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OPENSEQ.org
IscRHscB
Genes: A B A+B
Length: 162 171 326
Sequences: 5205 3234 333
Seq/Len: 32.13 18.91 1.02
MirrorTree (Pazo et al. 2001) 0.84
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.01 0.00
2 0.01 0.01 0.03
5 0.01 0.01 0.94
10 0.02 0.02 1.00
20 0.02 0.02 1.00
100 0.03 0.03 1.03
∞ 0.10 0.05 1.23
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
79_V 42_A 1.49 0.77 0.02
9_Y 88_D 1.45 0.74 0.02
36_G 44_Q 1.44 0.73 0.02
48_R 155_D 1.43 0.72 0.02
5_S 69_E 1.41 0.71 0.02
87_V 41_Q 1.38 0.69 0.01
68_G 162_E 1.28 0.60 0.01
5_S 56_Q 1.23 0.56 0.01
89_A 37_A 1.23 0.55 0.01
146_D 161_A 1.22 0.54 0.01
17_V 70_Y 1.19 0.52 0.01
143_H 167_K 1.15 0.48 0.01
2_R 42_A 1.15 0.48 0.01
73_S 135_Q 1.15 0.47 0.01
53_G 63_H 1.15 0.47 0.01
19_L 162_E 1.12 0.45 0.01
6_K 95_Q 1.11 0.45 0.01
117_L 152_R 1.11 0.44 0.01
131_N 134_E 1.11 0.44 0.01
2_R 70_Y 1.10 0.43 0.01
116_R 54_I 1.09 0.43 0.01
61_P 100_E 1.09 0.42 0.01
61_P 95_Q 1.09 0.42 0.01
116_R 83_Q 1.06 0.40 0.01
125_T 114_L 1.06 0.40 0.01
105_L 27_L 1.05 0.39 0.01
84_D 44_Q 1.04 0.38 0.01
2_R 3_Y 1.04 0.38 0.01
88_D 149_R 1.03 0.37 0.01
82_A 51_S 1.03 0.37 0.01
9_Y 165_E 1.02 0.36 0.01
5_S 71_L 1.02 0.36 0.01
114_S 88_D 1.02 0.36 0.01
128_E 83_Q 1.00 0.35 0.01
66_L 43_E 1.00 0.35 0.01
105_L 88_D 1.00 0.34 0.01
17_V 56_Q 0.99 0.33 0.01
84_D 165_E 0.98 0.33 0.01
27_P 45_L 0.98 0.33 0.01
27_P 48_V 0.98 0.33 0.01
17_V 3_Y 0.97 0.32 0.01
9_Y 50_Q 0.97 0.32 0.01
62_G 95_Q 0.97 0.32 0.01
2_R 148_V 0.96 0.32 0.01
114_S 42_A 0.96 0.31 0.01
118_T 152_R 0.96 0.31 0.01
90_T 37_A 0.96 0.31 0.01
23_A 146_D 0.95 0.31 0.01
78_E 35_K 0.95 0.31 0.00
75_A 152_R 0.95 0.31 0.00
101_G 166_E 0.95 0.30 0.00
54_L 109_K 0.95 0.30 0.00
15_L 152_R 0.94 0.30 0.00
2_R 65_L 0.93 0.29 0.00
15_L 72_L 0.93 0.29 0.00
14_M 58_W 0.93 0.29 0.00
114_S 165_E 0.93 0.29 0.00
99_Q 170_D 0.92 0.28 0.00
76_V 111_E 0.92 0.28 0.00
51_K 98_L 0.92 0.28 0.00
22_E 167_K 0.92 0.28 0.00
25_P 82_E 0.92 0.28 0.00
84_D 76_G 0.92 0.28 0.00
12_T 91_F 0.91 0.28 0.00
51_K 45_L 0.91 0.27 0.00
117_L 150_K 0.91 0.27 0.00
79_V 18_Q 0.91 0.27 0.00
46_F 91_F 0.91 0.27 0.00
17_V 69_E 0.91 0.27 0.00
73_S 162_E 0.90 0.27 0.00
122_N 23_R 0.90 0.26 0.00
132_N 160_S 0.90 0.26 0.00
56_S 161_A 0.90 0.26 0.00
73_S 118_I 0.90 0.26 0.00
51_K 124_M 0.90 0.26 0.00
105_L 152_R 0.89 0.26 0.00
26_V 98_L 0.89 0.26 0.00
2_R 121_V 0.89 0.26 0.00
99_Q 121_V 0.88 0.25 0.00
75_A 164_L 0.88 0.25 0.00
48_R 45_L 0.88 0.25 0.00
61_P 93_M 0.88 0.25 0.00
97_G 117_F 0.87 0.25 0.00
71_A 159_S 0.87 0.24 0.00
108_A 56_Q 0.87 0.24 0.00
132_N 24_F 0.86 0.24 0.00
128_E 136_L 0.86 0.24 0.00
124_I 8_G 0.86 0.24 0.00
33_E 40_S 0.86 0.24 0.00
76_V 120_R 0.86 0.24 0.00
144_T 167_K 0.86 0.24 0.00
23_A 131_L 0.86 0.24 0.00
29_A 82_E 0.86 0.23 0.00
137_D 156_K 0.85 0.23 0.00
76_V 161_A 0.85 0.23 0.00
30_D 29_R 0.85 0.23 0.00
116_R 49_Q 0.85 0.23 0.00
17_V 1_M 0.85 0.23 0.00
32_S 95_Q 0.85 0.23 0.00
89_A 84_H 0.85 0.23 0.00
33_E 156_K 0.84 0.23 0.00
108_A 69_E 0.84 0.23 0.00
125_T 18_Q 0.84 0.23 0.00
47_S 21_S 0.84 0.22 0.00
119_G 164_L 0.84 0.22 0.00
50_R 95_Q 0.83 0.22 0.00
2_R 149_R 0.83 0.22 0.00
21_S 15_L 0.83 0.22 0.00
27_P 85_T 0.83 0.22 0.00
136_L 146_D 0.83 0.22 0.00
78_E 31_Y 0.83 0.22 0.00
33_E 150_K 0.83 0.22 0.00
94_G 7_F 0.83 0.22 0.00
54_L 99_R 0.83 0.22 0.00
126_L 110_D 0.82 0.21 0.00
58_V 156_K 0.82 0.21 0.00
22_E 79_L 0.82 0.21 0.00
149_R 44_Q 0.81 0.21 0.00
125_T 53_T 0.81 0.21 0.00
62_G 93_M 0.81 0.21 0.00
4_T 47_A 0.81 0.21 0.00
128_E 132_M 0.81 0.21 0.00
28_L 91_F 0.81 0.20 0.00
137_D 15_L 0.80 0.20 0.00
93_Q 35_K 0.80 0.20 0.00
120_F 105_I 0.80 0.20 0.00
122_N 115_E 0.80 0.20 0.00
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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