| pengfei tian |
| ID: | 1478204291 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 99 (95) | ||
| Sequences: | 10408 (7035) | ||
| Seq/Len: | 109.558 | ||
| Nf(neff/√len): | 721.8 |
HHblits Results: (2016_02)
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: 109.558).
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 |
| 22_A | 83_N | 4.492 | 1.00 |
| 31_T | 88_N | 3.538 | 1.00 |
| 13_I | 22_A | 3.303 | 1.00 |
| 14_K | 65_E | 2.988 | 1.00 |
| 65_E | 70_K | 2.737 | 1.00 |
| 63_L | 70_K | 2.508 | 1.00 |
| 31_T | 75_V | 2.419 | 1.00 |
| 37_N | 41_R | 2.395 | 1.00 |
| 14_K | 19_L | 2.070 | 1.00 |
| 12_T | 19_L | 2.028 | 1.00 |
| 89_L | 93_I | 2.011 | 1.00 |
| 24_L | 90_L | 1.840 | 1.00 |
| 20_K | 37_N | 1.823 | 1.00 |
| 30_D | 88_N | 1.765 | 1.00 |
| 12_T | 21_E | 1.735 | 1.00 |
| 65_E | 68_G | 1.667 | 1.00 |
| 59_Y | 74_T | 1.630 | 1.00 |
| 85_I | 89_L | 1.612 | 1.00 |
| 35_E | 39_P | 1.580 | 1.00 |
| 35_E | 79_P | 1.569 | 1.00 |
| 61_Q | 74_T | 1.514 | 1.00 |
| 10_L | 21_E | 1.489 | 1.00 |
| 33_L | 83_N | 1.380 | 0.99 |
| 20_K | 83_N | 1.318 | 0.99 |
| 23_L | 84_I | 1.271 | 0.99 |
| 32_V | 78_G | 1.250 | 0.99 |
| 16_G | 62_I | 1.250 | 0.99 |
| 63_L | 72_I | 1.185 | 0.98 |
| 38_L | 41_R | 1.178 | 0.98 |
| 34_E | 37_N | 1.144 | 0.97 |
| 90_L | 95_C | 1.133 | 0.97 |
| 13_I | 83_N | 1.127 | 0.97 |
| 48_G | 52_G | 1.126 | 0.97 |
| 73_G | 89_L | 1.120 | 0.96 |
| 47_I | 50_I | 1.114 | 0.96 |
| 46_M | 53_F | 1.110 | 0.96 |
| 47_I | 56_V | 1.103 | 0.96 |
| 64_I | 73_G | 1.091 | 0.96 |
| 37_N | 40_G | 1.080 | 0.95 |
| 48_G | 53_F | 1.077 | 0.95 |
| 20_K | 82_V | 1.069 | 0.95 |
| 37_N | 83_N | 1.069 | 0.95 |
| 18_Q | 40_G | 1.068 | 0.95 |
| 25_D | 28_A | 1.067 | 0.95 |
| 33_L | 38_L | 1.054 | 0.95 |
| 61_Q | 72_I | 1.051 | 0.94 |
| 38_L | 42_W | 1.042 | 0.94 |
| 71_A | 89_L | 1.033 | 0.94 |
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 | |
| 2hs1A | 2 | 1 | 99.3 | 0.085 | Contact Map |
| 1fmbA | 1 | 0.9798 | 99.3 | 0.104 | Contact Map |
| 2hahA | 1 | 1 | 99.2 | 0.116 | Contact Map |
| 3ec0A | 2 | 1 | 99.2 | 0.136 | Contact Map |
| 3slzA | 2 | 0.9697 | 99.2 | 0.144 | Contact Map |
| 3ka2A | 1 | 0.9495 | 99.1 | 0.149 | Contact Map |
| 3s8iA | 2 | 0.9192 | 99.1 | 0.158 | Contact Map |
| 2i1aA | 4 | 0.899 | 99 | 0.187 | Contact Map |
| 3liyA | 6 | 1 | 98.9 | 0.238 | Contact Map |
| 3sqfA | 2 | 0.8889 | 98.7 | 0.28 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)