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OPENSEQ.org
fliPflhB
Genes: A B A+B
Length: 215 211 420
Sequences: 1428 1992 1359
Seq/Len: 6.64 9.44 3.24
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.00 0.00
2 0.00 0.00 0.22
5 0.01 0.01 2.63
10 0.01 0.01 2.90
20 0.02 0.02 3.19
100 0.03 0.03 3.55
∞ 0.07 0.07 3.83
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
157_F 131_G 1.37 0.93 0.49
22_T 199_F 1.11 0.78 0.27
120_F 15_K 1.10 0.77 0.27
50_T 181_L 1.08 0.76 0.25
39_I 135_L 1.04 0.72 0.22
159_I 180_Q 1.03 0.70 0.21
51_P 16_K 1.03 0.70 0.21
64_L 125_K 1.01 0.68 0.20
75_I 170_P 1.01 0.68 0.20
146_T 109_Q 1.00 0.67 0.19
205_L 87_V 1.00 0.67 0.19
183_P 208_F 1.00 0.67 0.19
37_I 144_S 0.96 0.63 0.17
70_I 209_L 0.96 0.63 0.17
23_F 71_F 0.96 0.62 0.17
212_S 105_G 0.94 0.60 0.16
180_M 147_I 0.94 0.60 0.16
183_P 109_Q 0.92 0.57 0.14
168_L 207_V 0.91 0.57 0.14
175_M 16_K 0.91 0.56 0.14
38_I 91_L 0.90 0.55 0.14
100_G 28_K 0.89 0.53 0.13
87_S 88_L 0.89 0.53 0.13
187_I 93_P 0.89 0.53 0.13
26_A 8_K 0.89 0.53 0.13
58_V 100_I 0.88 0.53 0.13
193_L 120_M 0.88 0.53 0.13
187_I 9_T 0.88 0.52 0.12
31_M 203_A 0.87 0.51 0.12
111_Q 32_A 0.87 0.51 0.12
104_L 126_I 0.87 0.51 0.12
55_P 150_K 0.87 0.51 0.12
150_K 199_F 0.87 0.51 0.12
9_S 139_K 0.86 0.50 0.12
197_V 121_P 0.86 0.50 0.12
119_L 137_S 0.85 0.49 0.11
103_P 21_R 0.85 0.49 0.11
136_P 202_I 0.85 0.48 0.11
158_T 6_Q 0.85 0.48 0.11
117_L 204_V 0.85 0.48 0.11
198_L 150_K 0.84 0.48 0.11
74_V 93_P 0.84 0.48 0.11
187_I 147_I 0.84 0.47 0.11
123_L 192_A 0.84 0.47 0.11
168_L 184_L 0.83 0.47 0.10
146_T 131_G 0.83 0.47 0.10
157_F 15_K 0.83 0.47 0.10
62_L 31_D 0.83 0.47 0.10
198_L 28_K 0.83 0.46 0.10
35_T 131_G 0.83 0.46 0.10
108_M 97_S 0.83 0.46 0.10
168_L 169_L 0.82 0.45 0.10
12_V 191_L 0.82 0.45 0.10
53_A 17_I 0.82 0.45 0.10
182_V 112_F 0.82 0.45 0.10
77_K 16_K 0.82 0.45 0.10
125_N 55_R 0.82 0.44 0.10
137_M 16_K 0.82 0.44 0.10
199_V 203_A 0.82 0.44 0.10
52_S 195_V 0.82 0.44 0.10
64_L 108_M 0.81 0.43 0.09
106_A 155_F 0.81 0.43 0.09
205_L 14_S 0.81 0.43 0.09
97_L 18_E 0.80 0.42 0.09
175_M 110_F 0.79 0.41 0.09
27_I 115_T 0.79 0.41 0.09
92_S 116_T 0.79 0.41 0.09
115_A 127_N 0.79 0.41 0.09
100_G 25_N 0.79 0.41 0.09
88_E 107_I 0.79 0.41 0.09
143_A 10_E 0.79 0.41 0.09
10_L 40_I 0.78 0.40 0.08
43_L 194_I 0.78 0.40 0.08
53_A 135_L 0.78 0.40 0.08
113_R 31_D 0.78 0.40 0.08
135_V 153_I 0.78 0.39 0.08
