| T0815 |
| ID: | 1402517900 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (104) | ||
| Sequences: | 250 (211.2) | ||
| Seq/Len: | 2.404 | ||
| Nf(neff/√len): | 20.7 |
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: 2.404).
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 |
| 32_V | 48_W | 3.114 | 1.00 |
| 11_F | 74_V | 2.122 | 1.00 |
| 27_A | 101_A | 1.950 | 0.99 |
| 35_E | 61_E | 1.927 | 0.99 |
| 51_A | 55_A | 1.845 | 0.99 |
| 35_E | 48_W | 1.841 | 0.99 |
| 32_V | 35_E | 1.490 | 0.93 |
| 77_K | 88_T | 1.479 | 0.93 |
| 62_P | 85_S | 1.438 | 0.91 |
| 49_W | 53_K | 1.421 | 0.91 |
| 28_P | 69_G | 1.405 | 0.90 |
| 19_T | 74_V | 1.383 | 0.89 |
| 94_T | 102_R | 1.379 | 0.89 |
| 3_L | 95_I | 1.369 | 0.89 |
| 7_V | 72_A | 1.320 | 0.86 |
| 47_R | 91_Y | 1.313 | 0.86 |
| 10_Y | 74_V | 1.288 | 0.84 |
| 30_A | 69_G | 1.286 | 0.84 |
| 11_F | 86_P | 1.251 | 0.82 |
| 11_F | 104_E | 1.232 | 0.80 |
| 6_I | 95_I | 1.222 | 0.80 |
| 20_D | 31_V | 1.208 | 0.78 |
| 49_W | 52_A | 1.207 | 0.78 |
| 87_V | 99_R | 1.206 | 0.78 |
| 32_V | 39_H | 1.193 | 0.77 |
| 29_D | 40_Q | 1.186 | 0.77 |
| 79_S | 85_S | 1.179 | 0.76 |
| 78_V | 86_P | 1.161 | 0.75 |
| 3_L | 6_I | 1.137 | 0.72 |
| 74_V | 97_D | 1.124 | 0.71 |
| 57_S | 81_R | 1.123 | 0.71 |
| 20_D | 46_L | 1.120 | 0.71 |
| 63_L | 77_K | 1.117 | 0.70 |
| 25_T | 81_R | 1.100 | 0.69 |
| 38_R | 59_V | 1.093 | 0.68 |
| 10_Y | 26_F | 1.088 | 0.67 |
| 2_D | 47_R | 1.086 | 0.67 |
| 11_F | 76_A | 1.083 | 0.67 |
| 54_K | 60_A | 1.079 | 0.67 |
| 62_P | 86_P | 1.078 | 0.66 |
| 7_V | 100_I | 1.071 | 0.66 |
| 5_D | 46_L | 1.068 | 0.65 |
| 40_Q | 50_V | 1.064 | 0.65 |
| 52_A | 62_P | 1.060 | 0.65 |
| 26_F | 70_D | 1.048 | 0.63 |
| 31_V | 101_A | 1.020 | 0.60 |
| 35_E | 100_I | 1.020 | 0.60 |
| 4_P | 44_A | 1.019 | 0.60 |
| 61_E | 75_R | 1.011 | 0.59 |
| 54_K | 79_S | 1.010 | 0.59 |
| 30_A | 35_E | 1.009 | 0.59 |
| 13_A | 18_D | 1.004 | 0.58 |
| 78_V | 85_S | 1.001 | 0.58 |
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 | |
| 3mg1A | 2 | 1 | 99.3 | 0.672 | Contact Map |
| 4h3uA | 2 | 1 | 99.3 | 0.675 | Contact Map |
| 3dm8A | 1 | 1 | 99.2 | 0.691 | Contact Map |
| 4mjdA | 2 | 0.9811 | 99.2 | 0.694 | Contact Map |
| 2a15A | 1 | 0.9811 | 99.1 | 0.7 | Contact Map |
| 3g16A | 2 | 1 | 99.1 | 0.7 | Contact Map |
| 3ff2A | 1 | 1 | 99.1 | 0.701 | Contact Map |
| 1ohpA | 4 | 0.9906 | 99.1 | 0.702 | Contact Map |
| 3dmcA | 2 | 1 | 99.1 | 0.703 | Contact Map |
| 2k54A | 1 | 1 | 99.1 | 0.706 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)