| sub10 |
| ID: | 1404141654 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (171) | ||
| Sequences: | 2180 (1477.6) | ||
| Seq/Len: | 12.749 | ||
| Nf(neff/√len): | 113.0 |
Jackhmmer Results: (2014_04_16)
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: 12.749).
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 |
| 44_V | 52_G | 3.327 | 1.00 |
| 12_L | 38_V | 3.151 | 1.00 |
| 8_A | 41_G | 2.350 | 1.00 |
| 12_L | 35_N | 2.299 | 1.00 |
| 17_V | 21_T | 2.217 | 1.00 |
| 5_E | 9_L | 2.116 | 1.00 |
| 22_L | 31_A | 2.103 | 1.00 |
| 25_A | 70_V | 1.960 | 1.00 |
| 150_T | 154_V | 1.916 | 1.00 |
| 140_L | 143_G | 1.869 | 1.00 |
| 167_E | 172_E | 1.758 | 1.00 |
| 90_R | 93_A | 1.756 | 1.00 |
| 33_I | 64_V | 1.747 | 1.00 |
| 43_Y | 55_Q | 1.701 | 1.00 |
| 18_L | 21_T | 1.623 | 1.00 |
| 10_F | 14_L | 1.618 | 1.00 |
| 18_L | 31_A | 1.599 | 1.00 |
| 67_F | 70_V | 1.581 | 1.00 |
| 168_A | 171_R | 1.568 | 1.00 |
| 126_A | 129_P | 1.559 | 1.00 |
| 115_F | 119_L | 1.545 | 1.00 |
| 70_V | 74_L | 1.480 | 1.00 |
| 18_L | 22_L | 1.480 | 1.00 |
| 25_A | 74_L | 1.472 | 1.00 |
| 48_A | 140_L | 1.461 | 1.00 |
| 136_L | 140_L | 1.438 | 1.00 |
| 16_G | 35_N | 1.396 | 0.99 |
| 3_L | 7_L | 1.373 | 0.99 |
| 4_L | 8_A | 1.356 | 0.99 |
| 40_A | 56_V | 1.344 | 0.99 |
| 15_S | 31_A | 1.332 | 0.99 |
| 138_V | 143_G | 1.323 | 0.99 |
| 22_L | 28_A | 1.322 | 0.99 |
| 63_I | 70_V | 1.299 | 0.99 |
| 49_R | 123_L | 1.271 | 0.99 |
| 164_R | 167_E | 1.269 | 0.99 |
| 43_Y | 152_V | 1.267 | 0.99 |
| 8_A | 11_L | 1.245 | 0.98 |
| 130_L | 134_D | 1.242 | 0.98 |
| 66_L | 69_F | 1.242 | 0.98 |
| 147_M | 150_T | 1.227 | 0.98 |
| 100_V | 104_L | 1.221 | 0.98 |
| 65_V | 70_V | 1.216 | 0.98 |
| 12_L | 39_L | 1.215 | 0.98 |
| 36_F | 132_Y | 1.213 | 0.98 |
| 9_L | 45_A | 1.208 | 0.98 |
| 28_A | 152_V | 1.197 | 0.98 |
| 129_P | 134_D | 1.156 | 0.97 |
| 58_V | 67_F | 1.138 | 0.97 |
| 8_A | 38_V | 1.135 | 0.97 |
| 153_A | 157_V | 1.132 | 0.97 |
| 101_A | 105_A | 1.131 | 0.97 |
| 165_A | 168_A | 1.131 | 0.97 |
| 99_G | 103_I | 1.129 | 0.97 |
| 167_E | 170_K | 1.128 | 0.97 |
| 139_L | 143_G | 1.120 | 0.96 |
| 70_V | 76_A | 1.119 | 0.96 |
| 102_G | 106_A | 1.112 | 0.96 |
| 15_S | 34_L | 1.108 | 0.96 |
| 44_V | 68_L | 1.107 | 0.96 |
| 11_L | 38_V | 1.103 | 0.96 |
| 97_A | 101_A | 1.091 | 0.96 |
| 94_A | 100_V | 1.090 | 0.96 |
| 93_A | 97_A | 1.082 | 0.96 |
| 57_I | 63_I | 1.079 | 0.95 |
| 43_Y | 48_A | 1.070 | 0.95 |
| 53_F | 60_A | 1.063 | 0.95 |
| 114_A | 118_D | 1.063 | 0.95 |
| 67_F | 74_L | 1.057 | 0.95 |
| 32_L | 147_M | 1.056 | 0.95 |
| 31_A | 34_L | 1.055 | 0.95 |
| 51_L | 143_G | 1.053 | 0.95 |
| 33_I | 62_A | 1.050 | 0.94 |
| 43_Y | 54_I | 1.046 | 0.94 |
| 25_A | 76_A | 1.043 | 0.94 |
| 36_F | 62_A | 1.039 | 0.94 |
| 14_L | 18_L | 1.034 | 0.94 |
| 49_R | 124_P | 1.032 | 0.94 |
| 165_A | 169_E | 1.029 | 0.94 |
| 25_A | 58_V | 1.025 | 0.93 |
| 61_G | 66_L | 1.024 | 0.93 |
| 135_W | 138_V | 1.023 | 0.93 |
| 122_G | 125_Q | 1.020 | 0.93 |
| 165_A | 172_E | 1.011 | 0.93 |
| 47_D | 142_V | 1.007 | 0.93 |
| 30_L | 34_L | 1.007 | 0.93 |
| 62_A | 154_V | 1.007 | 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 | |
| 4he8J | 2 | 0.9091 | 100 | 0.163 | Contact Map |
| 3rkoJ | 2 | 0.9375 | 100 | 0.219 | Contact Map |
| 3j5pB | 4 | 0.9205 | 25.3 | 0.926 | Contact Map |
| 4djkA | 2 | 0.8125 | 10.3 | 0.938 | Contact Map |
| 4oh3A | 2 | 0.9261 | 8.1 | 0.941 | Contact Map |
| 3giaA | 1 | 0.7784 | 7.4 | 0.942 | Contact Map |
| 3w9iA | 6 | 0.858 | 7.4 | 0.942 | Contact Map |
| 3l1lA | 1 | 0.7898 | 6.9 | 0.943 | Contact Map |
| 4gycB | 1 | 0.3352 | 5.5 | 0.945 | Contact Map |
| 2kluA | 1 | 0.2727 | 5.4 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)