| d3jstb_ |
| ID: | 1451491670 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (94) | ||
| Sequences: | 2070 (1506.1) | ||
| Seq/Len: | 22.021 | ||
| Nf(neff/√len): | 155.3 |
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: 22.021).
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 |
| 75_E | 79_T | 2.780 | 1.00 |
| 40_F | 47_A | 2.396 | 1.00 |
| 68_V | 89_M | 2.266 | 1.00 |
| 29_R | 90_N | 2.233 | 1.00 |
| 43_M | 61_N | 2.160 | 1.00 |
| 46_A | 89_M | 2.153 | 1.00 |
| 70_L | 89_M | 2.112 | 1.00 |
| 30_S | 67_D | 2.067 | 1.00 |
| 17_G | 29_R | 2.028 | 1.00 |
| 4_T | 7_E | 1.928 | 1.00 |
| 80_E | 84_K | 1.823 | 1.00 |
| 58_E | 62_A | 1.787 | 1.00 |
| 11_A | 83_I | 1.775 | 1.00 |
| 40_F | 44_A | 1.768 | 1.00 |
| 26_A | 69_T | 1.754 | 1.00 |
| 35_D | 38_T | 1.701 | 1.00 |
| 70_L | 85_M | 1.692 | 1.00 |
| 33_F | 42_F | 1.622 | 1.00 |
| 81_L | 84_K | 1.576 | 1.00 |
| 56_H | 73_H | 1.490 | 1.00 |
| 20_K | 78_V | 1.482 | 1.00 |
| 50_A | 57_P | 1.482 | 1.00 |
| 43_M | 59_W | 1.469 | 1.00 |
| 42_F | 66_V | 1.421 | 1.00 |
| 49_Y | 88_K | 1.384 | 0.99 |
| 83_I | 87_R | 1.374 | 0.99 |
| 49_Y | 53_L | 1.352 | 0.99 |
| 6_S | 10_E | 1.350 | 0.99 |
| 21_V | 28_T | 1.303 | 0.99 |
| 40_F | 43_M | 1.271 | 0.99 |
| 34_K | 38_T | 1.263 | 0.99 |
| 30_S | 65_R | 1.257 | 0.99 |
| 3_L | 8_M | 1.244 | 0.98 |
| 85_M | 89_M | 1.238 | 0.98 |
| 53_L | 84_K | 1.217 | 0.98 |
| 36_F | 39_A | 1.192 | 0.98 |
| 40_F | 61_N | 1.175 | 0.98 |
| 37_S | 45_Q | 1.175 | 0.98 |
| 28_T | 69_T | 1.174 | 0.98 |
| 72_T | 81_L | 1.159 | 0.97 |
| 28_T | 67_D | 1.152 | 0.97 |
| 31_F | 89_M | 1.142 | 0.97 |
| 59_W | 68_V | 1.112 | 0.96 |
| 17_G | 90_N | 1.105 | 0.96 |
| 5_E | 9_N | 1.101 | 0.96 |
| 5_E | 8_M | 1.059 | 0.95 |
| 37_S | 51_E | 1.056 | 0.95 |
| 32_K | 64_N | 1.045 | 0.94 |
| 53_L | 81_L | 1.040 | 0.94 |
| 5_E | 20_K | 1.036 | 0.94 |
| 39_A | 66_V | 1.022 | 0.93 |
| 63_Y | 73_H | 1.016 | 0.93 |
| 8_M | 20_K | 1.015 | 0.93 |
| 41_G | 44_A | 1.008 | 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 | |
| 3jstA | 2 | 1 | 100 | -0.011 | Contact Map |
| 2v6uA | 2 | 1 | 100 | -0.009 | Contact Map |
| 2ebbA | 1 | 0.9894 | 100 | -0.005 | Contact Map |
| 4wilA | 2 | 1 | 100 | 0.001 | Contact Map |
| 3hxaA | 8 | 1 | 100 | 0.005 | Contact Map |
| 1usmA | 1 | 0.8085 | 99.9 | 0.107 | Contact Map |
| 4lowA | 2 | 0.8617 | 99.9 | 0.174 | Contact Map |
| 3j4jA | 1 | 1 | 19.3 | 0.892 | Contact Map |
| 2qt7A | 2 | 0.7553 | 16.5 | 0.895 | Contact Map |
| 4kjzA | 4 | 0.8617 | 16.1 | 0.896 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)