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OPENSEQ.org
1RM6_A_C
Genes: A B A+B
Length: 769 161 902
Sequences: 4230 4844 2714
Seq/Len: 5.5 30.09 3.01
MirrorTree (Pazo et al. 2001) 0.74
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 1.71
2 0.03 0.02 2.83
5 0.04 0.03 2.88
10 0.05 0.04 2.90
20 0.11 0.06 2.92
100 0.14 0.10 2.95
∞ 0.22 0.19 3.02
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
696_V 134_L 2.83 1.00 1.00
699_I 130_L 1.52 0.96 0.90
24_V 108_I 1.46 0.95 0.88
20_G 93_H 1.42 0.94 0.86
24_V 93_H 1.40 0.93 0.85
24_V 85_L 1.35 0.92 0.83
664_Q 142_K 1.25 0.87 0.76
33_D 102_F 1.21 0.84 0.72
660_E 142_K 1.16 0.81 0.68
704_D 123_R 1.15 0.80 0.66
699_I 144_I 1.13 0.78 0.65
16_P 94_E 1.06 0.71 0.56
270_R 30_E 1.00 0.65 0.49
21_V 85_L 0.94 0.57 0.42
25_T 89_Q 0.90 0.53 0.37
16_P 93_H 0.90 0.52 0.36
24_V 98_T 0.88 0.50 0.34
661_G 138_T 0.88 0.50 0.34
24_V 89_Q 0.86 0.48 0.32
661_G 139_G 0.84 0.46 0.30
118_K 21_N 0.84 0.45 0.30
25_T 80_A 0.83 0.44 0.29
664_Q 141_V 0.81 0.41 0.27
657_L 96_L 0.80 0.40 0.26
29_K 35_T 0.79 0.39 0.25
21_V 93_H 0.77 0.37 0.23
27_K 80_A 0.77 0.37 0.23
275_R 40_G 0.74 0.33 0.20
692_L 43_G 0.73 0.33 0.19
28_A 38_K 0.70 0.30 0.17
25_T 85_L 0.70 0.29 0.16
690_N 97_G 0.66 0.26 0.14
632_V 105_P 0.66 0.25 0.14
25_T 93_H 0.66 0.25 0.13
144_A 5_L 0.64 0.24 0.12
699_I 147_V 0.64 0.23 0.12
21_V 90_A 0.63 0.23 0.12
698_T 134_L 0.63 0.22 0.11
699_I 107_M 0.63 0.22 0.11
56_A 15_E 0.62 0.22 0.11
580_E 54_D 0.62 0.22 0.11
702_S 144_I 0.62 0.22 0.11
16_P 90_A 0.61 0.21 0.10
598_Y 138_T 0.58 0.18 0.09
669_M 138_T 0.58 0.18 0.09
164_G 44_G 0.58 0.18 0.09
111_I 12_R 0.57 0.18 0.08
661_G 96_L 0.57 0.18 0.08
63_E 147_V 0.57 0.18 0.08
240_F 38_K 0.57 0.18 0.08
26_G 36_G 0.57 0.18 0.08
542_G 152_A 0.56 0.17 0.08
493_A 109_M 0.56 0.17 0.08
276_E 43_G 0.56 0.17 0.08
25_T 86_S 0.55 0.17 0.07
699_I 127_K 0.55 0.16 0.07
668_W 138_T 0.55 0.16 0.07
25_T 87_K 0.55 0.16 0.07
223_V 87_K 0.54 0.16 0.07
253_H 145_K 0.54 0.15 0.07
121_A 60_A 0.54 0.15 0.07
536_A 145_K 0.54 0.15 0.07
168_A 124_D 0.53 0.15 0.07
56_A 144_I 0.53 0.15 0.07
169_A 27_Y 0.53 0.15 0.06
19_D 96_L 0.53 0.15 0.06
53_R 13_A 0.53 0.15 0.06
246_G 99_Q 0.52 0.15 0.06
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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