| 3kll Lactobacillus reuteri N-ter truncated glucansucrase 983-08 18-45 55-145 179-240 a3A |
| ID: | 1510610535 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (199) | ||
| Sequences: | 13531 (7583.8) | ||
| Seq/Len: | 67.995 | ||
| Nf(neff/√len): | 537.6 |
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: 67.995).
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 |
| 12_Q | 46_I | 4.632 | 1.00 |
| 133_R | 174_D | 3.597 | 1.00 |
| 157_Y | 193_I | 3.296 | 1.00 |
| 161_L | 197_L | 3.238 | 1.00 |
| 20_Y | 50_Y | 3.202 | 1.00 |
| 23_M | 58_H | 2.573 | 1.00 |
| 154_P | 192_T | 2.539 | 1.00 |
| 132_V | 156_A | 2.484 | 1.00 |
| 198_K | 202_K | 2.445 | 1.00 |
| 13_A | 17_N | 2.385 | 1.00 |
| 48_R | 52_N | 2.313 | 1.00 |
| 19_L | 47_A | 2.268 | 1.00 |
| 177_Q | 189_Y | 2.151 | 1.00 |
| 5_D | 8_N | 2.142 | 1.00 |
| 6_N | 15_E | 2.111 | 1.00 |
| 16_L | 46_I | 2.110 | 1.00 |
| 24_N | 54_A | 1.979 | 1.00 |
| 190_F | 194_T | 1.967 | 1.00 |
| 21_Y | 25_F | 1.955 | 1.00 |
| 16_L | 50_Y | 1.922 | 1.00 |
| 20_Y | 24_N | 1.864 | 1.00 |
| 191_D | 194_T | 1.810 | 1.00 |
| 20_Y | 54_A | 1.797 | 1.00 |
| 10_V | 13_A | 1.742 | 1.00 |
| 21_Y | 26_G | 1.728 | 1.00 |
| 52_N | 80_Q | 1.720 | 1.00 |
| 4_I | 11_V | 1.718 | 1.00 |
| 9_P | 13_A | 1.701 | 1.00 |
| 131_F | 134_A | 1.681 | 1.00 |
| 50_Y | 53_A | 1.656 | 1.00 |
| 14_E | 18_W | 1.599 | 1.00 |
| 13_A | 50_Y | 1.593 | 1.00 |
| 35_A | 38_N | 1.573 | 1.00 |
| 34_D | 136_D | 1.573 | 1.00 |
| 158_T | 192_T | 1.551 | 1.00 |
| 191_D | 195_N | 1.518 | 1.00 |
| 195_N | 198_K | 1.516 | 1.00 |
| 59_I | 81_L | 1.514 | 1.00 |
| 18_W | 21_Y | 1.511 | 1.00 |
| 63_E | 135_H | 1.504 | 1.00 |
| 187_T | 191_D | 1.489 | 1.00 |
| 52_N | 84_D | 1.483 | 1.00 |
| 34_D | 63_E | 1.474 | 1.00 |
| 34_D | 135_H | 1.470 | 1.00 |
| 129_Y | 169_R | 1.448 | 1.00 |
| 46_I | 50_Y | 1.441 | 1.00 |
| 45_S | 78_N | 1.432 | 1.00 |
| 153_M | 177_Q | 1.422 | 1.00 |
| 27_N | 55_A | 1.408 | 1.00 |
| 197_L | 201_V | 1.400 | 0.99 |
| 95_L | 156_A | 1.396 | 0.99 |
| 63_E | 136_D | 1.386 | 0.99 |
| 32_R | 136_D | 1.381 | 0.99 |
| 46_I | 49_D | 1.379 | 0.99 |
| 194_T | 198_K | 1.365 | 0.99 |
| 132_V | 160_L | 1.364 | 0.99 |
| 48_R | 60_N | 1.360 | 0.99 |
| 199_T | 203_Y | 1.357 | 0.99 |
| 14_E | 17_N | 1.355 | 0.99 |
| 83_M | 169_R | 1.351 | 0.99 |
| 170_V | 193_I | 1.335 | 0.99 |
| 154_P | 188_R | 1.329 | 0.99 |
| 172_Y | 183_M | 1.321 | 0.99 |
| 157_Y | 174_D | 1.297 | 0.99 |
| 18_W | 22_L | 1.275 | 0.99 |
| 104_A | 107_K | 1.270 | 0.99 |
| 32_R | 63_E | 1.265 | 0.99 |
| 16_L | 47_A | 1.251 | 0.99 |
| 161_L | 168_P | 1.247 | 0.99 |
| 154_P | 189_Y | 1.241 | 0.98 |
| 43_L | 47_A | 1.229 | 0.98 |
| 87_L | 91_I | 1.224 | 0.98 |
| 112_S | 163_N | 1.224 | 0.98 |
| 158_T | 196_L | 1.199 | 0.98 |
| 150_L | 154_P | 1.196 | 0.98 |
| 51_F | 58_H | 1.194 | 0.98 |
| 176_Y | 183_M | 1.175 | 0.98 |
| 190_F | 193_I | 1.171 | 0.98 |
| 49_D | 53_A | 1.168 | 0.97 |
| 39_V | 44_L | 1.166 | 0.97 |
| 187_T | 190_F | 1.162 | 0.97 |
| 157_Y | 196_L | 1.161 | 0.97 |
| 16_L | 20_Y | 1.153 | 0.97 |
| 19_L | 31_I | 1.148 | 0.97 |
| 159_I | 163_N | 1.146 | 0.97 |
| 23_M | 55_A | 1.145 | 0.97 |
| 50_Y | 54_A | 1.130 | 0.97 |
| 61_I | 169_R | 1.125 | 0.97 |
| 194_T | 197_L | 1.123 | 0.97 |
| 84_D | 130_N | 1.110 | 0.96 |
| 4_I | 15_E | 1.092 | 0.96 |
| 19_L | 51_F | 1.088 | 0.96 |
| 32_R | 135_H | 1.086 | 0.96 |
| 157_Y | 189_Y | 1.085 | 0.96 |
| 170_V | 174_D | 1.074 | 0.95 |
| 130_N | 166_S | 1.066 | 0.95 |
| 127_P | 167_V | 1.056 | 0.95 |
| 65_W | 137_S | 1.033 | 0.94 |
| 153_M | 189_Y | 1.030 | 0.94 |
| 189_Y | 192_T | 1.030 | 0.94 |
| 192_T | 196_L | 1.027 | 0.94 |
| 176_Y | 190_F | 1.020 | 0.93 |
| 81_L | 167_V | 1.008 | 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 | |
| 3aieA | 8 | 1 | 100 | 0.149 | Contact Map |
| 3klkA | 1 | 1 | 100 | 0.157 | Contact Map |
| 1j0hA | 2 | 0.9565 | 100 | 0.175 | Contact Map |
| 1ea9C | 2 | 0.9565 | 100 | 0.175 | Contact Map |
| 1wzlA | 2 | 0.9517 | 100 | 0.187 | Contact Map |
| 3bh4A | 2 | 0.9469 | 100 | 0.2 | Contact Map |
| 3edfA | 2 | 0.9565 | 100 | 0.206 | Contact Map |
| 4e2oA | 1 | 0.9565 | 100 | 0.209 | Contact Map |
| 4aeeA | 2 | 0.9372 | 100 | 0.211 | Contact Map |
| 1ud2A | 1 | 0.9324 | 100 | 0.214 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)