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OPENSEQ.org
1rm6
Genes: A B A+B
Length: 761 323 1020
Sequences: 4233 3395 2533
Seq/Len: 5.56 10.51 2.48
MirrorTree (Pazo et al. 2001) 0.79
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.01 1.67
2 0.03 0.01 2.27
5 0.04 0.02 2.32
10 0.05 0.03 2.33
20 0.11 0.04 2.34
100 0.14 0.07 2.34
∞ 0.22 0.17 2.37
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
625_D 315_K 2.09 1.00 0.98
627_I 311_A 1.57 0.96 0.89
627_I 314_R 1.52 0.94 0.86
755_D 307_R 1.51 0.94 0.86
627_I 315_K 1.38 0.90 0.78
687_R 232_D 1.35 0.88 0.76
748_D 301_G 1.30 0.85 0.72
751_T 307_R 1.27 0.84 0.69
751_T 308_V 0.91 0.48 0.30
752_E 303_K 0.90 0.48 0.29
690_T 228_R 0.85 0.42 0.25
283_K 14_T 0.83 0.39 0.22
456_L 171_D 0.81 0.37 0.20
747_P 227_I 0.75 0.30 0.15
496_I 287_L 0.74 0.30 0.15
747_P 304_Y 0.73 0.28 0.14
42_A 282_E 0.72 0.28 0.14
201_L 321_W 0.72 0.28 0.14
630_K 223_S 0.72 0.27 0.14
58_E 240_A 0.71 0.27 0.13
630_K 225_V 0.71 0.27 0.13
732_V 186_P 0.71 0.27 0.13
116_K 180_A 0.70 0.26 0.12
63_V 320_L 0.69 0.25 0.12
92_Y 313_S 0.69 0.25 0.12
682_N 42_R 0.67 0.23 0.10
747_P 308_V 0.67 0.23 0.10
496_I 8_R 0.66 0.22 0.10
120_E 190_L 0.65 0.21 0.10
359_A 112_L 0.65 0.21 0.09
183_M 112_L 0.65 0.21 0.09
147_I 252_L 0.64 0.21 0.09
304_A 12_P 0.63 0.20 0.09
514_S 316_V 0.63 0.20 0.09
293_K 186_P 0.63 0.20 0.08
424_P 315_K 0.62 0.20 0.08
22_Y 54_T 0.62 0.19 0.08
216_A 74_A 0.62 0.19 0.08
205_T 308_V 0.62 0.19 0.08
732_V 93_A 0.62 0.19 0.08
286_I 116_L 0.61 0.18 0.07
51_T 292_S 0.60 0.18 0.07
3_V 12_P 0.60 0.18 0.07
229_I 51_V 0.60 0.18 0.07
498_V 212_V 0.60 0.18 0.07
693_E 228_R 0.60 0.17 0.07
34_G 31_G 0.59 0.17 0.07
13_V 50_L 0.59 0.17 0.07
202_N 55_G 0.59 0.17 0.07
116_K 243_Q 0.59 0.17 0.07
504_A 72_I 0.59 0.17 0.07
659_V 98_A 0.58 0.17 0.07
454_V 20_N 0.58 0.17 0.06
56_A 275_N 0.58 0.16 0.06
115_I 62_I 0.58 0.16 0.06
512_S 234_P 0.58 0.16 0.06
111_A 16_A 0.57 0.16 0.06
383_N 30_L 0.57 0.16 0.06
687_R 228_R 0.57 0.16 0.06
549_E 80_A 0.57 0.16 0.06
11_D 259_S 0.57 0.15 0.06
351_G 191_F 0.56 0.15 0.06
502_D 97_A 0.56 0.15 0.06
751_T 311_A 0.56 0.15 0.06
112_L 74_A 0.56 0.15 0.06
371_E 116_L 0.56 0.15 0.06
229_I 254_V 0.56 0.15 0.06
62_A 212_V 0.56 0.15 0.06
131_A 111_T 0.55 0.15 0.05
158_V 29_P 0.55 0.15 0.05
123_P 320_L 0.55 0.15 0.05
687_R 227_I 0.55 0.15 0.05
212_H 189_Q 0.55 0.15 0.05
172_T 184_T 0.55 0.15 0.05
648_P 30_L 0.55 0.15 0.05
382_I 280_A 0.55 0.14 0.05
296_A 219_S 0.55 0.14 0.05
632_T 229_D 0.55 0.14 0.05
38_R 79_E 0.55 0.14 0.05
728_I 239_A 0.55 0.14 0.05
565_D 210_I 0.55 0.14 0.05
5_V 171_D 0.55 0.14 0.05
524_A 12_P 0.55 0.14 0.05
426_G 181_G 0.55 0.14 0.05
728_I 269_D 0.54 0.14 0.05
644_K 31_G 0.54 0.14 0.05
33_V 113_G 0.54 0.14 0.05
193_D 173_R 0.54 0.14 0.05
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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