | 1.00 |
| 132_N | 135_K | 1.847 | 1.00 |
| 13_L | 29_I | 1.825 | 1.00 |
| 31_H | 104_F | 1.824 | 1.00 |
| 144_N | 148_R | 1.802 | 1.00 |
| 58_I | 66_L | 1.756 | 1.00 |
| 28_G | 63_A | 1.729 | 1.00 |
| 29_I | 63_A | 1.697 | 1.00 |
| 120_M | 125_R | 1.689 | 1.00 |
| 142_T | 149_V | 1.676 | 1.00 |
| 74_A | 103_V | 1.621 | 1.00 |
| 58_I | 63_A | 1.618 | 1.00 |
| 8_R | 29_I | 1.609 | 1.00 |
| 143_P | 146_A | 1.605 | 1.00 |
| 103_V | 111_V | 1.559 | 1.00 |
| 120_M | 128_E | 1.532 | 1.00 |
| 15_L | 63_A | 1.506 | 1.00 |
| 142_T | 148_R | 1.460 | 0.99 |
| 149_V | 152_T | 1.447 | 0.99 |
| 27_I | 58_I | 1.387 | 0.99 |
| 116_N | 132_N | 1.386 | 0.99 |
| 70_D | 104_F | 1.362 | 0.99 |
| 102_M | 106_M | 1.360 | 0.99 |
| 95_R | 126_W | 1.342 | 0.99 |
| 13_L | 60_K | 1.318 | 0.98 |
| 74_A | 78_I | 1.294 | 0.98 |
| 91_L | 121_L | 1.283 | 0.98 |
| 59_T | 62_E | 1.278 | 0.98 |
| 151_T | 154_R | 1.274 | 0.98 |
| 18_Y | 26_T | 1.270 | 0.98 |
| 29_I | 67_F | 1.259 | 0.98 |
| 138_W | 141_Q | 1.253 | 0.98 |
| 60_K | 63_A | 1.231 | 0.97 |
| 111_V | 118_L | 1.226 | 0.97 |
| 17_I | 27_I | 1.223 | 0.97 |
| 93_A | 96_R | 1.220 | 0.97 |
| 28_G | 58_I | 1.214 | 0.97 |
| 143_P | 148_R | 1.193 | 0.96 |
| 143_P | 149_V | 1.191 | 0.96 |
| 17_I | 25_Y | 1.178 | 0.96 |
| 87_V | 91_L | 1.171 | 0.96 |
| 121_L | 126_W | 1.153 | 0.96 |
| 149_V | 153_F | 1.145 | 0.95 |
| 148_R | 152_T | 1.137 | 0.95 |
| 128_E | 132_N | 1.136 | 0.95 |
| 29_I | 104_F | 1.128 | 0.95 |
| 19_K | 23_G | 1.127 | 0.95 |
| 15_L | 58_I | 1.126 | 0.95 |
| 116_N | 119_R | 1.123 | 0.95 |
| 87_V | 122_Q | 1.106 | 0.94 |
| 105_Q | 143_P | 1.106 | 0.94 |
| 33_L | 36_S | 1.104 | 0.94 |
| 60_K | 64_E | 1.094 | 0.94 |
| 76_R | 80_R | 1.090 | 0.93 |
| 16_K | 57_V | 1.083 | 0.93 |
| 96_R | 100_I | 1.073 | 0.93 |
| 133_L | 153_F | 1.070 | 0.93 |
| 6_M | 10_D | 1.064 | 0.92 |
| 29_I | 64_E | 1.056 | 0.92 |
| 116_N | 120_M | 1.053 | 0.92 |
| 143_P | 147_K | 1.052 | 0.92 |
| 106_M | 111_V | 1.044 | 0.91 |
| 17_I | 55_N | 1.025 | 0.90 |
| 6_M | 101_N | 1.024 | 0.90 |
| 74_A | 104_F | 1.021 | 0.90 |
| 10_D | 101_N | 1.019 | 0.90 |
| 25_Y | 54_T | 1.006 | 0.89 |
| 19_K | 24_Y | 1.005 | 0.89 |
| 134_A | 139_Y | 1.001 | 0.89 |
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 | |
| 1swyA | 1 | 1 | 100 | 0.122 | Contact Map |
| 4httA | 2 | 0 | 100 | 0.135 | Contact Map |
| 4e97A | 2 | 1 | 100 | 0.137 | Contact Map |
| 4epiA | 1 | 1 | 100 | 0.138 | Contact Map |
| 4zwjA | 4 | 0 | 100 | 0.152 | Contact Map |
| 2qb0B | 2 | 0.9878 | 100 | 0.154 | Contact Map |
| 4yx7C | 2 | 0 | 100 | 0.164 | Contact Map |
| 1wthA | 1 | 1 | 100 | 0.169 | Contact Map |
| 4xesA | 1 | 0 | 100 | 0.196 | Contact Map |
| 4iapA | 2 | 0.9939 | 100 | 0.221 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)