| Rv3499c_cter |
| ID: | 1443085296 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (94) | ||
| Sequences: | 164 (145.8) | ||
| Seq/Len: | 1.745 | ||
| Nf(neff/√len): | 15.0 |
HHblits Results: (2015_06)
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: 1.745).
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 |
| 37_A | 66_T | 2.464 | 1.00 |
| 46_W | 73_F | 2.138 | 0.99 |
| 51_P | 55_E | 1.843 | 0.97 |
| 43_G | 58_A | 1.778 | 0.96 |
| 76_C | 115_C | 1.758 | 0.96 |
| 30_H | 116_N | 1.636 | 0.94 |
| 94_R | 98_E | 1.554 | 0.91 |
| 94_R | 113_W | 1.546 | 0.91 |
| 46_W | 114_A | 1.526 | 0.90 |
| 87_Q | 90_T | 1.479 | 0.88 |
| 37_A | 61_K | 1.458 | 0.87 |
| 77_G | 87_Q | 1.452 | 0.87 |
| 80_A | 102_V | 1.435 | 0.86 |
| 30_H | 47_H | 1.366 | 0.82 |
| 31_Y | 73_F | 1.343 | 0.80 |
| 41_A | 114_A | 1.334 | 0.80 |
| 80_A | 110_I | 1.327 | 0.79 |
| 50_T | 53_R | 1.303 | 0.78 |
| 78_A | 98_E | 1.287 | 0.76 |
| 91_G | 100_D | 1.270 | 0.75 |
| 39_S | 50_T | 1.263 | 0.74 |
| 31_Y | 89_G | 1.240 | 0.72 |
| 31_Y | 72_R | 1.224 | 0.71 |
| 31_Y | 108_G | 1.223 | 0.71 |
| 79_V | 104_R | 1.204 | 0.69 |
| 95_R | 99_D | 1.192 | 0.68 |
| 30_H | 112_N | 1.183 | 0.67 |
| 73_F | 112_N | 1.171 | 0.66 |
| 93_T | 103_N | 1.138 | 0.63 |
| 29_I | 47_H | 1.129 | 0.62 |
| 37_A | 40_G | 1.124 | 0.61 |
| 35_A | 88_G | 1.117 | 0.61 |
| 67_C | 101_A | 1.114 | 0.60 |
| 55_E | 88_G | 1.113 | 0.60 |
| 55_E | 69_V | 1.107 | 0.60 |
| 75_R | 87_Q | 1.104 | 0.59 |
| 34_I | 67_C | 1.100 | 0.59 |
| 68_K | 87_Q | 1.094 | 0.58 |
| 31_Y | 75_R | 1.083 | 0.57 |
| 39_S | 64_D | 1.080 | 0.57 |
| 52_A | 79_V | 1.072 | 0.56 |
| 45_A | 48_Q | 1.063 | 0.55 |
| 34_I | 78_A | 1.062 | 0.55 |
| 37_A | 73_F | 1.055 | 0.54 |
| 63_G | 78_A | 1.042 | 0.53 |
| 82_N | 108_G | 1.039 | 0.52 |
| 46_W | 110_I | 1.033 | 0.52 |
| 50_T | 98_E | 1.031 | 0.52 |
| 35_A | 76_C | 1.016 | 0.50 |
| 35_A | 43_G | 1.011 | 0.49 |
| 82_N | 87_Q | 1.005 | 0.49 |
| 28_I | 49_R | 1.001 | 0.48 |
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 | |
| 2gkpA | 1 | 0.4655 | 5.2 | 0.941 | Contact Map |
| 3ocrA | 2 | 0.8276 | 1.8 | 0.954 | Contact Map |
| 2z7bA | 1 | 0.8707 | 1.7 | 0.954 | Contact Map |
| 4kzsA | 1 | 0.3017 | 1.5 | 0.955 | Contact Map |
| 2b3zA | 4 | 0.8966 | 1.5 | 0.956 | Contact Map |
| 2fk5A | 2 | 0.819 | 1.5 | 0.956 | Contact Map |
| 4c24A | 1 | 0.819 | 1.4 | 0.956 | Contact Map |
| 4nl7A | 1 | 0.4483 | 1.2 | 0.958 | Contact Map |
| 2gx1A | 1 | 0.0862 | 1.2 | 0.958 | Contact Map |
| 3lvgA | 3 | 0 | 1.2 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)