| 3kll Lactobacillus reuteri N-ter truncated glucansucrase GTF180 1392-1512 Ab3 |
| ID: | 1510605489 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (111) | ||
| Sequences: | 6851 (3410.1) | ||
| Seq/Len: | 61.721 | ||
| Nf(neff/√len): | 323.7 |
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: 61.721).
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 |
| 41_D | 106_A | 3.665 | 1.00 |
| 92_S | 95_D | 3.237 | 1.00 |
| 83_G | 89_K | 2.715 | 1.00 |
| 102_A | 105_K | 2.660 | 1.00 |
| 102_A | 106_A | 2.543 | 1.00 |
| 34_V | 98_N | 2.431 | 1.00 |
| 37_A | 98_N | 2.241 | 1.00 |
| 44_K | 106_A | 2.203 | 1.00 |
| 37_A | 102_A | 2.110 | 1.00 |
| 34_V | 95_D | 2.068 | 1.00 |
| 17_G | 36_I | 2.055 | 1.00 |
| 36_I | 99_A | 2.034 | 1.00 |
| 100_L | 110_A | 1.950 | 1.00 |
| 43_F | 48_I | 1.949 | 1.00 |
| 58_N | 88_N | 1.947 | 1.00 |
| 17_G | 22_I | 1.907 | 1.00 |
| 39_N | 42_L | 1.786 | 1.00 |
| 56_Q | 112_A | 1.693 | 1.00 |
| 103_L | 110_A | 1.693 | 1.00 |
| 34_V | 37_A | 1.690 | 1.00 |
| 103_L | 108_L | 1.664 | 1.00 |
| 51_F | 103_L | 1.627 | 1.00 |
| 14_I | 50_T | 1.581 | 1.00 |
| 12_N | 49_T | 1.543 | 1.00 |
| 40_A | 106_A | 1.508 | 1.00 |
| 40_A | 103_L | 1.505 | 1.00 |
| 22_I | 39_N | 1.490 | 1.00 |
| 96_L | 112_A | 1.475 | 1.00 |
| 12_N | 50_T | 1.419 | 1.00 |
| 16_E | 54_A | 1.380 | 0.99 |
| 23_Y | 39_N | 1.368 | 0.99 |
| 93_D | 97_R | 1.345 | 0.99 |
| 13_V | 48_I | 1.317 | 0.99 |
| 21_F | 71_D | 1.271 | 0.99 |
| 56_Q | 96_L | 1.268 | 0.99 |
| 94_E | 97_R | 1.265 | 0.99 |
| 83_G | 88_N | 1.263 | 0.99 |
| 58_N | 77_T | 1.261 | 0.99 |
| 33_N | 82_L | 1.242 | 0.98 |
| 73_G | 90_Y | 1.222 | 0.98 |
| 36_I | 53_L | 1.219 | 0.98 |
| 98_N | 102_A | 1.195 | 0.98 |
| 33_N | 91_G | 1.152 | 0.97 |
| 50_T | 111_I | 1.152 | 0.97 |
| 96_L | 99_A | 1.143 | 0.97 |
| 57_Y | 76_F | 1.134 | 0.97 |
| 99_A | 103_L | 1.132 | 0.97 |
| 58_N | 81_D | 1.119 | 0.96 |
| 19_S | 36_I | 1.103 | 0.96 |
| 115_V | 118_Q | 1.098 | 0.96 |
| 41_D | 45_S | 1.077 | 0.95 |
| 32_T | 35_R | 1.047 | 0.94 |
| 101_Q | 105_K | 1.046 | 0.94 |
| 81_D | 93_D | 1.027 | 0.94 |
| 82_L | 96_L | 1.020 | 0.93 |
| 42_L | 45_S | 1.018 | 0.93 |
| 44_K | 108_L | 1.011 | 0.93 |
| 12_N | 109_Q | 1.005 | 0.93 |
| 14_I | 111_I | 1.003 | 0.93 |
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 | |
| 2z1kA | 4 | 0.843 | 100 | 0.019 | Contact Map |
| 4wf7A | 4 | 0.8595 | 100 | 0.021 | Contact Map |
| 3zo9A | 2 | 0.9008 | 100 | 0.029 | Contact Map |
| 4mb1A | 1 | 0.8512 | 100 | 0.031 | Contact Map |
| 2wc7A | 1 | 0.876 | 100 | 0.031 | Contact Map |
| 1uokA | 1 | 0.876 | 100 | 0.032 | Contact Map |
| 3aj7A | 1 | 0.9008 | 100 | 0.033 | Contact Map |
| 2ze0A | 1 | 0.8678 | 100 | 0.033 | Contact Map |
| 2zicA | 1 | 0.876 | 100 | 0.036 | Contact Map |
| 3wy2A | 2 | 0 | 100 | 0.041 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)