| 4m70A |
| ID: | 1458923185 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (103) | ||
| Sequences: | 3845 (2733.8) | ||
| Seq/Len: | 37.330 | ||
| Nf(neff/√len): | 269.4 |
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: 37.330).
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 |
| 30_E | 47_E | 2.999 | 1.00 |
| 37_A | 43_I | 2.802 | 1.00 |
| 101_M | 105_D | 2.688 | 1.00 |
| 27_P | 102_A | 2.448 | 1.00 |
| 43_I | 47_E | 2.415 | 1.00 |
| 33_K | 43_I | 2.262 | 1.00 |
| 9_S | 12_R | 2.138 | 1.00 |
| 24_D | 94_D | 2.090 | 1.00 |
| 54_T | 99_Q | 2.052 | 1.00 |
| 58_M | 96_T | 1.908 | 1.00 |
| 41_L | 44_L | 1.796 | 1.00 |
| 4_Y | 8_T | 1.689 | 1.00 |
| 24_D | 97_V | 1.651 | 1.00 |
| 33_K | 47_E | 1.508 | 1.00 |
| 34_S | 43_I | 1.503 | 1.00 |
| 77_R | 82_I | 1.494 | 1.00 |
| 29_Y | 33_K | 1.375 | 0.99 |
| 61_S | 92_C | 1.355 | 0.99 |
| 4_Y | 9_S | 1.307 | 0.99 |
| 78_A | 81_E | 1.304 | 0.99 |
| 44_L | 48_I | 1.292 | 0.99 |
| 53_Y | 57_D | 1.256 | 0.99 |
| 38_I | 45_E | 1.237 | 0.98 |
| 33_K | 46_V | 1.231 | 0.98 |
| 77_R | 80_W | 1.223 | 0.98 |
| 31_K | 34_S | 1.222 | 0.98 |
| 49_V | 56_E | 1.153 | 0.97 |
| 64_R | 67_F | 1.150 | 0.97 |
| 7_V | 10_L | 1.146 | 0.97 |
| 65_N | 68_L | 1.141 | 0.97 |
| 5_A | 14_I | 1.097 | 0.96 |
| 31_K | 35_L | 1.097 | 0.96 |
| 98_K | 101_M | 1.090 | 0.96 |
| 5_A | 10_L | 1.088 | 0.96 |
| 56_E | 60_D | 1.067 | 0.95 |
| 78_A | 82_I | 1.054 | 0.95 |
| 75_R | 84_F | 1.052 | 0.95 |
| 87_E | 91_E | 1.051 | 0.94 |
| 23_C | 95_S | 1.051 | 0.94 |
| 53_Y | 56_E | 1.043 | 0.94 |
| 30_E | 99_Q | 1.042 | 0.94 |
| 59_V | 63_S | 1.042 | 0.94 |
| 21_T | 62_E | 1.035 | 0.94 |
| 86_L | 90_L | 1.031 | 0.94 |
| 51_V | 103_T | 1.030 | 0.94 |
| 25_L | 52_A | 1.027 | 0.94 |
| 12_R | 16_Q | 1.020 | 0.93 |
| 79_M | 84_F | 1.019 | 0.93 |
| 75_R | 78_A | 1.014 | 0.93 |
| 96_T | 99_Q | 1.002 | 0.92 |
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 | |
| 3qflA | 1 | 0.8491 | 98.8 | 0.34 | Contact Map |
| 4m70A | 5 | 0.9906 | 96.8 | 0.582 | Contact Map |
| 2qywA | 1 | 0.8868 | 22.8 | 0.819 | Contact Map |
| 1vcsA | 1 | 0.8396 | 14.6 | 0.835 | Contact Map |
| 4ev6A | 5 | 0.9245 | 7.3 | 0.855 | Contact Map |
| 4i0uA | 10 | 0.9906 | 7.2 | 0.856 | Contact Map |
| 2msvA | 1 | 0.934 | 7.2 | 0.856 | Contact Map |
| 3l39A | 1 | 0.9057 | 7 | 0.857 | Contact Map |
| 4n78D | 1 | 0.6792 | 6.5 | 0.859 | Contact Map |
| 3nvoA | 2 | 0.9906 | 5.5 | 0.863 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)