| Student |
| ID: | 1509988487 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 173 (171) | ||
| Sequences: | 2552 (1442.6) | ||
| Seq/Len: | 14.924 | ||
| Nf(neff/√len): | 110.3 |
HHblits Results: (2016_02)
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: 14.924).
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 |
| 21_E | 25_K | 3.181 | 1.00 |
| 22_K | 25_K | 2.715 | 1.00 |
| 153_L | 156_E | 2.573 | 1.00 |
| 116_Q | 119_K | 2.418 | 1.00 |
| 55_K | 59_Q | 2.223 | 1.00 |
| 102_D | 105_K | 2.207 | 1.00 |
| 85_N | 88_K | 2.128 | 1.00 |
| 26_K | 30_E | 2.039 | 1.00 |
| 17_Q | 61_D | 1.869 | 1.00 |
| 88_K | 105_K | 1.845 | 1.00 |
| 81_K | 85_N | 1.788 | 1.00 |
| 121_E | 125_E | 1.758 | 1.00 |
| 32_K | 36_K | 1.746 | 1.00 |
| 95_K | 112_E | 1.726 | 1.00 |
| 19_S | 23_K | 1.685 | 1.00 |
| 40_K | 44_L | 1.675 | 1.00 |
| 51_K | 54_E | 1.583 | 1.00 |
| 142_L | 146_L | 1.580 | 1.00 |
| 108_K | 112_E | 1.569 | 1.00 |
| 30_E | 34_L | 1.568 | 1.00 |
| 28_E | 32_K | 1.533 | 1.00 |
| 121_E | 124_E | 1.532 | 1.00 |
| 29_A | 33_K | 1.469 | 1.00 |
| 151_Q | 155_D | 1.458 | 1.00 |
| 39_N | 42_R | 1.451 | 1.00 |
| 28_E | 50_K | 1.407 | 0.99 |
| 86_A | 90_G | 1.396 | 0.99 |
| 27_L | 30_E | 1.365 | 0.99 |
| 28_E | 35_A | 1.363 | 0.99 |
| 144_A | 148_A | 1.338 | 0.99 |
| 49_Q | 56_Q | 1.320 | 0.99 |
| 34_L | 39_N | 1.317 | 0.99 |
| 107_D | 111_D | 1.294 | 0.99 |
| 14_E | 64_L | 1.288 | 0.99 |
| 25_K | 29_A | 1.281 | 0.99 |
| 88_K | 92_K | 1.271 | 0.99 |
| 91_A | 95_K | 1.251 | 0.99 |
| 32_K | 35_A | 1.241 | 0.98 |
| 92_K | 95_K | 1.230 | 0.98 |
| 167_E | 170_S | 1.214 | 0.98 |
| 143_E | 147_D | 1.213 | 0.98 |
| 34_L | 46_L | 1.196 | 0.98 |
| 117_M | 121_E | 1.184 | 0.98 |
| 10_E | 67_L | 1.181 | 0.98 |
| 164_K | 167_E | 1.179 | 0.98 |
| 82_E | 85_N | 1.177 | 0.98 |
| 20_L | 23_K | 1.164 | 0.97 |
| 158_L | 162_S | 1.156 | 0.97 |
| 27_L | 46_L | 1.154 | 0.97 |
| 45_L | 49_Q | 1.152 | 0.97 |
| 10_E | 64_L | 1.148 | 0.97 |
| 22_K | 26_K | 1.146 | 0.97 |
| 14_E | 18_E | 1.143 | 0.97 |
| 162_S | 165_L | 1.141 | 0.97 |
| 33_K | 37_K | 1.136 | 0.97 |
| 10_E | 68_E | 1.135 | 0.97 |
| 95_K | 99_K | 1.134 | 0.97 |
| 63_Q | 83_V | 1.126 | 0.97 |
| 89_Q | 92_K | 1.126 | 0.97 |
| 164_K | 168_V | 1.119 | 0.96 |
| 144_A | 147_D | 1.117 | 0.96 |
| 166_P | 169_P | 1.114 | 0.96 |
| 24_I | 57_L | 1.113 | 0.96 |
| 4_R | 7_R | 1.109 | 0.96 |
| 161_E | 170_S | 1.105 | 0.96 |
| 111_D | 114_E | 1.104 | 0.96 |
| 6_L | 9_A | 1.097 | 0.96 |
| 25_K | 82_E | 1.090 | 0.96 |
| 58_D | 62_G | 1.083 | 0.96 |
| 23_K | 53_Y | 1.080 | 0.95 |
| 26_K | 29_A | 1.076 | 0.95 |
| 52_R | 72_L | 1.071 | 0.95 |
| 168_V | 171_E | 1.068 | 0.95 |
| 96_A | 99_K | 1.066 | 0.95 |
| 161_E | 165_L | 1.050 | 0.94 |
| 161_E | 164_K | 1.048 | 0.94 |
| 98_N | 116_Q | 1.047 | 0.94 |
| 35_A | 38_G | 1.047 | 0.94 |
| 160_D | 163_V | 1.046 | 0.94 |
| 155_D | 159_L | 1.046 | 0.94 |
| 166_P | 170_S | 1.033 | 0.94 |
| 16_K | 60_L | 1.030 | 0.94 |
| 44_L | 51_K | 1.025 | 0.93 |
| 43_A | 47_L | 1.010 | 0.93 |
| 71_R | 90_G | 1.010 | 0.93 |
| 162_S | 166_P | 1.004 | 0.93 |
| 68_E | 72_L | 1.001 | 0.92 |
| 23_K | 109_L | 1.001 | 0.92 |
| 127_L | 130_S | 1.000 | 0.92 |
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 | |
| 3frtA | 2 | 0.763 | 99.9 | 0.275 | Contact Map |
| 2gd5A | 4 | 0.8382 | 99.9 | 0.284 | Contact Map |
| 3um3B | 1 | 0 | 99.1 | 0.614 | Contact Map |
| 4abmA | 4 | 0.4277 | 99 | 0.627 | Contact Map |
| 2luhB | 1 | 0.3295 | 98.2 | 0.711 | Contact Map |
| 4txrC | 1 | 0.2139 | 97.3 | 0.764 | Contact Map |
| 3eabG | 6 | 0.1214 | 84.9 | 0.852 | Contact Map |
| 3ulyB | 1 | 0 | 84.4 | 0.853 | Contact Map |
| 3htuB | 4 | 0.1618 | 50.3 | 0.886 | Contact Map |
| 4jkvA | 2 | 0.5318 | 22.5 | 0.905 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)