| NDC80 80-200 |
| ID: | 1464761128 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (118) | ||
| Sequences: | 451 (334) | ||
| Seq/Len: | 3.822 | ||
| Nf(neff/√len): | 30.7 |
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: 3.822).
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 |
| 7_L | 104_A | 3.996 | 1.00 |
| 27_N | 52_F | 2.110 | 1.00 |
| 42_S | 46_F | 2.102 | 1.00 |
| 6_P | 12_F | 2.034 | 1.00 |
| 10_K | 13_I | 1.943 | 1.00 |
| 3_D | 53_L | 1.921 | 1.00 |
| 92_T | 95_A | 1.835 | 1.00 |
| 76_F | 105_A | 1.693 | 0.99 |
| 41_P | 99_W | 1.688 | 0.99 |
| 23_F | 56_F | 1.675 | 0.99 |
| 12_F | 16_C | 1.626 | 0.99 |
| 50_F | 54_Y | 1.623 | 0.99 |
| 20_L | 110_I | 1.555 | 0.98 |
| 45_D | 72_V | 1.529 | 0.98 |
| 49_I | 85_L | 1.462 | 0.97 |
| 67_K | 70_E | 1.440 | 0.96 |
| 38_L | 49_I | 1.424 | 0.96 |
| 11_A | 14_Q | 1.407 | 0.96 |
| 23_F | 113_I | 1.390 | 0.95 |
| 47_L | 68_F | 1.386 | 0.95 |
| 107_V | 111_D | 1.295 | 0.92 |
| 50_F | 76_F | 1.277 | 0.92 |
| 57_L | 116_H | 1.245 | 0.90 |
| 88_S | 113_I | 1.245 | 0.90 |
| 43_V | 102_I | 1.238 | 0.90 |
| 2_K | 92_T | 1.229 | 0.90 |
| 22_E | 112_C | 1.229 | 0.90 |
| 29_Y | 52_F | 1.228 | 0.90 |
| 56_F | 117_T | 1.201 | 0.88 |
| 90_M | 98_T | 1.201 | 0.88 |
| 75_I | 79_L | 1.195 | 0.88 |
| 105_A | 115_I | 1.154 | 0.85 |
| 30_A | 40_A | 1.149 | 0.85 |
| 74_R | 80_G | 1.126 | 0.83 |
| 54_Y | 75_I | 1.125 | 0.83 |
| 46_F | 105_A | 1.122 | 0.83 |
| 34_S | 37_S | 1.101 | 0.81 |
| 25_T | 93_V | 1.098 | 0.81 |
| 115_I | 119_M | 1.081 | 0.80 |
| 50_F | 106_L | 1.079 | 0.80 |
| 24_L | 45_D | 1.077 | 0.79 |
| 73_P | 91_Y | 1.070 | 0.79 |
| 14_Q | 33_V | 1.056 | 0.77 |
| 94_G | 106_L | 1.052 | 0.77 |
| 10_K | 77_K | 1.043 | 0.76 |
| 43_V | 94_G | 1.039 | 0.76 |
| 77_K | 100_P | 1.036 | 0.76 |
| 20_L | 112_C | 1.034 | 0.75 |
| 13_I | 107_V | 1.032 | 0.75 |
| 10_K | 36_K | 1.031 | 0.75 |
| 23_F | 117_T | 1.030 | 0.75 |
| 19_Q | 107_V | 1.021 | 0.74 |
| 99_W | 103_V | 1.021 | 0.74 |
| 27_N | 68_F | 1.011 | 0.73 |
| 95_A | 101_H | 1.010 | 0.73 |
| 32_N | 69_E | 1.007 | 0.73 |
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 | |
| 2ve7A | 2 | 1 | 100 | -0.007 | Contact Map |
| 2igpA | 1 | 0.9421 | 100 | 0.028 | Contact Map |
| 4lvpA | 1 | 0.8595 | 59.8 | 0.902 | Contact Map |
| 2lbcA | 1 | 0.843 | 23.3 | 0.922 | Contact Map |
| 2axiA | 1 | 0.1818 | 15.2 | 0.929 | Contact Map |
| 3dacM | 2 | 0.1488 | 15 | 0.929 | Contact Map |
| 4ae4A | 1 | 0.8017 | 12.5 | 0.931 | Contact Map |
| 2ve7C | 2 | 0.876 | 11.7 | 0.932 | Contact Map |
| 1sqwA | 1 | 0.6942 | 11 | 0.933 | Contact Map |
| 1vw4E | 1 | 0.6198 | 10.9 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)