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OPENSEQ.org
AtpF_AtpX
Genes: A B A+B
Length: 171 144 294
Sequences: 2855 2881 79
Seq/Len: 16.7 20.01 0.27
MirrorTree (Pazo et al. 2001) 0.90
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 0.09 0.11 0.25
2 0.09 0.11 0.25
5 0.09 0.11 0.25
10 0.09 0.11 0.25
20 0.09 0.11 0.25
100 0.09 0.11 0.25
∞ 0.09 0.11 0.25
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
66_L 43_I 2.30 0.84 0.42
37_L 63_Q 1.71 0.52 0.11
112_Y 83_I 1.70 0.52 0.11
76_S 53_D 1.68 0.50 0.10
152_E 45_D 1.62 0.47 0.09
33_S 53_D 1.60 0.45 0.08
108_I 139_A 1.58 0.44 0.07
138_I 65_D 1.41 0.33 0.04
137_K 123_L 1.39 0.32 0.04
137_K 23_A 1.38 0.32 0.04
29_I 53_D 1.37 0.31 0.04
80_K 116_K 1.35 0.30 0.04
37_L 104_E 1.34 0.29 0.03
54_F 51_K 1.30 0.28 0.03
112_Y 90_Y 1.30 0.28 0.03
106_Y 89_S 1.28 0.27 0.03
53_S 72_A 1.27 0.26 0.03
27_T 47_L 1.27 0.26 0.03
41_G 20_L 1.26 0.25 0.03
76_S 33_L 1.26 0.25 0.03
133_L 93_V 1.25 0.25 0.03
38_L 29_Y 1.25 0.25 0.02
33_S 44_K 1.24 0.25 0.02
44_W 27_W 1.24 0.24 0.02
69_I 35_F 1.23 0.24 0.02
170_R 24_M 1.22 0.23 0.02
40_A 9_L 1.22 0.23 0.02
88_E 116_K 1.21 0.23 0.02
91_K 63_Q 1.21 0.23 0.02
83_L 137_R 1.20 0.23 0.02
61_E 72_A 1.20 0.22 0.02
83_L 75_R 1.19 0.22 0.02
72_Q 48_A 1.18 0.22 0.02
170_R 25_N 1.18 0.22 0.02
97_I 71_A 1.18 0.22 0.02
167_L 92_A 1.18 0.22 0.02
38_L 93_V 1.18 0.22 0.02
68_E 60_I 1.18 0.21 0.02
140_R 47_L 1.18 0.21 0.02
117_K 114_N 1.17 0.21 0.02
119_D 131_E 1.17 0.21 0.02
13_L 9_L 1.16 0.21 0.02
40_A 138_V 1.16 0.21 0.02
163_C 71_A 1.15 0.20 0.02
132_D 114_N 1.14 0.20 0.02
39_F 112_L 1.14 0.20 0.02
70_Q 14_F 1.14 0.20 0.02
79_N 141_G 1.13 0.20 0.02
58_K 24_M 1.12 0.19 0.01
101_A 78_I 1.12 0.19 0.01
152_E 100_E 1.11 0.19 0.01
131_M 108_F 1.10 0.18 0.01
77_K 72_A 1.09 0.18 0.01
91_K 82_A 1.08 0.17 0.01
38_L 104_E 1.08 0.17 0.01
76_S 138_V 1.06 0.17 0.01
97_I 23_A 1.05 0.17 0.01
143_V 133_E 1.05 0.16 0.01
65_R 64_I 1.05 0.16 0.01
27_T 140_M 1.04 0.16 0.01
89_Q 137_R 1.04 0.16 0.01
141_E 36_M 1.04 0.16 0.01
74_K 72_A 1.04 0.16 0.01
84_L 29_Y 1.04 0.16 0.01
168_K 75_R 1.03 0.16 0.01
98_I 91_D 1.03 0.16 0.01
143_V 10_M 1.03 0.16 0.01
59_S 47_L 1.02 0.15 0.01
83_L 64_I 1.02 0.15 0.01
41_G 104_E 1.01 0.15 0.01
81_K 49_K 1.01 0.15 0.01
55_L 21_L 1.01 0.15 0.01
134_E 130_F 1.00 0.15 0.01
109_T 87_T 1.00 0.15 0.01
76_S 44_K 1.00 0.15 0.01
66_L 20_L 0.99 0.14 0.01
56_R 16_V 0.99 0.14 0.01
59_S 89_S 0.99 0.14 0.01
144_E 64_I 0.99 0.14 0.01
133_L 15_I 0.98 0.14 0.01
170_R 46_S 0.98 0.14 0.01
111_K 30_R 0.98 0.14 0.01
28_D 112_L 0.98 0.14 0.01
136_K 55_A 0.98 0.14 0.01
115_Q 27_W 0.97 0.14 0.01
41_G 114_N 0.97 0.14 0.01
46_F 75_R 0.97 0.14 0.01
16_P 67_L 0.97 0.14 0.01
61_E 69_K 0.97 0.14 0.01
40_A 139_A 0.96 0.14 0.01
92_E 66_A 0.96 0.14 0.01
82_K 81_E 0.96 0.14 0.01
136_K 30_R 0.96 0.14 0.01
154_K 100_E 0.96 0.14 0.01
156_V 58_V 0.96 0.14 0.01
52_R 63_Q 0.96 0.14 0.01
38_L 22_W 0.96 0.13 0.01
130_L 115_E 0.96 0.13 0.01
93_K 40_Q 0.95 0.13 0.01
149_D 79_I 0.95 0.13 0.01
