| 4CI0_B |
| ID: | 1488468542 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 228 (214) | ||
| Sequences: | 3259 (1406.4) | ||
| Seq/Len: | 15.229 | ||
| Nf(neff/√len): | 96.1 |
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: 15.229).
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 |
| 81_V | 117_I | 2.373 | 1.00 |
| 3_R | 35_D | 2.093 | 1.00 |
| 176_I | 216_R | 1.963 | 1.00 |
| 6_Y | 16_A | 1.942 | 1.00 |
| 15_D | 128_P | 1.934 | 1.00 |
| 8_H | 11_G | 1.917 | 1.00 |
| 60_V | 71_L | 1.853 | 1.00 |
| 54_A | 78_A | 1.853 | 1.00 |
| 164_D | 201_S | 1.823 | 1.00 |
| 8_H | 13_T | 1.773 | 1.00 |
| 10_S | 61_C | 1.696 | 1.00 |
| 114_A | 122_A | 1.629 | 1.00 |
| 191_D | 200_N | 1.605 | 1.00 |
| 164_D | 200_N | 1.565 | 1.00 |
| 8_H | 16_A | 1.510 | 1.00 |
| 191_D | 198_E | 1.505 | 1.00 |
| 16_A | 57_E | 1.481 | 1.00 |
| 9_L | 67_S | 1.472 | 1.00 |
| 54_A | 74_L | 1.470 | 1.00 |
| 60_V | 68_L | 1.439 | 1.00 |
| 68_L | 72_K | 1.425 | 1.00 |
| 56_V | 71_L | 1.422 | 1.00 |
| 16_A | 39_G | 1.421 | 1.00 |
| 17_M | 21_E | 1.404 | 0.99 |
| 28_E | 32_N | 1.398 | 0.99 |
| 8_H | 40_Q | 1.388 | 0.99 |
| 179_G | 182_A | 1.379 | 0.99 |
| 65_E | 69_H | 1.361 | 0.99 |
| 184_A | 209_I | 1.357 | 0.99 |
| 87_C | 126_C | 1.351 | 0.99 |
| 177_G | 192_M | 1.338 | 0.99 |
| 179_G | 192_M | 1.310 | 0.99 |
| 9_L | 41_T | 1.309 | 0.99 |
| 5_G | 51_M | 1.300 | 0.99 |
| 10_S | 59_S | 1.289 | 0.99 |
| 9_L | 60_V | 1.289 | 0.99 |
| 52_D | 77_K | 1.268 | 0.99 |
| 208_G | 212_V | 1.264 | 0.99 |
| 145_M | 149_Q | 1.263 | 0.99 |
| 133_I | 137_V | 1.249 | 0.99 |
| 180_T | 183_M | 1.245 | 0.98 |
| 52_D | 79_K | 1.245 | 0.98 |
| 4_I | 34_V | 1.239 | 0.98 |
| 10_S | 67_S | 1.228 | 0.98 |
| 9_L | 16_A | 1.228 | 0.98 |
| 12_C | 87_C | 1.227 | 0.98 |
| 180_T | 184_A | 1.201 | 0.98 |
| 12_C | 15_D | 1.196 | 0.98 |
| 22_N | 25_I | 1.188 | 0.98 |
| 8_H | 41_T | 1.184 | 0.98 |
| 3_R | 37_V | 1.171 | 0.98 |
| 4_I | 53_L | 1.171 | 0.98 |
| 13_T | 16_A | 1.166 | 0.97 |
| 177_G | 197_P | 1.166 | 0.97 |
| 171_N | 174_L | 1.161 | 0.97 |
| 19_L | 26_L | 1.150 | 0.97 |
| 161_C | 206_K | 1.148 | 0.97 |
| 31_T | 35_D | 1.147 | 0.97 |
| 11_G | 40_Q | 1.145 | 0.97 |
| 163_C | 176_I | 1.130 | 0.97 |
| 11_G | 17_M | 1.126 | 0.97 |
| 175_C | 185_C | 1.124 | 0.97 |
| 164_D | 189_A | 1.119 | 0.96 |
| 16_A | 41_T | 1.116 | 0.96 |
| 189_A | 200_N | 1.116 | 0.96 |
| 169_V | 172_Q | 1.114 | 0.96 |
| 5_G | 20_T | 1.114 | 0.96 |
| 13_T | 40_Q | 1.113 | 0.96 |
| 25_I | 28_E | 1.108 | 0.96 |
| 192_M | 197_P | 1.108 | 0.96 |
| 193_T | 198_E | 1.107 | 0.96 |
| 30_L | 42_L | 1.106 | 0.96 |
| 19_L | 55_L | 1.095 | 0.96 |
| 206_K | 213_Q | 1.092 | 0.96 |
| 128_P | 133_I | 1.090 | 0.96 |
| 5_G | 16_A | 1.083 | 0.96 |
| 182_A | 192_M | 1.079 | 0.95 |
| 123_L | 128_P | 1.077 | 0.95 |
| 21_E | 24_D | 1.077 | 0.95 |
| 87_C | 92_C | 1.070 | 0.95 |
| 9_L | 71_L | 1.069 | 0.95 |
| 182_A | 191_D | 1.066 | 0.95 |
| 177_G | 195_G | 1.065 | 0.95 |
| 8_H | 20_T | 1.065 | 0.95 |
| 187_T | 205_I | 1.064 | 0.95 |
| 110_F | 113_I | 1.062 | 0.95 |
| 201_S | 216_R | 1.060 | 0.95 |
| 2_P | 53_L | 1.046 | 0.94 |
| 8_H | 57_E | 1.041 | 0.94 |
| 69_H | 73_E | 1.041 | 0.94 |
| 6_Y | 55_L | 1.040 | 0.94 |
| 6_Y | 17_M | 1.037 | 0.94 |
| 85_G | 161_C | 1.035 | 0.94 |
| 184_A | 213_Q | 1.034 | 0.94 |
| 112_P | 115_D | 1.022 | 0.93 |
| 117_I | 120_D | 1.021 | 0.93 |
| 20_T | 42_L | 1.019 | 0.93 |
| 24_D | 27_A | 1.019 | 0.93 |
| 11_G | 15_D | 1.019 | 0.93 |
| 8_H | 21_E | 1.018 | 0.93 |
| 38_Y | 45_L | 1.016 | 0.93 |
| 201_S | 205_I | 1.015 | 0.93 |
| 209_I | 213_Q | 1.008 | 0.93 |
| 209_I | 212_V | 1.003 | 0.93 |
| 32_N | 35_D | 1.002 | 0.92 |
| 201_S | 213_Q | 1.001 | 0.92 |
| 7_I | 13_T | 1.001 | 0.92 |
| 65_E | 70_E | 1.000 | 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 | |
| 4omfG | 1 | 1 | 100 | 0.214 | Contact Map |
| 4iucS | 1 | 0.9474 | 100 | 0.439 | Contact Map |
| 4uqlA | 2 | 0.9386 | 100 | 0.441 | Contact Map |
| 1h2aS | 1 | 0.9342 | 100 | 0.442 | Contact Map |
| 4ue3S | 2 | 0.943 | 100 | 0.457 | Contact Map |
| 4u9hS | 1 | 0.9342 | 100 | 0.463 | Contact Map |
| 3ayxB | 2 | 0.9605 | 100 | 0.468 | Contact Map |
| 3ze9A | 1 | 0.9298 | 100 | 0.477 | Contact Map |
| 1yq9A | 2 | 0.9386 | 100 | 0.478 | Contact Map |
| 2wpnA | 1 | 0.9386 | 100 | 0.48 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)