| Rv2633c |
| ID: | 1518566728 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 161 (146) | ||
| Sequences: | 2176 (1581.3) | ||
| Seq/Len: | 14.904 | ||
| Nf(neff/√len): | 130.9 |
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: 14.904).
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 |
| 12_T | 15_K | 3.290 | 1.00 |
| 7_L | 114_I | 3.147 | 1.00 |
| 10_H | 138_I | 2.467 | 1.00 |
| 80_T | 94_E | 2.229 | 1.00 |
| 123_T | 126_E | 2.217 | 1.00 |
| 31_R | 92_E | 2.001 | 1.00 |
| 15_K | 106_A | 1.935 | 1.00 |
| 15_K | 103_E | 1.895 | 1.00 |
| 48_I | 134_M | 1.770 | 1.00 |
| 2_N | 119_P | 1.696 | 1.00 |
| 137_R | 141_L | 1.643 | 1.00 |
| 32_H | 36_D | 1.632 | 1.00 |
| 51_D | 137_R | 1.570 | 1.00 |
| 99_R | 103_E | 1.563 | 1.00 |
| 56_A | 60_A | 1.525 | 1.00 |
| 129_E | 133_K | 1.500 | 1.00 |
| 70_E | 104_A | 1.494 | 1.00 |
| 73_Q | 101_V | 1.475 | 1.00 |
| 126_E | 129_E | 1.460 | 1.00 |
| 72_R | 76_D | 1.445 | 1.00 |
| 21_V | 92_E | 1.400 | 0.99 |
| 43_D | 75_V | 1.396 | 0.99 |
| 143_G | 146_L | 1.385 | 0.99 |
| 18_G | 102_L | 1.366 | 0.99 |
| 20_K | 34_L | 1.340 | 0.99 |
| 22_G | 103_E | 1.337 | 0.99 |
| 77_Q | 94_E | 1.336 | 0.99 |
| 137_R | 140_Q | 1.319 | 0.99 |
| 27_N | 30_E | 1.317 | 0.99 |
| 14_L | 38_M | 1.308 | 0.99 |
| 2_N | 127_L | 1.294 | 0.99 |
| 107_D | 111_R | 1.288 | 0.99 |
| 132_D | 136_A | 1.277 | 0.99 |
| 144_S | 147_Y | 1.270 | 0.99 |
| 22_G | 96_N | 1.255 | 0.99 |
| 133_K | 136_A | 1.253 | 0.99 |
| 7_L | 134_M | 1.235 | 0.98 |
| 46_F | 74_V | 1.234 | 0.98 |
| 2_N | 5_D | 1.232 | 0.98 |
| 14_L | 106_A | 1.231 | 0.98 |
| 69_A | 73_Q | 1.204 | 0.98 |
| 64_I | 68_H | 1.203 | 0.98 |
| 71_H | 109_E | 1.194 | 0.98 |
| 53_Y | 118_T | 1.188 | 0.98 |
| 65_T | 69_A | 1.184 | 0.98 |
| 21_V | 95_W | 1.171 | 0.98 |
| 4_Y | 119_P | 1.169 | 0.97 |
| 33_V | 37_E | 1.169 | 0.97 |
| 102_L | 106_A | 1.153 | 0.97 |
| 8_K | 110_E | 1.153 | 0.97 |
| 128_E | 132_D | 1.148 | 0.97 |
| 74_V | 102_L | 1.144 | 0.97 |
| 3_A | 134_M | 1.143 | 0.97 |
| 39_L | 82_L | 1.142 | 0.97 |
| 8_K | 12_T | 1.136 | 0.97 |
| 30_E | 33_V | 1.127 | 0.97 |
| 8_K | 119_P | 1.124 | 0.97 |
| 54_Y | 108_V | 1.099 | 0.96 |
| 35_F | 81_L | 1.097 | 0.96 |
| 124_D | 128_E | 1.095 | 0.96 |
| 24_A | 31_R | 1.092 | 0.96 |
| 81_L | 95_W | 1.092 | 0.96 |
| 42_L | 98_F | 1.083 | 0.96 |
| 39_L | 78_L | 1.082 | 0.96 |
| 38_M | 95_W | 1.077 | 0.95 |
| 56_A | 130_L | 1.071 | 0.95 |
| 6_V | 135_A | 1.070 | 0.95 |
| 96_N | 100_T | 1.069 | 0.95 |
| 127_L | 131_G | 1.066 | 0.95 |
| 3_A | 48_I | 1.066 | 0.95 |
| 143_G | 147_Y | 1.056 | 0.95 |
| 46_F | 71_H | 1.052 | 0.95 |
| 142_R | 145_P | 1.041 | 0.94 |
| 36_D | 82_L | 1.040 | 0.94 |
| 136_A | 140_Q | 1.039 | 0.94 |
| 11_H | 45_H | 1.033 | 0.94 |
| 20_K | 23_E | 1.031 | 0.94 |
| 35_F | 82_L | 1.026 | 0.94 |
| 108_V | 112_D | 1.024 | 0.93 |
| 66_G | 108_V | 1.016 | 0.93 |
| 104_A | 107_D | 1.012 | 0.93 |
| 97_V | 100_T | 1.009 | 0.93 |
| 47_R | 51_D | 1.009 | 0.93 |
| 141_L | 145_P | 1.002 | 0.92 |
| 20_K | 30_E | 1.001 | 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 | |
| 2p0nA | 2 | 0.8571 | 99.7 | 0.424 | Contact Map |
| 3caxA | 1 | 0.9752 | 99.7 | 0.451 | Contact Map |
| 2hmqA | 4 | 0.5901 | 94 | 0.819 | Contact Map |
| 4xpxA | 1 | 0 | 93.4 | 0.823 | Contact Map |
| 3agtA | 2 | 0.7143 | 92.7 | 0.828 | Contact Map |
| 2mhrA | 1 | 0.6211 | 91.8 | 0.832 | Contact Map |
| 3u9jA | 2 | 0.8571 | 78 | 0.862 | Contact Map |
| 3d5aX | 1 | 0.6957 | 9.8 | 0.92 | Contact Map |
| 3zeyT | 1 | 0.2671 | 7.5 | 0.924 | Contact Map |
| 2b3tB | 1 | 0.4658 | 5.4 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)