| job_1 |
| ID: | 1430132493 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 203 (201) | ||
| Sequences: | 947 (726.4) | ||
| Seq/Len: | 4.711 | ||
| Nf(neff/√len): | 51.2 |
HHblits Results: (2013_03)
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: 4.711).
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_N | 117_I | 3.913 | 1.00 |
| 52_I | 56_L | 3.863 | 1.00 |
| 109_D | 112_Q | 3.003 | 1.00 |
| 60_N | 63_R | 2.894 | 1.00 |
| 186_D | 189_S | 2.767 | 1.00 |
| 162_R | 166_E | 2.593 | 1.00 |
| 47_S | 54_D | 2.545 | 1.00 |
| 3_I | 164_I | 2.467 | 1.00 |
| 154_E | 193_G | 2.444 | 1.00 |
| 171_K | 174_Q | 2.442 | 1.00 |
| 173_E | 176_T | 2.366 | 1.00 |
| 4_L | 134_V | 2.347 | 1.00 |
| 135_I | 164_I | 2.321 | 1.00 |
| 61_A | 65_H | 2.212 | 1.00 |
| 186_D | 198_K | 2.159 | 1.00 |
| 5_I | 161_S | 2.067 | 1.00 |
| 191_S | 194_E | 1.991 | 1.00 |
| 116_D | 120_N | 1.975 | 1.00 |
| 104_N | 107_G | 1.943 | 1.00 |
| 38_A | 64_F | 1.896 | 1.00 |
| 26_E | 121_K | 1.843 | 1.00 |
| 189_S | 198_K | 1.828 | 1.00 |
| 164_I | 169_L | 1.795 | 1.00 |
| 176_T | 195_L | 1.773 | 1.00 |
| 118_I | 145_S | 1.747 | 1.00 |
| 172_P | 195_L | 1.747 | 1.00 |
| 58_G | 62_A | 1.744 | 1.00 |
| 5_I | 75_L | 1.740 | 1.00 |
| 31_S | 67_W | 1.709 | 0.99 |
| 59_I | 63_R | 1.688 | 0.99 |
| 135_I | 158_P | 1.631 | 0.99 |
| 52_I | 57_A | 1.505 | 0.98 |
| 159_L | 181_E | 1.493 | 0.98 |
| 46_I | 52_I | 1.482 | 0.98 |
| 8_A | 11_L | 1.475 | 0.98 |
| 108_K | 112_Q | 1.462 | 0.98 |
| 76_R | 125_A | 1.451 | 0.98 |
| 161_S | 165_I | 1.429 | 0.97 |
| 164_I | 175_L | 1.403 | 0.97 |
| 140_D | 157_K | 1.389 | 0.97 |
| 185_F | 195_L | 1.374 | 0.97 |
| 37_E | 102_L | 1.370 | 0.97 |
| 158_P | 195_L | 1.350 | 0.96 |
| 62_A | 66_D | 1.346 | 0.96 |
| 37_E | 41_L | 1.344 | 0.96 |
| 184_F | 200_Y | 1.343 | 0.96 |
| 35_I | 81_L | 1.304 | 0.95 |
| 121_K | 124_E | 1.300 | 0.95 |
| 31_S | 113_F | 1.288 | 0.95 |
| 98_M | 142_Y | 1.278 | 0.94 |
| 192_N | 195_L | 1.271 | 0.94 |
| 166_E | 180_S | 1.260 | 0.94 |
| 42_T | 45_Q | 1.254 | 0.94 |
| 80_G | 98_M | 1.248 | 0.93 |
| 116_D | 147_K | 1.236 | 0.93 |
| 26_E | 125_A | 1.195 | 0.91 |
| 2_L | 132_N | 1.183 | 0.91 |
| 132_N | 154_E | 1.176 | 0.90 |
| 159_L | 180_S | 1.154 | 0.89 |
| 118_I | 146_V | 1.131 | 0.88 |
| 25_P | 89_D | 1.116 | 0.87 |
| 13_Y | 91_M | 1.105 | 0.86 |
| 25_P | 85_L | 1.104 | 0.86 |
| 133_V | 154_E | 1.102 | 0.86 |
| 80_G | 142_Y | 1.095 | 0.86 |
| 195_L | 198_K | 1.084 | 0.85 |
| 28_L | 70_D | 1.080 | 0.84 |
| 125_A | 129_Q | 1.077 | 0.84 |
| 136_N | 139_S | 1.075 | 0.84 |
| 174_Q | 177_G | 1.071 | 0.84 |
| 7_P | 142_Y | 1.070 | 0.84 |
| 119_T | 148_P | 1.065 | 0.83 |
| 4_L | 122_L | 1.061 | 0.83 |
| 6_S | 136_N | 1.061 | 0.83 |
| 119_T | 153_A | 1.051 | 0.82 |
| 27_L | 84_V | 1.048 | 0.82 |
| 47_S | 57_A | 1.047 | 0.82 |
| 115_G | 147_K | 1.038 | 0.81 |
| 53_S | 99_G | 1.033 | 0.81 |
| 80_G | 97_E | 1.032 | 0.81 |
| 115_G | 118_I | 1.025 | 0.80 |
| 62_A | 65_H | 1.019 | 0.79 |
| 82_Y | 87_P | 1.016 | 0.79 |
| 44_P | 48_T | 1.011 | 0.79 |
| 33_Q | 106_R | 1.010 | 0.79 |
| 135_I | 157_K | 1.009 | 0.78 |
| 71_F | 90_L | 1.008 | 0.78 |
| 169_L | 172_P | 1.008 | 0.78 |
| 9_K | 97_E | 1.007 | 0.78 |
| 132_N | 152_N | 1.007 | 0.78 |
| 98_M | 141_E | 1.006 | 0.78 |
| 157_K | 194_E | 1.003 | 0.78 |
| 111_Y | 144_K | 1.002 | 0.78 |
| 169_L | 174_Q | 1.002 | 0.78 |
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 | |
| 3c65A | 1 | 0.0443 | 22.8 | 0.952 | Contact Map |
| 2yufA | 1 | 0.6798 | 15.3 | 0.956 | Contact Map |
| 2ia0A | 2 | 0.7438 | 14.4 | 0.956 | Contact Map |
| 1fseA | 6 | 0.335 | 10.3 | 0.959 | Contact Map |
| 1x3uA | 1 | 0.3793 | 10.2 | 0.959 | Contact Map |
| 1je8A | 4 | 0.3202 | 9.7 | 0.96 | Contact Map |
| 4e1pA | 2 | 0.202 | 9.1 | 0.96 | Contact Map |
| 2htjA | 1 | 0.3645 | 8.4 | 0.961 | Contact Map |
| 1fs1B | 2 | 0.2463 | 8.2 | 0.961 | Contact Map |
| 2duyA | 1 | 0.3153 | 8 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)