| T0846 |
| ID: | 1404840905 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (135) | ||
| Sequences: | 170 (153.7) | ||
| Seq/Len: | 1.259 | ||
| Nf(neff/√len): | 13.2 |
HHblits Results: (2013_03)
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: 1.259).
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 |
| 94_K | 102_E | 2.467 | 1.00 |
| 47_V | 86_A | 2.467 | 1.00 |
| 13_Q | 48_F | 1.993 | 0.97 |
| 23_F | 123_M | 1.959 | 0.97 |
| 44_S | 54_L | 1.798 | 0.94 |
| 98_R | 101_A | 1.684 | 0.91 |
| 43_L | 104_N | 1.628 | 0.89 |
| 39_E | 91_F | 1.514 | 0.83 |
| 48_F | 56_N | 1.491 | 0.82 |
| 56_N | 95_N | 1.453 | 0.80 |
| 61_I | 112_I | 1.389 | 0.75 |
| 119_V | 126_I | 1.387 | 0.75 |
| 40_I | 43_L | 1.385 | 0.75 |
| 60_Q | 63_E | 1.320 | 0.70 |
| 59_S | 71_I | 1.307 | 0.69 |
| 110_E | 116_A | 1.305 | 0.68 |
| 23_F | 95_N | 1.299 | 0.68 |
| 78_S | 82_F | 1.269 | 0.65 |
| 65_P | 116_A | 1.267 | 0.65 |
| 103_K | 121_N | 1.266 | 0.65 |
| 87_G | 101_A | 1.243 | 0.63 |
| 27_V | 53_Q | 1.237 | 0.62 |
| 34_Q | 107_K | 1.219 | 0.61 |
| 133_E | 139_Q | 1.205 | 0.59 |
| 37_E | 48_F | 1.201 | 0.59 |
| 34_Q | 104_N | 1.185 | 0.58 |
| 13_Q | 75_L | 1.185 | 0.58 |
| 33_I | 121_N | 1.169 | 0.56 |
| 24_I | 33_I | 1.139 | 0.53 |
| 86_A | 101_A | 1.127 | 0.52 |
| 12_P | 48_F | 1.113 | 0.50 |
| 33_I | 72_S | 1.112 | 0.50 |
| 58_L | 111_A | 1.109 | 0.50 |
| 27_V | 110_E | 1.104 | 0.50 |
| 22_E | 126_I | 1.093 | 0.48 |
| 47_V | 123_M | 1.090 | 0.48 |
| 47_V | 93_I | 1.084 | 0.48 |
| 19_S | 22_E | 1.075 | 0.47 |
| 63_E | 74_T | 1.074 | 0.47 |
| 24_I | 84_K | 1.060 | 0.45 |
| 12_P | 142_E | 1.059 | 0.45 |
| 13_Q | 144_P | 1.057 | 0.45 |
| 16_V | 136_R | 1.056 | 0.45 |
| 83_A | 118_A | 1.055 | 0.45 |
| 59_S | 115_Y | 1.050 | 0.44 |
| 96_S | 119_V | 1.049 | 0.44 |
| 41_R | 52_N | 1.048 | 0.44 |
| 24_I | 89_K | 1.048 | 0.44 |
| 15_I | 141_V | 1.047 | 0.44 |
| 48_F | 52_N | 1.046 | 0.44 |
| 26_K | 34_Q | 1.042 | 0.43 |
| 22_E | 51_Q | 1.041 | 0.43 |
| 57_Q | 135_K | 1.037 | 0.43 |
| 40_I | 135_K | 1.034 | 0.43 |
| 26_K | 136_R | 1.031 | 0.42 |
| 50_N | 92_G | 1.027 | 0.42 |
| 16_V | 45_Q | 1.024 | 0.42 |
| 39_E | 86_A | 1.017 | 0.41 |
| 49_G | 68_T | 1.014 | 0.41 |
| 31_H | 40_I | 1.012 | 0.41 |
| 68_T | 116_A | 1.009 | 0.40 |
| 35_E | 39_E | 1.007 | 0.40 |
| 43_L | 133_E | 1.007 | 0.40 |
| 78_S | 139_Q | 1.005 | 0.40 |
| 33_I | 37_E | 1.004 | 0.40 |
| 98_R | 143_L | 1.004 | 0.40 |
| 105_I | 124_G | 1.003 | 0.40 |
| 37_E | 40_I | 1.001 | 0.40 |
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 | |
| 2lnmA | 1 | 0.4041 | 39.6 | 0.931 | Contact Map |
| 2llvA | 1 | 0.4863 | 30.7 | 0.935 | Contact Map |
| 2llwA | 1 | 0.4863 | 24.9 | 0.938 | Contact Map |
| 2zbcA | 8 | 0.5274 | 13.2 | 0.945 | Contact Map |
| 3hwsA | 6 | 0.637 | 10 | 0.948 | Contact Map |
| 2djwA | 10 | 0.5205 | 7.2 | 0.951 | Contact Map |
| 2oeqA | 4 | 0.4658 | 6 | 0.953 | Contact Map |
| 4o4fA | 1 | 0.9452 | 5.2 | 0.954 | Contact Map |
| 2lmdA | 1 | 0.4658 | 5.2 | 0.954 | Contact Map |
| 2f4mB | 1 | 0.411 | 4.7 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)