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OPENSEQ.org
S7-vs-RsfS
Genes: A B A+B
Length: 179 105 260
Sequences: 1685 2682 987
Seq/Len: 9.41 25.54 3.8
MirrorTree (Pazo et al. 2001) 0.58
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 0.11 0.01 0.00
2 0.11 0.01 0.00
5 0.11 0.01 0.01
10 0.11 0.01 0.02
20 0.11 0.01 0.04
100 0.11 0.01 0.31
∞ 0.11 0.01 3.48
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
101_M 90_M 1.09 0.81 0.05
138_R 15_D 1.06 0.78 0.05
84_T 97_L 1.06 0.78 0.05
129_E 90_M 1.04 0.76 0.04
131_K 37_M 0.94 0.65 0.03
149_K 11_I 0.93 0.64 0.03
143_R 85_V 0.93 0.64 0.03
98_A 25_L 0.91 0.61 0.03
124_L 29_G 0.89 0.59 0.03
110_K 22_I 0.89 0.58 0.03
58_E 100_L 0.89 0.58 0.03
143_R 51_I 0.86 0.55 0.03
4_R 42_G 0.86 0.54 0.03
12_I 12_D 0.85 0.53 0.02
70_R 42_G 0.84 0.52 0.02
49_T 24_A 0.84 0.52 0.02
66_L 40_C 0.82 0.49 0.02
118_L 89_V 0.80 0.47 0.02
69_V 47_H 0.80 0.47 0.02
107_A 74_S 0.80 0.46 0.02
96_R 103_L 0.79 0.46 0.02
138_R 33_I 0.79 0.45 0.02
96_R 18_K 0.79 0.45 0.02
100_A 42_G 0.78 0.44 0.02
101_M 43_T 0.77 0.43 0.02
142_H 35_D 0.77 0.43 0.02
83_S 92_E 0.77 0.43 0.02
63_E 48_V 0.76 0.42 0.02
61_A 24_A 0.75 0.41 0.02
38_T 14_I 0.75 0.40 0.02
119_R 16_D 0.75 0.40 0.02
134_A 6_L 0.74 0.40 0.02
152_A 94_S 0.74 0.39 0.02
156_W 13_K 0.74 0.39 0.02
121_A 93_E 0.73 0.38 0.02
38_T 51_I 0.73 0.38 0.02
113_D 89_V 0.73 0.38 0.02
49_T 30_K 0.73 0.38 0.02
53_R 40_C 0.73 0.38 0.02
135_V 59_S 0.73 0.38 0.02
76_K 43_T 0.71 0.35 0.01
80_V 7_Q 0.71 0.35 0.01
154_Y 83_G 0.70 0.34 0.01
124_L 72_E 0.70 0.34 0.01
108_A 16_D 0.69 0.33 0.01
121_A 24_A 0.69 0.33 0.01
100_A 69_V 0.69 0.33 0.01
131_K 94_S 0.69 0.33 0.01
83_S 103_L 0.69 0.32 0.01
111_R 84_D 0.68 0.32 0.01
104_I 12_D 0.68 0.31 0.01
93_P 87_V 0.68 0.31 0.01
58_E 97_L 0.67 0.31 0.01
37_S 55_V 0.67 0.31 0.01
61_A 57_Q 0.67 0.30 0.01
45_S 87_V 0.67 0.30 0.01
119_R 29_G 0.67 0.30 0.01
84_T 47_H 0.66 0.30 0.01
66_L 80_V 0.66 0.29 0.01
12_I 21_D 0.66 0.29 0.01
21_E 6_L 0.66 0.29 0.01
96_R 31_S 0.65 0.29 0.01
40_E 41_T 0.65 0.29 0.01
152_A 103_L 0.65 0.29 0.01
19_G 78_I 0.65 0.28 0.01
76_K 90_M 0.65 0.28 0.01
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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