| Fz4CRD |
| ID: | 1499875641 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 122 (117) | ||
| Sequences: | 1389 (881.6) | ||
| Seq/Len: | 11.872 | ||
| Nf(neff/√len): | 81.5 |
Jackhmmer Results: (2016_04)
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: 11.872).
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 |
| 11_I | 64_V | 3.172 | 1.00 |
| 7_D | 33_Q | 2.570 | 1.00 |
| 8_P | 21_V | 2.026 | 1.00 |
| 79_G | 111_P | 1.980 | 1.00 |
| 80_G | 111_P | 1.933 | 1.00 |
| 16_N | 56_Q | 1.928 | 1.00 |
| 52_S | 85_V | 1.921 | 1.00 |
| 79_G | 83_L | 1.889 | 1.00 |
| 19_Y | 22_T | 1.857 | 1.00 |
| 32_L | 35_D | 1.730 | 1.00 |
| 52_S | 88_R | 1.670 | 1.00 |
| 54_Q | 84_S | 1.638 | 1.00 |
| 85_V | 88_R | 1.630 | 1.00 |
| 62_V | 109_F | 1.600 | 1.00 |
| 26_N | 30_H | 1.578 | 1.00 |
| 90_E | 94_K | 1.556 | 1.00 |
| 51_C | 89_C | 1.552 | 1.00 |
| 24_M | 36_A | 1.549 | 1.00 |
| 66_M | 120_M | 1.540 | 1.00 |
| 114_D | 117_H | 1.488 | 1.00 |
| 84_S | 88_R | 1.483 | 1.00 |
| 59_L | 63_Y | 1.468 | 1.00 |
| 101_P | 104_L | 1.454 | 1.00 |
| 93_L | 98_F | 1.414 | 1.00 |
| 25_P | 30_H | 1.414 | 1.00 |
| 62_V | 104_L | 1.409 | 1.00 |
| 83_L | 87_R | 1.393 | 0.99 |
| 9_I | 19_Y | 1.334 | 0.99 |
| 37_E | 41_T | 1.309 | 0.99 |
| 57_F | 61_S | 1.245 | 0.98 |
| 13_M | 47_I | 1.238 | 0.98 |
| 44_T | 48_Q | 1.235 | 0.98 |
| 33_Q | 36_A | 1.233 | 0.98 |
| 66_M | 75_I | 1.226 | 0.98 |
| 112_Q | 117_H | 1.226 | 0.98 |
| 66_M | 81_M | 1.197 | 0.98 |
| 25_P | 28_V | 1.191 | 0.98 |
| 77_P | 120_M | 1.179 | 0.98 |
| 51_C | 67_C | 1.163 | 0.97 |
| 86_K | 90_E | 1.130 | 0.97 |
| 35_D | 46_L | 1.123 | 0.97 |
| 9_I | 17_L | 1.122 | 0.97 |
| 42_T | 49_Y | 1.120 | 0.96 |
| 40_L | 47_I | 1.100 | 0.96 |
| 52_S | 84_S | 1.085 | 0.96 |
| 24_M | 33_Q | 1.075 | 0.95 |
| 83_L | 86_K | 1.074 | 0.95 |
| 11_I | 36_A | 1.058 | 0.95 |
| 14_C | 60_C | 1.057 | 0.95 |
| 41_T | 55_L | 1.047 | 0.94 |
| 67_C | 78_C | 1.043 | 0.94 |
| 29_G | 35_D | 1.040 | 0.94 |
| 50_G | 92_V | 1.032 | 0.94 |
| 106_C | 110_P | 1.025 | 0.93 |
| 22_T | 33_Q | 1.023 | 0.93 |
| 41_T | 48_Q | 1.023 | 0.93 |
| 99_A | 102_E | 1.020 | 0.93 |
| 86_K | 100_W | 1.015 | 0.93 |
| 7_D | 36_A | 1.011 | 0.93 |
| 78_C | 82_C | 1.008 | 0.93 |
| 49_Y | 96_F | 1.007 | 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 | |
| 1ijyA | 2 | 0.9836 | 100 | 0.058 | Contact Map |
| 5bpbA | 4 | 0 | 100 | 0.061 | Contact Map |
| 1ijxA | 6 | 0.959 | 100 | 0.087 | Contact Map |
| 4c7aA | 2 | 0.8934 | 100 | 0.187 | Contact Map |
| 2mahA | 1 | 0.8934 | 100 | 0.196 | Contact Map |
| 3hklA | 2 | 0.9672 | 97.9 | 0.739 | Contact Map |
| 4ywtA | 4 | 0 | 55.4 | 0.885 | Contact Map |
| 3odnA | 1 | 0.8689 | 33.2 | 0.899 | Contact Map |
| 1hdlA | 1 | 0.4016 | 2.9 | 0.939 | Contact Map |
| 1ug2A | 1 | 0.4754 | 2.2 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)