| ProTa |
| ID: | 1454426347 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 110 (97) | ||
| Sequences: | 155 (110.7) | ||
| Seq/Len: | 1.598 | ||
| Nf(neff/√len): | 11.2 |
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: 1.598).
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 |
| 67_E | 71_A | 2.690 | 1.00 |
| 77_Q | 82_A | 1.999 | 0.98 |
| 59_K | 65_A | 1.848 | 0.97 |
| 93_K | 96_K | 1.822 | 0.96 |
| 10_A | 14_V | 1.793 | 0.96 |
| 9_T | 14_V | 1.638 | 0.93 |
| 30_K | 41_T | 1.613 | 0.92 |
| 93_K | 97_T | 1.542 | 0.89 |
| 11_T | 16_A | 1.419 | 0.83 |
| 50_V | 54_T | 1.400 | 0.82 |
| 1_M | 17_K | 1.386 | 0.81 |
| 44_A | 49_K | 1.385 | 0.81 |
| 23_K | 31_T | 1.365 | 0.80 |
| 44_A | 50_V | 1.343 | 0.78 |
| 45_E | 48_D | 1.310 | 0.76 |
| 20_K | 23_K | 1.307 | 0.75 |
| 59_K | 63_G | 1.272 | 0.73 |
| 2_A | 7_D | 1.266 | 0.72 |
| 74_T | 79_V | 1.250 | 0.71 |
| 64_N | 67_E | 1.244 | 0.70 |
| 22_K | 64_N | 1.244 | 0.70 |
| 9_T | 17_K | 1.224 | 0.68 |
| 29_E | 41_T | 1.213 | 0.67 |
| 18_E | 23_K | 1.211 | 0.67 |
| 43_G | 51_E | 1.207 | 0.67 |
| 13_E | 17_K | 1.207 | 0.67 |
| 10_A | 17_K | 1.197 | 0.66 |
| 27_V | 30_K | 1.192 | 0.65 |
| 7_D | 11_T | 1.189 | 0.65 |
| 58_H | 62_E | 1.189 | 0.65 |
| 8_T | 13_E | 1.181 | 0.64 |
| 88_E | 91_E | 1.140 | 0.60 |
| 55_E | 66_E | 1.132 | 0.60 |
| 3_D | 17_K | 1.124 | 0.59 |
| 84_E | 87_E | 1.119 | 0.58 |
| 13_E | 16_A | 1.101 | 0.56 |
| 42_N | 58_H | 1.101 | 0.56 |
| 92_T | 95_Q | 1.099 | 0.56 |
| 45_E | 52_E | 1.095 | 0.56 |
| 18_E | 25_A | 1.091 | 0.55 |
| 44_A | 48_D | 1.078 | 0.54 |
| 45_E | 75_D | 1.078 | 0.54 |
| 48_D | 52_E | 1.060 | 0.52 |
| 74_T | 77_Q | 1.056 | 0.52 |
| 35_D | 39_N | 1.042 | 0.50 |
| 87_E | 99_E | 1.040 | 0.50 |
| 31_T | 39_N | 1.038 | 0.50 |
| 60_N | 63_G | 1.035 | 0.49 |
| 3_D | 10_A | 1.029 | 0.49 |
| 14_V | 36_A | 1.027 | 0.49 |
| 11_T | 17_K | 1.012 | 0.47 |
| 85_E | 94_K | 1.008 | 0.47 |
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 | |
| 2l9iA | 1 | 0.2545 | 98.1 | 0.706 | Contact Map |
| 4u7aA | 1 | 0 | 35.4 | 0.891 | Contact Map |
| 4fp9B | 4 | 0.2636 | 5.8 | 0.924 | Contact Map |
| 1i5jA | 1 | 0.2455 | 1.4 | 0.945 | Contact Map |
| 4gyiA | 1 | 0.2727 | 1.4 | 0.945 | Contact Map |
| 4kblA | 2 | 0 | 1.1 | 0.948 | Contact Map |
| 3btpA | 1 | 0 | 0.7 | 0.955 | Contact Map |
| 1pjnA | 1 | 0.1727 | 0.6 | 0.957 | Contact Map |
| 3ukwC | 1 | 0.2 | 0.5 | 0.959 | Contact Map |
| 3ul0C | 1 | 0.2 | 0.5 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)