| zbtb7a_gremlin |
| ID: | 1449077296 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (122) | ||
| Sequences: | 5872 (3935.5) | ||
| Seq/Len: | 48.131 | ||
| Nf(neff/√len): | 356.3 |
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: 48.131).
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 |
| 34_T | 93_L | 3.160 | 1.00 |
| 31_T | 38_E | 3.018 | 1.00 |
| 30_L | 41_T | 2.557 | 1.00 |
| 39_Y | 90_P | 2.451 | 1.00 |
| 33_R | 82_V | 2.425 | 1.00 |
| 88_V | 118_A | 2.386 | 1.00 |
| 38_E | 82_V | 2.319 | 1.00 |
| 33_R | 38_E | 2.118 | 1.00 |
| 37_L | 94_G | 2.075 | 1.00 |
| 89_G | 114_A | 1.980 | 1.00 |
| 42_H | 101_Y | 1.968 | 1.00 |
| 120_R | 128_I | 1.958 | 1.00 |
| 19_N | 22_R | 1.866 | 1.00 |
| 49_C | 100_A | 1.847 | 1.00 |
| 87_F | 121_L | 1.813 | 1.00 |
| 33_R | 84_E | 1.807 | 1.00 |
| 88_V | 93_L | 1.763 | 1.00 |
| 25_G | 40_R | 1.762 | 1.00 |
| 21_Q | 44_A | 1.701 | 1.00 |
| 52_Y | 122_L | 1.682 | 1.00 |
| 37_L | 90_P | 1.680 | 1.00 |
| 31_T | 40_R | 1.662 | 1.00 |
| 39_Y | 97_L | 1.662 | 1.00 |
| 100_A | 124_I | 1.610 | 1.00 |
| 26_H | 54_K | 1.586 | 1.00 |
| 96_L | 124_I | 1.558 | 1.00 |
| 96_L | 118_A | 1.532 | 1.00 |
| 51_H | 123_E | 1.526 | 1.00 |
| 96_L | 127_V | 1.519 | 1.00 |
| 32_I | 93_L | 1.506 | 1.00 |
| 53_F | 57_F | 1.464 | 1.00 |
| 39_Y | 94_G | 1.418 | 1.00 |
| 94_G | 98_E | 1.403 | 0.99 |
| 35_Q | 90_P | 1.392 | 0.99 |
| 132_M | 136_Q | 1.353 | 0.99 |
| 17_C | 49_C | 1.327 | 0.99 |
| 32_I | 41_T | 1.327 | 0.99 |
| 116_L | 132_M | 1.302 | 0.99 |
| 22_R | 98_E | 1.279 | 0.99 |
| 19_N | 23_Q | 1.269 | 0.99 |
| 103_A | 126_C | 1.233 | 0.98 |
| 112_M | 134_I | 1.228 | 0.98 |
| 30_L | 57_F | 1.203 | 0.98 |
| 26_H | 58_T | 1.175 | 0.98 |
| 30_L | 46_L | 1.158 | 0.97 |
| 22_R | 25_G | 1.157 | 0.97 |
| 43_R | 81_G | 1.147 | 0.97 |
| 11_S | 15_L | 1.147 | 0.97 |
| 34_T | 39_Y | 1.108 | 0.96 |
| 91_E | 111_N | 1.095 | 0.96 |
| 28_C | 41_T | 1.095 | 0.96 |
| 95_A | 98_E | 1.093 | 0.96 |
| 89_G | 92_A | 1.093 | 0.96 |
| 7_F | 99_F | 1.089 | 0.96 |
| 18_L | 44_A | 1.083 | 0.96 |
| 19_N | 98_E | 1.072 | 0.95 |
| 17_C | 20_E | 1.071 | 0.95 |
| 41_T | 97_L | 1.068 | 0.95 |
| 47_A | 58_T | 1.053 | 0.95 |
| 105_L | 127_V | 1.048 | 0.94 |
| 93_L | 97_L | 1.033 | 0.94 |
| 14_L | 18_L | 1.027 | 0.94 |
| 96_L | 122_L | 1.012 | 0.93 |
| 62_G | 80_A | 1.012 | 0.93 |
| 31_T | 82_V | 1.008 | 0.93 |
| 23_Q | 98_E | 1.007 | 0.93 |
| 43_R | 57_F | 1.005 | 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 | |
| 3i3nA | 2 | 0.8913 | 99.9 | 0.13 | Contact Map |
| 4hxiA | 1 | 0.8333 | 99.9 | 0.136 | Contact Map |
| 3hveA | 1 | 0.7754 | 99.9 | 0.14 | Contact Map |
| 2ppiA | 1 | 0.8406 | 99.9 | 0.154 | Contact Map |
| 2if5A | 1 | 0.8333 | 99.9 | 0.159 | Contact Map |
| 4cxiA | 1 | 0.8986 | 99.9 | 0.16 | Contact Map |
| 4u77A | 1 | 0.8623 | 99.9 | 0.165 | Contact Map |
| 2z8hA | 1 | 0.8841 | 99.9 | 0.176 | Contact Map |
| 4u2mA | 4 | 0.8841 | 99.9 | 0.177 | Contact Map |
| 3ohuA | 6 | 0.8623 | 99.9 | 0.18 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)