| Sudipto Basu |
| ID: | 1473069726 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (122) | ||
| Sequences: | 498 (165.2) | ||
| Seq/Len: | 4.082 | ||
| Nf(neff/√len): | 15.0 |
HHblits Results: (2016_02)
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: 4.082).
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 |
| 31_E | 35_R | 3.075 | 1.00 |
| 86_L | 100_I | 2.240 | 1.00 |
| 23_V | 87_E | 1.966 | 1.00 |
| 69_W | 93_Y | 1.696 | 0.99 |
| 31_E | 79_A | 1.635 | 0.99 |
| 89_A | 100_I | 1.583 | 0.98 |
| 87_E | 90_K | 1.565 | 0.98 |
| 69_W | 92_A | 1.530 | 0.98 |
| 35_R | 79_A | 1.487 | 0.97 |
| 33_L | 102_G | 1.469 | 0.97 |
| 11_K | 17_Y | 1.345 | 0.95 |
| 14_T | 112_I | 1.323 | 0.94 |
| 41_C | 82_V | 1.319 | 0.94 |
| 9_I | 97_F | 1.315 | 0.94 |
| 50_V | 57_S | 1.309 | 0.94 |
| 51_Y | 55_H | 1.292 | 0.93 |
| 27_L | 86_L | 1.282 | 0.93 |
| 42_L | 100_I | 1.270 | 0.92 |
| 90_K | 98_V | 1.267 | 0.92 |
| 20_P | 79_A | 1.265 | 0.92 |
| 15_L | 118_K | 1.263 | 0.92 |
| 88_E | 93_Y | 1.258 | 0.92 |
| 1_M | 4_W | 1.251 | 0.92 |
| 30_I | 82_V | 1.241 | 0.91 |
| 71_L | 110_Q | 1.239 | 0.91 |
| 103_F | 109_V | 1.213 | 0.90 |
| 76_C | 81_Q | 1.211 | 0.90 |
| 103_F | 107_R | 1.201 | 0.89 |
| 34_L | 81_Q | 1.200 | 0.89 |
| 35_R | 68_M | 1.182 | 0.88 |
| 46_K | 95_D | 1.181 | 0.88 |
| 70_K | 108_Q | 1.181 | 0.88 |
| 73_M | 110_Q | 1.178 | 0.88 |
| 32_Y | 36_S | 1.173 | 0.88 |
| 22_T | 25_D | 1.170 | 0.88 |
| 102_G | 112_I | 1.166 | 0.87 |
| 117_Y | 121_G | 1.159 | 0.87 |
| 6_I | 29_Q | 1.158 | 0.87 |
| 27_L | 83_L | 1.143 | 0.86 |
| 44_F | 93_Y | 1.139 | 0.86 |
| 21_L | 113_S | 1.127 | 0.85 |
| 5_P | 11_K | 1.123 | 0.84 |
| 96_A | 107_R | 1.120 | 0.84 |
| 75_G | 94_P | 1.117 | 0.84 |
| 34_L | 96_A | 1.111 | 0.84 |
| 52_R | 58_P | 1.101 | 0.83 |
| 18_L | 21_L | 1.094 | 0.82 |
| 40_P | 70_K | 1.092 | 0.82 |
| 44_F | 67_T | 1.082 | 0.81 |
| 107_R | 119_P | 1.078 | 0.81 |
| 54_N | 58_P | 1.078 | 0.81 |
| 60_Y | 64_R | 1.070 | 0.80 |
| 53_E | 56_R | 1.066 | 0.80 |
| 27_L | 79_A | 1.055 | 0.79 |
| 103_F | 110_Q | 1.050 | 0.79 |
| 42_L | 86_L | 1.049 | 0.78 |
| 71_L | 82_V | 1.049 | 0.78 |
| 16_S | 19_P | 1.047 | 0.78 |
| 49_F | 53_E | 1.022 | 0.76 |
| 97_F | 119_P | 1.020 | 0.76 |
| 51_Y | 56_R | 1.012 | 0.75 |
| 40_P | 110_Q | 1.009 | 0.75 |
| 107_R | 120_P | 1.009 | 0.75 |
| 25_D | 57_S | 1.001 | 0.74 |
| 6_I | 37_K | 1.001 | 0.74 |
| 2_Q | 102_G | 1.000 | 0.74 |
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 | |
| 1wddS | 2 | 0.9453 | 100 | 0.1 | Contact Map |
| 1gk8I | 4 | 0.9219 | 100 | 0.11 | Contact Map |
| 1rblM | 8 | 0.8438 | 100 | 0.232 | Contact Map |
| 3zxwB | 4 | 0.7266 | 100 | 0.233 | Contact Map |
| 1svdM | 1 | 0.8359 | 100 | 0.251 | Contact Map |
| 1bxnI | 4 | 0.8594 | 100 | 0.284 | Contact Map |
| 4f0hB | 1 | 0.8594 | 100 | 0.296 | Contact Map |
| 2do7A | 1 | 0.4375 | 19.3 | 0.955 | Contact Map |
| 2l4dA | 1 | 0.3906 | 12.5 | 0.958 | Contact Map |
| 1co6A | 1 | 0.3359 | 10 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)