| 1CBI |
| ID: | 1471613502 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 136 (133) | ||
| Sequences: | 1276 (758.3) | ||
| Seq/Len: | 9.594 | ||
| Nf(neff/√len): | 65.8 |
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: 9.594).
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 |
| 66_K | 69_E | 3.954 | 1.00 |
| 70_G | 82_R | 2.919 | 1.00 |
| 75_T | 79_R | 2.714 | 1.00 |
| 7_W | 113_L | 2.675 | 1.00 |
| 49_Q | 64_N | 2.256 | 1.00 |
| 17_E | 20_K | 2.182 | 1.00 |
| 83_S | 95_C | 2.136 | 1.00 |
| 72_E | 80_K | 2.068 | 1.00 |
| 92_K | 112_E | 2.057 | 1.00 |
| 53_K | 62_E | 2.043 | 1.00 |
| 49_Q | 66_K | 2.000 | 1.00 |
| 74_E | 80_K | 1.953 | 1.00 |
| 112_E | 121_T | 1.853 | 1.00 |
| 116_D | 135_R | 1.832 | 1.00 |
| 27_M | 31_V | 1.812 | 1.00 |
| 121_T | 130_T | 1.798 | 1.00 |
| 51_Y | 64_N | 1.798 | 1.00 |
| 3_F | 113_L | 1.754 | 1.00 |
| 6_T | 42_E | 1.724 | 1.00 |
| 72_E | 82_R | 1.710 | 1.00 |
| 73_E | 95_C | 1.679 | 1.00 |
| 43_I | 52_I | 1.678 | 1.00 |
| 73_E | 83_S | 1.668 | 1.00 |
| 5_G | 135_R | 1.645 | 1.00 |
| 110_T | 121_T | 1.621 | 1.00 |
| 30_K | 33_V | 1.601 | 1.00 |
| 19_L | 32_A | 1.557 | 1.00 |
| 123_G | 128_V | 1.538 | 1.00 |
| 55_S | 60_T | 1.512 | 1.00 |
| 48_D | 66_K | 1.507 | 1.00 |
| 46_D | 49_Q | 1.473 | 1.00 |
| 14_N | 17_E | 1.468 | 1.00 |
| 87_W | 93_I | 1.451 | 1.00 |
| 110_T | 123_G | 1.445 | 1.00 |
| 91_N | 112_E | 1.445 | 1.00 |
| 109_W | 120_L | 1.432 | 1.00 |
| 13_E | 130_T | 1.388 | 0.99 |
| 42_E | 55_S | 1.363 | 0.99 |
| 92_K | 110_T | 1.363 | 0.99 |
| 86_T | 96_T | 1.334 | 0.99 |
| 14_N | 18_L | 1.272 | 0.99 |
| 15_F | 19_L | 1.263 | 0.99 |
| 9_M | 12_S | 1.225 | 0.98 |
| 16_D | 20_K | 1.204 | 0.98 |
| 16_D | 29_R | 1.191 | 0.98 |
| 31_V | 37_S | 1.180 | 0.97 |
| 114_A | 117_E | 1.159 | 0.97 |
| 10_R | 117_E | 1.156 | 0.97 |
| 124_A | 127_V | 1.145 | 0.97 |
| 4_A | 45_Q | 1.144 | 0.97 |
| 121_T | 132_I | 1.141 | 0.97 |
| 7_W | 14_N | 1.067 | 0.95 |
| 45_Q | 50_F | 1.059 | 0.94 |
| 116_D | 134_V | 1.056 | 0.94 |
| 2_N | 5_G | 1.049 | 0.94 |
| 128_V | 131_R | 1.037 | 0.94 |
| 79_R | 97_Q | 1.028 | 0.93 |
| 2_N | 135_R | 1.015 | 0.93 |
| 70_G | 98_T | 1.012 | 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 | |
| 2g7bA | 1 | 0.9853 | 100 | -0.055 | Contact Map |
| 3wbgA | 4 | 0.9559 | 100 | -0.055 | Contact Map |
| 3q6lA | 1 | 0.9559 | 100 | -0.055 | Contact Map |
| 4a60A | 1 | 0.9485 | 100 | -0.054 | Contact Map |
| 4aznA | 2 | 0.9559 | 100 | -0.054 | Contact Map |
| 1vyfA | 1 | 0.9632 | 100 | -0.047 | Contact Map |
| 3p6dA | 1 | 0.9559 | 100 | -0.046 | Contact Map |
| 4bvmA | 1 | 0.9559 | 100 | -0.045 | Contact Map |
| 2a0aA | 1 | 0.9559 | 100 | -0.045 | Contact Map |
| 4tkbA | 1 | 0.9559 | 100 | -0.044 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)