| 1xt8_cys_id95_min100 |
| ID: | 1394220350 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 4146 (2759.6) | ||
| Seq/Len: | 39.113 | ||
| Nf(neff/√len): | 268.0 |
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: 39.113).
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 |
| 35_P | 38_A | 4.097 | 1.00 |
| 33_Q | 100_A | 4.077 | 1.00 |
| 28_L | 101_P | 3.393 | 1.00 |
| 62_D | 66_T | 3.068 | 1.00 |
| 62_D | 70_K | 3.064 | 1.00 |
| 80_H | 85_L | 2.729 | 1.00 |
| 4_G | 16_L | 2.290 | 1.00 |
| 49_L | 61_A | 2.091 | 1.00 |
| 33_Q | 38_A | 2.079 | 1.00 |
| 73_Q | 76_T | 2.043 | 1.00 |
| 27_I | 31_F | 1.998 | 1.00 |
| 52_A | 69_L | 1.987 | 1.00 |
| 23_V | 31_F | 1.963 | 1.00 |
| 56_N | 59_T | 1.931 | 1.00 |
| 54_L | 71_Y | 1.913 | 1.00 |
| 12_Y | 16_L | 1.892 | 1.00 |
| 9_F | 45_M | 1.852 | 1.00 |
| 46_K | 98_V | 1.814 | 1.00 |
| 17_V | 25_L | 1.811 | 1.00 |
| 57_K | 72_D | 1.651 | 1.00 |
| 82_N | 86_F | 1.624 | 1.00 |
| 66_T | 70_K | 1.617 | 1.00 |
| 36_Q | 39_V | 1.609 | 1.00 |
| 72_D | 76_T | 1.567 | 1.00 |
| 53_L | 77_F | 1.559 | 1.00 |
| 2_V | 29_A | 1.556 | 1.00 |
| 63_A | 67_Q | 1.520 | 1.00 |
| 31_F | 102_A | 1.478 | 1.00 |
| 51_V | 79_S | 1.416 | 1.00 |
| 55_L | 62_D | 1.381 | 0.99 |
| 21_N | 25_L | 1.290 | 0.99 |
| 47_V | 82_N | 1.275 | 0.99 |
| 51_V | 77_F | 1.270 | 0.99 |
| 38_A | 105_F | 1.257 | 0.99 |
| 22_R | 27_I | 1.227 | 0.98 |
| 33_Q | 43_P | 1.217 | 0.98 |
| 74_N | 80_H | 1.188 | 0.98 |
| 64_Y | 68_N | 1.181 | 0.98 |
| 19_A | 22_R | 1.177 | 0.98 |
| 4_G | 10_G | 1.170 | 0.97 |
| 65_F | 79_S | 1.167 | 0.97 |
| 6_K | 9_F | 1.167 | 0.97 |
| 17_V | 22_R | 1.156 | 0.97 |
| 1_G | 22_R | 1.151 | 0.97 |
| 41_C | 103_V | 1.147 | 0.97 |
| 26_I | 102_A | 1.146 | 0.97 |
| 10_G | 29_A | 1.121 | 0.97 |
| 50_G | 82_N | 1.099 | 0.96 |
| 63_A | 66_T | 1.088 | 0.96 |
| 47_V | 83_T | 1.080 | 0.95 |
| 41_C | 101_P | 1.051 | 0.94 |
| 18_E | 21_N | 1.051 | 0.94 |
| 10_G | 16_L | 1.041 | 0.94 |
| 4_G | 12_Y | 1.018 | 0.93 |
| 64_Y | 67_Q | 1.008 | 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 | |
| 1wdnA | 1 | 1 | 98.5 | 0.588 | Contact Map |
| 4oenA | 2 | 1 | 98.1 | 0.636 | Contact Map |
| 2rc8A | 2 | 1 | 97.6 | 0.673 | Contact Map |
| 1pb7A | 1 | 0.9245 | 97.5 | 0.682 | Contact Map |
| 1yaeA | 6 | 1 | 96.9 | 0.709 | Contact Map |
| 3vv5A | 2 | 1 | 96.6 | 0.719 | Contact Map |
| 3i6vA | 1 | 1 | 96.4 | 0.726 | Contact Map |
| 4jwxA | 1 | 1 | 96.1 | 0.732 | Contact Map |
| 2ylnA | 1 | 1 | 95.9 | 0.739 | Contact Map |
| 3g3kA | 2 | 0.9906 | 95.8 | 0.741 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)