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OPENSEQ.org
1xr
Genes: A B A+B
Length: 135 308 440
Sequences: 2589 2588 1549
Seq/Len: 19.18 8.4 3.52
MirrorTree (Pazo et al. 2001) 0.73
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 0.08 3.15
2 0.09 0.08 3.32
5 0.09 0.08 3.43
10 0.09 0.08 3.47
20 0.09 0.08 3.50
100 0.09 0.08 3.61
∞ 0.09 0.09 4.21
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
17_F 168_E 1.02 0.72 0.02
41_G 58_L 0.94 0.62 0.01
3_R 163_Y 0.93 0.61 0.01
128_K 222_I 0.90 0.57 0.01
84_V 129_R 0.90 0.57 0.01
109_L 72_K 0.89 0.56 0.01
17_F 253_I 0.87 0.54 0.01
128_K 61_N 0.87 0.53 0.01
106_A 291_L 0.84 0.50 0.01
49_H 40_F 0.84 0.49 0.01
105_D 110_M 0.83 0.49 0.01
87_A 236_L 0.82 0.47 0.01
68_L 256_F 0.82 0.47 0.01
76_S 286_I 0.81 0.47 0.01
27_F 208_R 0.81 0.46 0.01
126_E 122_G 0.81 0.46 0.01
78_S 303_L 0.81 0.45 0.01
83_K 120_G 0.80 0.45 0.01
119_L 130_L 0.80 0.44 0.01
66_E 8_D 0.79 0.44 0.01
60_Y 54_I 0.78 0.42 0.01
41_G 291_L 0.78 0.42 0.01
51_L 19_K 0.78 0.42 0.01
106_A 158_V 0.78 0.42 0.01
47_H 56_H 0.77 0.41 0.01
20_L 51_A 0.77 0.40 0.01
67_N 163_Y 0.76 0.40 0.01
87_A 188_A 0.76 0.39 0.01
37_A 250_E 0.75 0.39 0.01
80_V 115_M 0.75 0.39 0.01
17_F 131_E 0.75 0.38 0.01
68_L 10_Y 0.75 0.38 0.01
124_A 23_Y 0.75 0.38 0.01
79_G 72_K 0.75 0.38 0.01
125_L 204_K 0.75 0.38 0.01
134_H 148_T 0.75 0.38 0.01
124_A 42_P 0.73 0.36 0.01
105_D 158_V 0.73 0.36 0.01
125_L 176_D 0.73 0.36 0.01
49_H 158_V 0.73 0.36 0.01
79_G 108_P 0.73 0.36 0.01
121_E 180_L 0.73 0.36 0.01
80_V 33_P 0.73 0.35 0.01
28_L 275_G 0.72 0.35 0.01
42_K 25_E 0.72 0.35 0.01
134_H 263_L 0.72 0.34 0.01
123_I 118_V 0.72 0.34 0.01
55_E 278_E 0.71 0.34 0.01
40_E 166_P 0.71 0.34 0.01
25_G 67_G 0.71 0.33 0.01
60_Y 79_I 0.71 0.33 0.01
82_P 139_G 0.70 0.33 0.01
80_V 54_I 0.70 0.33 0.01
45_G 186_E 0.70 0.33 0.01
95_R 196_S 0.70 0.32 0.01
108_L 138_I 0.70 0.32 0.01
133_P 15_R 0.70 0.32 0.01
119_L 117_I 0.70 0.32 0.01
92_L 179_L 0.69 0.32 0.01
122_R 30_R 0.69 0.32 0.01
73_L 20_L 0.69 0.32 0.01
105_D 115_M 0.69 0.31 0.01
121_E 121_Q 0.69 0.31 0.01
80_V 131_E 0.69 0.31 0.01
76_S 265_T 0.69 0.31 0.01
37_A 167_E 0.69 0.31 0.01
57_L 115_M 0.69 0.31 0.01
48_T 239_L 0.68 0.30 0.01
98_A 16_L 0.68 0.30 0.01
100_A 20_L 0.68 0.30 0.01
44_V 228_L 0.68 0.30 0.01
111_S 138_I 0.68 0.30 0.01
91_A 11_I 0.68 0.30 0.01
4_Y 40_F 0.67 0.29 0.01
115_V 56_H 0.67 0.29 0.01
69_A 187_E 0.67 0.29 0.01
92_L 279_E 0.67 0.29 0.01
97_L 121_Q 0.67 0.29 0.01
131_V 250_E 0.67 0.28 0.01
84_V 162_E 0.66 0.28 0.01
49_H 286_I 0.66 0.28 0.01
73_L 223_T 0.66 0.28 0.01
6_R 165_T 0.66 0.28 0.01
41_G 167_E 0.66 0.28 0.01
2_I 126_R 0.66 0.28 0.01
57_L 70_I 0.66 0.28 0.01
87_A 78_A 0.66 0.27 0.01
31_P 254_L 0.65 0.27 0.01
19_L 64_V 0.65 0.27 0.01
60_Y 192_I 0.65 0.27 0.01
42_K 171_Q 0.65 0.27 0.01
107_R 115_M 0.65 0.27 0.01
101_L 217_A 0.65 0.27 0.01
31_P 252_L 0.65 0.27 0.01
8_L 210_V 0.65 0.26 0.01
121_E 29_A 0.65 0.26 0.01
80_V 81_A 0.64 0.26 0.01
16_G 168_E 0.64 0.26 0.01
6_R 306_R 0.64 0.26 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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