111_K 94_I 0.95 0.13 0.01
168_K 44_K 0.95 0.13 0.01
161_Q 57_S 0.95 0.13 0.01
169_Q 74_K 0.94 0.13 0.01
41_G 29_Y 0.94 0.13 0.01
41_G 12_V 0.93 0.13 0.01
117_K 68_L 0.93 0.13 0.01
126_N 81_E 0.93 0.12 0.01
146_V 121_E 0.93 0.12 0.01
87_L 10_M 0.92 0.12 0.01
108_I 35_F 0.92 0.12 0.01
34_L 91_D 0.92 0.12 0.01
31_E 106_E 0.92 0.12 0.01
83_L 46_S 0.92 0.12 0.01
140_R 79_I 0.92 0.12 0.01
171_L 24_M 0.92 0.12 0.01
123_L 15_I 0.92 0.12 0.01
97_I 20_L 0.91 0.12 0.01
128_K 29_Y 0.91 0.12 0.01
112_Y 79_I 0.91 0.12 0.01
157_S 66_A 0.91 0.12 0.01
81_K 59_E 0.91 0.12 0.01
30_I 94_I 0.90 0.12 0.01
40_A 62_H 0.90 0.12 0.01
62_I 24_M 0.90 0.12 0.01
165_N 23_A 0.90 0.12 0.01
162_D 53_D 0.90 0.12 0.01
140_R 21_L 0.90 0.12 0.01
171_L 46_S 0.90 0.12 0.01
13_L 23_A 0.90 0.12 0.01
145_S 42_E 0.90 0.12 0.01
98_I 110_K 0.89 0.12 0.01
92_E 64_I 0.89 0.12 0.01
106_Y 12_V 0.89 0.12 0.01
35_N 31_P 0.89 0.11 0.01
35_N 39_R 0.89 0.11 0.01
102_N 24_M 0.89 0.11 0.01
29_I 13_V 0.89 0.11 0.01
144_E 94_I 0.89 0.11 0.01
123_L 114_N 0.89 0.11 0.01
92_E 94_I 0.88 0.11 0.01
124_I 85_K 0.88 0.11 0.01
132_D 110_K 0.88 0.11 0.01
101_A 67_L 0.88 0.11 0.01
171_L 57_S 0.88 0.11 0.01
56_R 74_K 0.88 0.11 0.01
167_L 110_K 0.88 0.11 0.01
96_L 107_A 0.88 0.11 0.01
98_I 78_I 0.87 0.11 0.01
125_K 16_V 0.87 0.11 0.01
27_T 32_L 0.87 0.11 0.01
69_I 47_L 0.87 0.11 0.01
45_Y 86_A 0.87 0.11 0.01
88_E 106_E 0.87 0.11 0.01
37_L 70_E 0.87 0.11 0.01
168_K 16_V 0.87 0.11 0.01
70_Q 18_V 0.87 0.11 0.01
141_E 116_K 0.87 0.11 0.01
148_K 94_I 0.87 0.11 0.01
105_A 78_I 0.87 0.11 0.01
143_V 13_V 0.87 0.11 0.01
75_V 125_V 0.86 0.11 0.01
50_K 50_I 0.86 0.11 0.01
52_R 24_M 0.86 0.11 0.01
143_V 112_L 0.86 0.11 0.01
73_L 112_L 0.86 0.11 0.01
84_L 40_Q 0.86 0.11 0.01
57_S 73_E 0.86 0.11 0.01
68_E 125_V 0.86 0.11 0.01
52_R 48_A 0.86 0.11 0.01
78_E 21_L 0.86 0.11 0.01
50_K 87_T 0.85 0.10 0.01
64_K 126_Q 0.85 0.10 0.01
70_Q 6_N 0.85 0.10 0.01
84_L 68_L 0.85 0.10 0.01
42_I 30_R 0.85 0.10 0.01
24_I 79_I 0.85 0.10 0.01
135_V 80_A 0.85 0.10 0.01
108_I 49_K 0.85 0.10 0.01
44_W 14_F 0.84 0.10 0.01
73_L 43_I 0.84 0.10 0.01
30_I 140_M 0.84 0.10 0.01
63_S 91_D 0.84 0.10 0.01
98_I 128_P 0.84 0.10 0.01
136_K 114_N 0.84 0.10 0.01
131_M 92_A 0.84 0.10 0.01
89_Q 22_W 0.84 0.10 0.01
87_L 40_Q 0.84 0.10 0.01
151_R 109_A 0.84 0.10 0.01
119_D 52_T 0.84 0.10 0.01
62_I 56_Q 0.84 0.10 0.01
97_I 13_V 0.84 0.10 0.01
77_K 35_F 0.83 0.10 0.01
153_S 120_K 0.83 0.10 0.01
134_E 82_A 0.83 0.10 0.01
123_L 37_D 0.83 0.10 0.01
74_K 47_L 0.83 0.10 0.00
132_D 141_G 0.83 0.10 0.00
25_S 41_A 0.83 0.10 0.00
73_L 128_P 0.83 0.10 0.00
140_R 57_S 0.83 0.10 0.00
30_I 107_A 0.83 0.10 0.00
159_N 125_V 0.82 0.10 0.00
164_V 132_D 0.82 0.10 0.00
75_V 121_E 0.82 0.10 0.00
124_I 50_I 0.82 0.10 0.00
81_K 68_L 0.82 0.10 0.00
89_Q 103_Q 0.82 0.10 0.00
117_K 14_F 0.82 0.10 0.00
165_N 88_E 0.82 0.10 0.00
40_A 32_L 0.82 0.10 0.00
90_A 55_A 0.82 0.10 0.00
91_K 78_I 0.82 0.10 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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