| CcdB GREMLIN |
| ID: | 1385998643 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (101) | ||
| Sequences: | 159 (131.9) | ||
| Seq/Len: | 1.574 | ||
| Nf(neff/√len): | 13.1 |
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: 1.574).
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 |
| 8_Y | 15_R | 2.180 | 0.99 |
| 33_V | 76_I | 2.159 | 0.99 |
| 4_K | 82_D | 1.942 | 0.98 |
| 20_V | 34_I | 1.898 | 0.97 |
| 34_I | 63_M | 1.792 | 0.96 |
| 54_V | 63_M | 1.708 | 0.94 |
| 2_Q | 67_D | 1.617 | 0.92 |
| 3_F | 6_Y | 1.573 | 0.90 |
| 28_P | 65_T | 1.509 | 0.88 |
| 19_D | 31_R | 1.481 | 0.86 |
| 2_Q | 8_Y | 1.478 | 0.86 |
| 54_V | 94_I | 1.441 | 0.84 |
| 2_Q | 98_F | 1.415 | 0.83 |
| 5_V | 97_M | 1.408 | 0.82 |
| 32_M | 97_M | 1.398 | 0.82 |
| 56_I | 68_M | 1.388 | 0.81 |
| 39_A | 60_S | 1.367 | 0.79 |
| 18_V | 90_I | 1.358 | 0.79 |
| 2_Q | 99_W | 1.357 | 0.79 |
| 37_A | 43_S | 1.305 | 0.75 |
| 32_M | 98_F | 1.298 | 0.74 |
| 34_I | 65_T | 1.277 | 0.73 |
| 2_Q | 64_M | 1.275 | 0.72 |
| 1_M | 94_I | 1.272 | 0.72 |
| 72_P | 83_L | 1.268 | 0.72 |
| 24_I | 100_G | 1.237 | 0.69 |
| 36_L | 50_L | 1.218 | 0.67 |
| 67_D | 91_K | 1.204 | 0.66 |
| 64_M | 67_D | 1.203 | 0.66 |
| 51_Y | 66_T | 1.198 | 0.66 |
| 18_V | 65_T | 1.187 | 0.65 |
| 7_T | 56_I | 1.177 | 0.64 |
| 8_Y | 17_F | 1.177 | 0.64 |
| 8_Y | 16_L | 1.176 | 0.63 |
| 87_E | 95_N | 1.150 | 0.61 |
| 56_I | 83_L | 1.143 | 0.60 |
| 74_S | 98_F | 1.141 | 0.60 |
| 22_S | 77_G | 1.123 | 0.58 |
| 25_I | 91_K | 1.103 | 0.56 |
| 62_R | 66_T | 1.096 | 0.55 |
| 48_R | 63_M | 1.095 | 0.55 |
| 47_S | 51_Y | 1.087 | 0.54 |
| 54_V | 83_L | 1.086 | 0.54 |
| 19_D | 96_L | 1.083 | 0.54 |
| 21_Q | 59_E | 1.066 | 0.52 |
| 53_V | 81_A | 1.059 | 0.52 |
| 12_S | 22_S | 1.049 | 0.51 |
| 17_F | 76_I | 1.036 | 0.49 |
| 7_T | 57_G | 1.033 | 0.49 |
| 4_K | 93_A | 1.023 | 0.48 |
| 76_I | 79_E | 1.011 | 0.47 |
| 25_I | 28_P | 1.006 | 0.46 |
| 55_H | 85_H | 1.000 | 0.45 |
| 47_S | 101_I | 1.000 | 0.45 |
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 | |
| 3vubA | 1 | 1 | 99.9 | 0.417 | Contact Map |
| 2kmtA | 2 | 1 | 99.7 | 0.518 | Contact Map |
| 4mdxA | 2 | 0.9802 | 86.3 | 0.87 | Contact Map |
| 1m1fA | 2 | 0.9307 | 83.4 | 0.875 | Contact Map |
| 1ub4A | 2 | 0.8713 | 82.9 | 0.876 | Contact Map |
| 3j32A | 2 | 0.9406 | 8.5 | 0.933 | Contact Map |
| 4eagA | 1 | 0.4059 | 7.3 | 0.935 | Contact Map |
| 3t4nA | 1 | 0.4455 | 6.3 | 0.936 | Contact Map |
| 2qrdA | 2 | 0.4752 | 6.1 | 0.937 | Contact Map |
| 4eaiA | 1 | 0.3366 | 5.8 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)