127_G 149_L 0.78 0.39 0.08
212_S 172_V 0.77 0.39 0.08
204_L 135_L 0.77 0.39 0.08
159_I 54_E 0.77 0.39 0.08
176_A 95_V 0.77 0.39 0.08
84_Q 64_Q 0.77 0.38 0.08
80_V 12_P 0.77 0.38 0.08
168_L 137_S 0.76 0.38 0.08
33_S 204_V 0.76 0.38 0.08
125_N 81_I 0.76 0.38 0.08
61_G 200_L 0.76 0.38 0.08
110_R 138_L 0.76 0.38 0.08
45_R 95_V 0.76 0.38 0.08
55_P 21_R 0.76 0.37 0.08
161_I 116_T 0.76 0.37 0.08
17_F 17_I 0.76 0.37 0.07
173_V 73_L 0.76 0.37 0.07
47_A 33_A 0.76 0.37 0.07
105_R 173_E 0.76 0.37 0.07
123_L 73_L 0.76 0.37 0.07
58_V 140_K 0.76 0.37 0.07
158_T 149_L 0.75 0.37 0.07
55_P 151_V 0.75 0.37 0.07
88_E 186_D 0.75 0.36 0.07
159_I 80_M 0.75 0.36 0.07
170_I 204_V 0.75 0.36 0.07
52_S 11_E 0.75 0.36 0.07
210_A 109_Q 0.75 0.36 0.07
131_G 39_I 0.74 0.36 0.07
47_A 119_I 0.74 0.36 0.07
24_L 109_Q 0.74 0.35 0.07
152_A 146_K 0.74 0.35 0.07
177_L 41_G 0.74 0.35 0.07
14_T 189_I 0.74 0.35 0.07
197_V 170_P 0.74 0.35 0.07
99_K 8_K 0.74 0.35 0.07
187_I 149_L 0.74 0.35 0.07
42_G 102_G 0.74 0.35 0.07
112_T 14_S 0.74 0.35 0.07
104_L 103_V 0.74 0.35 0.07
186_T 153_I 0.74 0.35 0.07
58_V 191_L 0.73 0.34 0.07
12_V 18_E 0.73 0.34 0.07
136_P 210_V 0.73 0.34 0.07
20_S 191_L 0.73 0.34 0.07
138_R 36_V 0.73 0.34 0.07
200_D 125_K 0.72 0.33 0.07
26_A 143_E 0.72 0.33 0.07
164_L 119_I 0.72 0.33 0.06
160_F 122_N 0.72 0.33 0.06
68_F 170_P 0.72 0.33 0.06
102_Q 186_D 0.72 0.33 0.06
59_L 146_K 0.72 0.33 0.06
131_G 127_N 0.72 0.33 0.06
145_V 64_Q 0.72 0.33 0.06
171_A 51_F 0.72 0.32 0.06
191_F 131_G 0.71 0.32 0.06
194_M 194_I 0.71 0.32 0.06
22_T 109_Q 0.71 0.32 0.06
101_A 103_V 0.71 0.32 0.06
55_P 168_E 0.71 0.32 0.06
83_Y 17_I 0.71 0.32 0.06
146_T 106_N 0.71 0.32 0.06
11_S 180_Q 0.71 0.32 0.06
160_F 16_K 0.71 0.31 0.06
12_V 119_I 0.71 0.31 0.06
129_L 30_Q 0.71 0.31 0.06
147_S 31_D 0.70 0.31 0.06
74_V 160_I 0.70 0.31 0.06
30_M 162_L 0.70 0.31 0.06
20_S 166_M 0.70 0.31 0.06
108_M 31_D 0.70 0.31 0.06
169_V 32_A 0.70 0.31 0.06
16_V 88_L 0.70 0.31 0.06
74_V 68_G 0.70 0.31 0.06
186_T 140_K 0.70 0.31 0.06
70_I 89_I 0.70 0.31 0.06
120_F 117_K 0.70 0.30 0.06
175_M 146_K 0.70 0.30 0.06
33_S 136_F 0.70 0.30 0.06
141_L 118_P 0.70 0.30 0.06
70_I 11_E 0.70 0.30 0.06
55_P 113_I 0.70 0.30 0.06
131_G 45_T 0.70 0.30 0.06
183_P 15_K 0.69 0.30 0.06
121_A 100_I 0.69 0.30 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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