| T0759 |
| ID: | 1398961255 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (101) | ||
| Sequences: | 1302 (814) | ||
| Seq/Len: | 12.891 | ||
| Nf(neff/√len): | 81.0 |
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: 12.891).
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 |
| 94_K | 97_S | 2.152 | 1.00 |
| 53_V | 56_P | 1.980 | 1.00 |
| 27_A | 31_G | 1.862 | 1.00 |
| 49_E | 52_S | 1.854 | 1.00 |
| 52_S | 55_G | 1.847 | 1.00 |
| 23_S | 26_E | 1.784 | 1.00 |
| 50_E | 54_K | 1.709 | 1.00 |
| 24_P | 27_A | 1.665 | 1.00 |
| 20_R | 30_A | 1.651 | 1.00 |
| 84_T | 87_H | 1.610 | 1.00 |
| 27_A | 32_L | 1.560 | 1.00 |
| 22_L | 27_A | 1.481 | 1.00 |
| 15_H | 18_P | 1.397 | 0.99 |
| 34_D | 37_M | 1.374 | 0.99 |
| 88_Y | 91_Y | 1.371 | 0.99 |
| 57_N | 60_S | 1.356 | 0.99 |
| 9_S | 14_I | 1.353 | 0.99 |
| 52_S | 56_P | 1.345 | 0.99 |
| 70_K | 80_S | 1.336 | 0.99 |
| 14_I | 21_E | 1.307 | 0.99 |
| 24_P | 31_G | 1.291 | 0.99 |
| 57_N | 62_V | 1.265 | 0.99 |
| 28_H | 38_F | 1.253 | 0.99 |
| 51_I | 54_K | 1.236 | 0.98 |
| 9_S | 12_V | 1.232 | 0.98 |
| 92_V | 95_D | 1.197 | 0.98 |
| 95_D | 100_E | 1.173 | 0.98 |
| 50_E | 53_V | 1.172 | 0.98 |
| 45_E | 48_W | 1.165 | 0.97 |
| 88_Y | 92_V | 1.156 | 0.97 |
| 95_D | 99_Q | 1.151 | 0.97 |
| 61_S | 64_H | 1.148 | 0.97 |
| 25_E | 29_R | 1.146 | 0.97 |
| 60_S | 63_I | 1.145 | 0.97 |
| 31_G | 39_V | 1.141 | 0.97 |
| 85_P | 89_D | 1.138 | 0.97 |
| 99_Q | 103_V | 1.136 | 0.97 |
| 48_W | 51_I | 1.135 | 0.97 |
| 8_H | 12_V | 1.132 | 0.97 |
| 55_G | 59_E | 1.108 | 0.96 |
| 75_E | 80_S | 1.108 | 0.96 |
| 11_M | 14_I | 1.106 | 0.96 |
| 91_Y | 94_K | 1.102 | 0.96 |
| 67_K | 70_K | 1.098 | 0.96 |
| 49_E | 53_V | 1.098 | 0.96 |
| 95_D | 101_L | 1.084 | 0.96 |
| 8_H | 11_M | 1.078 | 0.95 |
| 10_H | 14_I | 1.076 | 0.95 |
| 17_D | 21_E | 1.070 | 0.95 |
| 75_E | 79_Q | 1.052 | 0.95 |
| 89_D | 93_N | 1.051 | 0.94 |
| 49_E | 55_G | 1.048 | 0.94 |
| 99_Q | 104_L | 1.047 | 0.94 |
| 65_D | 68_S | 1.024 | 0.93 |
| 7_H | 10_H | 1.023 | 0.93 |
| 15_H | 30_A | 1.022 | 0.93 |
| 13_V | 20_R | 1.020 | 0.93 |
| 35_W | 39_V | 1.019 | 0.93 |
| 49_E | 56_P | 1.017 | 0.93 |
| 90_R | 93_N | 1.013 | 0.93 |
| 11_M | 27_A | 1.013 | 0.93 |
| 26_E | 42_R | 1.011 | 0.93 |
| 18_P | 30_A | 1.007 | 0.93 |
| 49_E | 54_K | 1.002 | 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 | |
| 1lm5A | 2 | 0.945 | 99.5 | 0.262 | Contact Map |
| 1lm7A | 2 | 0.8624 | 99.5 | 0.271 | Contact Map |
| 1oaoC | 2 | 0.9083 | 13.8 | 0.867 | Contact Map |
| 2j5gA | 11 | 0.8532 | 10.7 | 0.873 | Contact Map |
| 4gm2A | 7 | 0.3578 | 9.8 | 0.876 | Contact Map |
| 1y7oA | 7 | 0.3761 | 9.6 | 0.876 | Contact Map |
| 3fduA | 6 | 0.8991 | 9.5 | 0.876 | Contact Map |
| 4og1A | 1 | 0.945 | 8.8 | 0.878 | Contact Map |
| 3p2lA | 7 | 0.3761 | 8.2 | 0.88 | Contact Map |
| 4mouA | 3 | 0.9174 | 8.1 | 0.88 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)