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OPENSEQ.org
1IXR
Genes: A B A+B
Length: 135 308 440
Sequences: 2589 2596 1551
Seq/Len: 19.18 8.43 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 3.14
2 0.09 0.08 3.30
5 0.09 0.08 3.42
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 4.22
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
128_K 222_I 0.95 0.64 0.01
84_V 129_R 0.93 0.61 0.01
41_G 58_L 0.93 0.61 0.01
3_R 163_Y 0.92 0.60 0.01
17_F 168_E 0.90 0.57 0.01
128_K 61_N 0.86 0.53 0.01
109_L 72_K 0.86 0.52 0.01
66_E 8_D 0.85 0.52 0.01
126_E 122_G 0.85 0.51 0.01
49_H 40_F 0.84 0.50 0.01
41_G 291_L 0.83 0.49 0.01
78_S 303_L 0.83 0.49 0.01
106_A 291_L 0.83 0.49 0.01
83_K 120_G 0.83 0.48 0.00
87_A 236_L 0.82 0.47 0.00
51_L 19_K 0.81 0.47 0.00
68_L 256_F 0.81 0.46 0.00
119_L 130_L 0.81 0.46 0.00
105_D 115_M 0.80 0.44 0.00
76_S 286_I 0.78 0.41 0.00
105_D 110_M 0.77 0.41 0.00
67_N 163_Y 0.77 0.41 0.00
87_A 188_A 0.77 0.41 0.00
80_V 115_M 0.77 0.41 0.00
79_G 72_K 0.76 0.40 0.00
125_L 204_K 0.76 0.40 0.00
106_A 158_V 0.76 0.40 0.00
47_H 56_H 0.76 0.39 0.00
124_A 23_Y 0.76 0.39 0.00
20_L 51_A 0.75 0.38 0.00
27_F 208_R 0.75 0.38 0.00
79_G 108_P 0.75 0.38 0.00
80_V 33_P 0.75 0.38 0.00
60_Y 54_I 0.74 0.38 0.00
124_A 42_P 0.74 0.37 0.00
17_F 253_I 0.74 0.37 0.00
25_G 67_G 0.73 0.36 0.00
68_L 10_Y 0.73 0.36 0.00
57_L 115_M 0.73 0.36 0.00
121_E 180_L 0.73 0.36 0.00
49_H 158_V 0.73 0.35 0.00
133_P 15_R 0.73 0.35 0.00
95_R 196_S 0.73 0.35 0.00
63_P 79_I 0.72 0.35 0.00
98_A 16_L 0.72 0.35 0.00
92_L 179_L 0.72 0.34 0.00
125_L 176_D 0.72 0.34 0.00
87_A 78_A 0.72 0.34 0.00
55_E 278_E 0.71 0.34 0.00
31_P 254_L 0.71 0.34 0.00
134_H 263_L 0.71 0.34 0.00
40_E 166_P 0.71 0.34 0.00
76_S 265_T 0.71 0.34 0.00
134_H 148_T 0.70 0.33 0.00
105_D 158_V 0.70 0.33 0.00
122_R 30_R 0.70 0.32 0.00
82_P 139_G 0.70 0.32 0.00
73_L 20_L 0.70 0.32 0.00
37_A 250_E 0.70 0.32 0.00
4_Y 40_F 0.70 0.32 0.00
60_Y 79_I 0.70 0.32 0.00
8_L 210_V 0.69 0.31 0.00
108_L 138_I 0.69 0.31 0.00
101_L 217_A 0.69 0.31 0.00
92_L 279_E 0.69 0.31 0.00
91_A 11_I 0.69 0.31 0.00
100_A 20_L 0.69 0.31 0.00
37_A 167_E 0.68 0.30 0.00
42_K 25_E 0.68 0.30 0.00
97_L 121_Q 0.68 0.30 0.00
86_L 117_I 0.67 0.29 0.00
123_I 118_V 0.67 0.29 0.00
84_V 162_E 0.67 0.29 0.00
80_V 131_E 0.67 0.29 0.00
17_F 131_E 0.67 0.29 0.00
57_L 70_I 0.67 0.29 0.00
107_R 115_M 0.67 0.29 0.00
115_V 56_H 0.66 0.28 0.00
115_V 64_V 0.66 0.28 0.00
49_H 286_I 0.66 0.28 0.00
90_S 216_V 0.66 0.28 0.00
48_T 280_V 0.66 0.28 0.00
101_L 226_R 0.66 0.28 0.00
111_S 299_V 0.66 0.28 0.00
111_S 138_I 0.66 0.28 0.00
4_Y 121_Q 0.66 0.28 0.00
28_L 275_G 0.66 0.28 0.00
80_V 81_A 0.65 0.27 0.00
112_A 99_S 0.65 0.27 0.00
113_S 120_G 0.65 0.27 0.00
119_L 117_I 0.65 0.27 0.00
30_A 255_R 0.65 0.27 0.00
6_R 165_T 0.65 0.27 0.00
66_E 168_E 0.65 0.27 0.00
73_L 16_L 0.64 0.26 0.00
48_T 239_L 0.64 0.26 0.00
2_I 126_R 0.64 0.26 0.00
95_R 221_V 0.64 0.26 0.00
121_E 29_A 0.64 0.26 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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