| T0814 60-180 |
| ID: | 1404854169 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (118) | ||
| Sequences: | 228 (200.8) | ||
| Seq/Len: | 1.932 | ||
| Nf(neff/√len): | 18.5 |
Jackhmmer Results: (2014_04_16)
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: 1.932).
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 |
| 23_N | 27_T | 4.608 | 1.00 |
| 75_S | 101_E | 2.943 | 1.00 |
| 7_G | 15_Y | 2.437 | 1.00 |
| 82_V | 93_F | 2.264 | 1.00 |
| 15_Y | 92_I | 2.120 | 0.99 |
| 21_H | 29_S | 1.869 | 0.98 |
| 3_I | 95_A | 1.804 | 0.97 |
| 33_P | 41_Q | 1.780 | 0.97 |
| 42_G | 73_K | 1.777 | 0.97 |
| 20_V | 81_Q | 1.594 | 0.94 |
| 38_N | 71_Q | 1.514 | 0.91 |
| 22_C | 96_C | 1.433 | 0.88 |
| 65_L | 72_F | 1.415 | 0.87 |
| 36_Y | 99_V | 1.400 | 0.86 |
| 11_G | 91_I | 1.382 | 0.85 |
| 92_I | 106_I | 1.378 | 0.85 |
| 2_E | 69_D | 1.372 | 0.85 |
| 63_L | 80_I | 1.357 | 0.84 |
| 47_D | 62_R | 1.347 | 0.83 |
| 26_W | 77_N | 1.330 | 0.82 |
| 18_N | 81_Q | 1.317 | 0.81 |
| 15_Y | 93_F | 1.307 | 0.80 |
| 41_Q | 93_F | 1.305 | 0.80 |
| 17_Y | 67_N | 1.260 | 0.77 |
| 81_Q | 91_I | 1.235 | 0.75 |
| 56_T | 61_Y | 1.224 | 0.74 |
| 10_S | 57_Q | 1.220 | 0.74 |
| 17_Y | 39_G | 1.218 | 0.73 |
| 19_V | 72_F | 1.173 | 0.69 |
| 7_G | 96_C | 1.168 | 0.69 |
| 39_G | 67_N | 1.152 | 0.67 |
| 8_L | 101_E | 1.140 | 0.66 |
| 7_G | 80_I | 1.138 | 0.66 |
| 90_Q | 104_V | 1.135 | 0.66 |
| 35_E | 60_N | 1.132 | 0.65 |
| 16_A | 41_Q | 1.131 | 0.65 |
| 112_G | 119_N | 1.130 | 0.65 |
| 27_T | 62_R | 1.127 | 0.65 |
| 32_S | 73_K | 1.113 | 0.63 |
| 3_I | 94_T | 1.109 | 0.63 |
| 41_Q | 72_F | 1.109 | 0.63 |
| 18_N | 49_A | 1.095 | 0.62 |
| 25_D | 29_S | 1.084 | 0.60 |
| 43_T | 104_V | 1.079 | 0.60 |
| 87_T | 100_V | 1.079 | 0.60 |
| 34_I | 65_L | 1.078 | 0.60 |
| 14_R | 24_A | 1.074 | 0.59 |
| 13_T | 84_N | 1.065 | 0.58 |
| 50_N | 59_S | 1.045 | 0.56 |
| 36_Y | 110_V | 1.044 | 0.56 |
| 14_R | 44_T | 1.037 | 0.55 |
| 60_N | 110_V | 1.033 | 0.55 |
| 11_G | 82_V | 1.033 | 0.55 |
| 16_A | 52_I | 1.028 | 0.54 |
| 64_L | 91_I | 1.025 | 0.54 |
| 12_Y | 50_N | 1.023 | 0.54 |
| 29_S | 97_F | 1.018 | 0.53 |
| 69_D | 92_I | 1.004 | 0.52 |
| 107_S | 115_D | 1.001 | 0.51 |
| 113_N | 119_N | 1.000 | 0.51 |
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 | |
| 3v9fA | 4 | 0.562 | 28.7 | 0.935 | Contact Map |
| 2hr0A | 1 | 0.9504 | 13.6 | 0.944 | Contact Map |
| 3ottA | 2 | 0.6529 | 13.2 | 0.944 | Contact Map |
| 3cu7A | 2 | 0.9256 | 12.5 | 0.945 | Contact Map |
| 4a2lA | 6 | 0.5785 | 11.5 | 0.946 | Contact Map |
| 2pn5A | 1 | 0.9091 | 10.5 | 0.947 | Contact Map |
| 3prxB | 2 | 0.8512 | 9.3 | 0.948 | Contact Map |
| 2p9rA | 2 | 0.7934 | 8.1 | 0.949 | Contact Map |
| 3hrzA | 1 | 0.843 | 7.3 | 0.95 | Contact Map |
| 4acqA | 4 | 0.9339 | 6.6 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)