| CcmM SS1 |
| ID: | 1491330688 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (86) | ||
| Sequences: | 1049 (551.3) | ||
| Seq/Len: | 12.198 | ||
| Nf(neff/√len): | 59.4 |
Jackhmmer Results: (2016_04)
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: 12.198).
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 |
| 23_H | 59_H | 2.839 | 1.00 |
| 37_G | 55_C | 2.773 | 1.00 |
| 10_G | 14_A | 2.326 | 1.00 |
| 12_L | 68_G | 2.321 | 1.00 |
| 59_H | 62_E | 2.112 | 1.00 |
| 23_H | 62_E | 1.926 | 1.00 |
| 10_G | 45_T | 1.907 | 1.00 |
| 44_S | 47_E | 1.818 | 1.00 |
| 9_I | 52_L | 1.682 | 1.00 |
| 23_H | 37_G | 1.611 | 1.00 |
| 21_T | 37_G | 1.559 | 1.00 |
| 21_T | 66_L | 1.550 | 1.00 |
| 42_G | 48_V | 1.532 | 1.00 |
| 20_G | 69_I | 1.529 | 1.00 |
| 8_Q | 80_E | 1.484 | 1.00 |
| 52_L | 66_L | 1.390 | 0.99 |
| 69_I | 74_K | 1.379 | 0.99 |
| 55_C | 59_H | 1.371 | 0.99 |
| 56_L | 64_V | 1.310 | 0.99 |
| 61_G | 86_D | 1.304 | 0.99 |
| 42_G | 47_E | 1.279 | 0.99 |
| 12_L | 19_I | 1.247 | 0.99 |
| 68_G | 78_V | 1.246 | 0.98 |
| 24_A | 32_G | 1.237 | 0.98 |
| 29_F | 81_I | 1.228 | 0.98 |
| 18_K | 32_G | 1.204 | 0.98 |
| 63_Y | 85_P | 1.193 | 0.98 |
| 6_V | 53_E | 1.190 | 0.98 |
| 63_Y | 83_Q | 1.158 | 0.97 |
| 66_L | 82_I | 1.152 | 0.97 |
| 61_G | 83_Q | 1.149 | 0.97 |
| 24_A | 31_T | 1.147 | 0.97 |
| 24_A | 28_R | 1.147 | 0.97 |
| 6_V | 46_G | 1.140 | 0.97 |
| 17_F | 78_V | 1.125 | 0.97 |
| 38_S | 55_C | 1.075 | 0.95 |
| 65_R | 76_R | 1.064 | 0.95 |
| 7_Q | 10_G | 1.045 | 0.94 |
| 2_S | 26_A | 1.038 | 0.94 |
| 24_A | 27_R | 1.026 | 0.94 |
| 2_S | 51_A | 1.020 | 0.93 |
| 26_A | 86_D | 1.016 | 0.93 |
| 25_D | 30_R | 1.014 | 0.93 |
| 4_E | 7_Q | 1.004 | 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 | |
| 3zxwB | 4 | 0.9341 | 100 | 0.146 | Contact Map |
| 4f0hB | 1 | 1 | 100 | 0.149 | Contact Map |
| 1svdM | 1 | 0.9451 | 100 | 0.155 | Contact Map |
| 1bxnI | 4 | 1 | 100 | 0.165 | Contact Map |
| 1rblM | 8 | 0.956 | 100 | 0.167 | Contact Map |
| 1gk8I | 4 | 0.9341 | 100 | 0.187 | Contact Map |
| 1wddS | 2 | 0.967 | 100 | 0.199 | Contact Map |
| 2wy7A | 1 | 0.8571 | 40.6 | 0.908 | Contact Map |
| 1hzfA | 1 | 0.8681 | 36 | 0.91 | Contact Map |
| 1qqfA | 1 | 0.8571 | 34.5 | 0.911 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)