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OPENSEQ.org
fdxHscB
Genes: A B A+B
Length: 111 171 279
Sequences: 5163 2875 386
Seq/Len: 46.51 16.81 1.38
MirrorTree (Pazo et al. 2001) 0.73
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 0.02 0.01 0.06
2 0.04 0.01 1.26
5 0.05 0.01 1.37
10 0.05 0.01 1.44
20 0.06 0.02 1.46
100 0.08 0.02 1.67
∞ 0.13 0.05 2.28
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
95_D 102_L 1.39 0.78 0.03
28_L 69_E 1.35 0.74 0.03
31_A 88_D 1.27 0.68 0.02
102_R 40_S 1.26 0.67 0.02
4_I 104_E 1.25 0.67 0.02
19_L 135_Q 1.24 0.66 0.02
3_K 17_T 1.24 0.65 0.02
19_L 66_M 1.22 0.64 0.02
109_R 58_W 1.22 0.63 0.02
107_H 47_A 1.19 0.61 0.02
109_R 2_D 1.18 0.59 0.02
28_L 50_Q 1.17 0.59 0.02
100_I 161_A 1.17 0.58 0.02
3_K 133_V 1.16 0.58 0.02
31_A 50_Q 1.13 0.55 0.01
91_V 18_Q 1.12 0.54 0.01
28_L 56_Q 1.11 0.53 0.01
53_C 57_A 1.11 0.53 0.01
107_H 103_D 1.11 0.53 0.01
53_C 96_L 1.11 0.53 0.01
12_L 145_A 1.10 0.52 0.01
104_T 58_W 1.08 0.50 0.01
108_A 30_Q 1.08 0.49 0.01
55_V 12_R 1.06 0.48 0.01
44_K 24_F 1.06 0.48 0.01
17_A 3_Y 1.05 0.47 0.01
97_V 113_R 1.04 0.46 0.01
31_A 87_R 1.01 0.42 0.01
26_T 48_V 1.00 0.42 0.01
102_R 97_E 1.00 0.42 0.01
81_P 160_S 1.00 0.42 0.01
31_A 21_S 0.99 0.41 0.01
66_S 152_R 0.98 0.40 0.01
2_P 47_A 0.98 0.40 0.01
31_A 27_L 0.98 0.40 0.01
92_T 103_D 0.98 0.40 0.01
60_D 5_T 0.97 0.39 0.01
86_S 152_R 0.97 0.39 0.01
107_H 167_K 0.97 0.39 0.01
19_L 129_H 0.97 0.39 0.01
54_I 138_N 0.96 0.38 0.01
36_I 58_W 0.96 0.38 0.01
75_K 121_V 0.95 0.38 0.01
18_V 78_D 0.95 0.37 0.01
53_C 15_L 0.94 0.36 0.01
19_L 60_T 0.93 0.35 0.01
102_R 48_V 0.93 0.35 0.01
91_V 60_T 0.93 0.35 0.01
65_S 120_R 0.92 0.34 0.01
17_A 150_K 0.92 0.34 0.01
31_A 42_A 0.91 0.34 0.01
10_Q 148_V 0.91 0.33 0.01
96_L 97_E 0.90 0.33 0.01
38_I 49_Q 0.90 0.32 0.01
66_S 122_K 0.89 0.32 0.01
2_P 120_R 0.89 0.32 0.01
67_E 142_D 0.88 0.31 0.01
68_Q 161_A 0.88 0.30 0.01
91_V 166_E 0.88 0.30 0.01
91_V 103_D 0.87 0.30 0.01
98_V 106_E 0.87 0.30 0.01
5_V 166_E 0.87 0.30 0.01
4_I 44_Q 0.87 0.30 0.01
31_A 54_I 0.86 0.29 0.01
66_S 63_H 0.86 0.29 0.01
75_K 69_E 0.85 0.28 0.01
20_E 112_A 0.85 0.28 0.01
110_E 47_A 0.85 0.28 0.01
5_V 79_L 0.85 0.28 0.01
13_C 57_A 0.84 0.28 0.01
93_D 158_R 0.84 0.28 0.01
55_V 40_S 0.84 0.27 0.01
43_E 65_L 0.83 0.27 0.01
10_Q 57_A 0.83 0.27 0.01
6_I 62_R 0.83 0.26 0.01
20_E 143_A 0.83 0.26 0.01
94_E 39_G 0.82 0.26 0.01
105_I 45_L 0.82 0.26 0.01
65_S 18_Q 0.82 0.26 0.01
26_T 131_L 0.81 0.25 0.01
6_I 23_R 0.81 0.25 0.01
15_D 52_A 0.81 0.25 0.01
6_I 38_S 0.81 0.25 0.01
60_D 58_W 0.81 0.25 0.01
39_E 58_W 0.81 0.25 0.01
86_S 56_Q 0.80 0.25 0.01
22_N 46_A 0.80 0.24 0.01
9_H 126_D 0.80 0.24 0.01
22_N 72_L 0.80 0.24 0.01
25_E 86_V 0.80 0.24 0.01
55_V 38_S 0.80 0.24 0.01
37_E 51_S 0.80 0.24 0.01
21_A 62_R 0.80 0.24 0.01
89_A 8_G 0.80 0.24 0.01
31_A 69_E 0.79 0.24 0.01
109_R 132_M 0.79 0.24 0.01
66_S 50_Q 0.79 0.24 0.01
6_I 154_L 0.79 0.24 0.01
66_S 44_Q 0.79 0.23 0.01
10_Q 8_G 0.78 0.23 0.01
108_A 161_A 0.78 0.23 0.01
28_L 86_V 0.78 0.23 0.01
71_D 55_N 0.78 0.23 0.01
108_A 38_S 0.78 0.23 0.01
52_H 55_N 0.77 0.22 0.01
55_V 105_I 0.77 0.22 0.01
82_E 51_S 0.77 0.22 0.01
33_R 154_L 0.77 0.22 0.01
103_Y 91_F 0.77 0.22 0.01
70_D 80_A 0.77 0.22 0.01
5_V 8_G 0.77 0.22 0.01
4_I 161_A 0.77 0.22 0.01
90_R 5_T 0.77 0.22 0.01
54_I 101_E 0.76 0.22 0.01
97_V 140_T 0.76 0.22 0.01
25_E 41_Q 0.76 0.21 0.01
90_R 21_S 0.76 0.21 0.01
102_R 5_T 0.76 0.21 0.01
98_V 93_M 0.76 0.21 0.01
81_P 134_E 0.76 0.21 0.01
64_E 80_A 0.76 0.21 0.01
37_E 79_L 0.76 0.21 0.01
10_Q 2_D 0.75 0.21 0.00
37_E 152_R 0.75 0.21 0.00
21_A 23_R 0.74 0.20 0.00
94_E 97_E 0.74 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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