| T0768 |
| ID: | 1399485109 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (167) | ||
| Sequences: | 1066 (859.5) | ||
| Seq/Len: | 6.383 | ||
| Nf(neff/√len): | 66.5 |
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: 6.383).
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 |
| 118_L | 122_L | 4.018 | 1.00 |
| 148_M | 151_P | 3.651 | 1.00 |
| 141_I | 145_V | 3.093 | 1.00 |
| 102_I | 106_A | 2.972 | 1.00 |
| 91_T | 114_S | 2.951 | 1.00 |
| 133_C | 155_S | 2.913 | 1.00 |
| 125_I | 129_A | 2.877 | 1.00 |
| 114_S | 137_K | 2.426 | 1.00 |
| 95_V | 99_V | 2.272 | 1.00 |
| 110_C | 133_C | 2.176 | 1.00 |
| 137_K | 159_D | 2.156 | 1.00 |
| 72_G | 75_Y | 1.992 | 1.00 |
| 123_I | 146_E | 1.915 | 1.00 |
| 139_I | 161_V | 1.899 | 1.00 |
| 80_I | 84_A | 1.863 | 1.00 |
| 125_I | 151_P | 1.766 | 1.00 |
| 48_L | 53_E | 1.725 | 1.00 |
| 50_R | 53_E | 1.684 | 1.00 |
| 130_F | 152_F | 1.669 | 1.00 |
| 116_V | 139_I | 1.652 | 1.00 |
| 92_G | 115_D | 1.596 | 1.00 |
| 80_I | 106_A | 1.575 | 0.99 |
| 73_Q | 76_P | 1.476 | 0.99 |
| 64_P | 67_V | 1.455 | 0.99 |
| 112_S | 135_A | 1.433 | 0.99 |
| 101_S | 124_Y | 1.433 | 0.99 |
| 33_V | 36_Y | 1.388 | 0.98 |
| 125_I | 149_D | 1.365 | 0.98 |
| 100_I | 146_E | 1.356 | 0.98 |
| 95_V | 118_L | 1.355 | 0.98 |
| 79_V | 101_S | 1.351 | 0.98 |
| 100_I | 123_I | 1.337 | 0.98 |
| 78_T | 100_I | 1.328 | 0.98 |
| 96_P | 142_P | 1.322 | 0.98 |
| 141_I | 163_M | 1.320 | 0.98 |
| 137_K | 157_A | 1.319 | 0.97 |
| 124_Y | 147_K | 1.316 | 0.97 |
| 99_V | 145_V | 1.298 | 0.97 |
| 64_P | 77_V | 1.282 | 0.97 |
| 110_C | 155_S | 1.279 | 0.97 |
| 56_A | 60_Y | 1.275 | 0.97 |
| 46_A | 50_R | 1.274 | 0.97 |
| 138_E | 160_T | 1.267 | 0.97 |
| 50_R | 54_S | 1.236 | 0.96 |
| 90_I | 95_V | 1.231 | 0.96 |
| 106_A | 129_A | 1.215 | 0.95 |
| 152_F | 155_S | 1.201 | 0.95 |
| 85_F | 110_C | 1.198 | 0.95 |
| 46_A | 49_T | 1.180 | 0.94 |
| 145_V | 148_M | 1.178 | 0.94 |
| 122_L | 145_V | 1.175 | 0.94 |
| 116_V | 133_C | 1.150 | 0.93 |
| 49_T | 53_E | 1.145 | 0.93 |
| 126_N | 129_A | 1.131 | 0.93 |
| 163_M | 166_M | 1.116 | 0.92 |
| 121_N | 144_S | 1.111 | 0.92 |
| 96_P | 119_S | 1.103 | 0.91 |
| 80_I | 125_I | 1.103 | 0.91 |
| 94_T | 115_D | 1.100 | 0.91 |
| 16_L | 23_S | 1.097 | 0.91 |
| 51_Y | 56_A | 1.097 | 0.91 |
| 119_S | 142_P | 1.067 | 0.89 |
| 49_T | 52_D | 1.062 | 0.89 |
| 110_C | 113_L | 1.059 | 0.89 |
| 120_E | 139_I | 1.038 | 0.88 |
| 18_L | 24_A | 1.029 | 0.87 |
| 33_V | 38_F | 1.029 | 0.87 |
| 93_V | 116_V | 1.029 | 0.87 |
| 99_V | 103_G | 1.023 | 0.86 |
| 11_A | 21_A | 1.021 | 0.86 |
| 135_A | 157_A | 1.017 | 0.86 |
| 102_I | 129_A | 1.013 | 0.86 |
| 106_A | 151_P | 1.011 | 0.86 |
| 133_C | 136_L | 1.010 | 0.86 |
| 85_F | 130_F | 1.001 | 0.85 |
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 | |
| 4gt6A | 1 | 0.8353 | 99.7 | 0.497 | Contact Map |
| 4fs7A | 1 | 0.8 | 99.5 | 0.542 | Contact Map |
| 2lz0A | 1 | 0.5706 | 99.3 | 0.59 | Contact Map |
| 4fdwA | 1 | 0.9765 | 99.3 | 0.6 | Contact Map |
| 3t6qA | 2 | 0.7824 | 99.2 | 0.606 | Contact Map |
| 3zyiA | 1 | 0.8059 | 99.2 | 0.611 | Contact Map |
| 4h09A | 5 | 0.8353 | 99.2 | 0.613 | Contact Map |
| 4kt1A | 1 | 0.8059 | 99.2 | 0.614 | Contact Map |
| 3zyjA | 2 | 0.8059 | 99.2 | 0.618 | Contact Map |
| 3sb4A | 2 | 0.9588 | 99.1 | 0.622 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)