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OPENSEQ.org
cI_A_H_Ecoli
Genes: A B A+B
Length: 147 325 432
Sequences: 3884 4760 3227
Seq/Len: 26.42 14.65 7.47
MirrorTree (Pazo et al. 2001) 0.88
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 0.21
2 0.00 0.00 0.44
5 0.00 0.00 1.48
10 0.00 0.01 6.28
20 0.01 0.01 6.51
100 0.01 0.02 6.70
∞ 0.02 0.05 6.84
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
46_K 71_E 2.82 1.00 1.00
20_L 96_L 2.26 1.00 0.99
104_A 314_L 1.72 1.00 0.97
100_F 318_A 1.69 1.00 0.96
24_I 92_T 1.66 1.00 0.96
58_G 140_K 1.51 0.99 0.94
60_A 138_N 1.50 0.99 0.93
61_R 138_N 1.44 0.99 0.91
27_C 88_M 1.44 0.99 0.91
47_N 73_W 1.33 0.98 0.87
100_F 317_A 1.28 0.98 0.85
34_G 231_G 1.22 0.97 0.81
86_F 174_F 1.22 0.97 0.81
124_D 303_K 1.22 0.97 0.81
118_V 303_K 1.14 0.95 0.74
103_A 165_M 1.11 0.94 0.72
49_P 139_N 1.09 0.93 0.70
82_A 161_G 1.09 0.93 0.70
103_A 317_A 1.08 0.92 0.69
92_I 317_A 1.06 0.91 0.67
115_V 311_I 1.06 0.91 0.67
112_A 269_I 1.03 0.90 0.63
100_F 314_L 1.01 0.89 0.62
111_L 310_L 1.01 0.89 0.61
107_I 313_L 0.99 0.87 0.59
107_I 310_L 0.98 0.86 0.58
88_W 317_A 0.93 0.82 0.51
71_V 294_Y 0.92 0.81 0.50
100_F 321_L 0.92 0.81 0.50
82_A 120_L 0.91 0.80 0.48
74_F 64_M 0.90 0.80 0.48
60_A 140_K 0.90 0.79 0.48
89_S 168_V 0.90 0.79 0.47
48_V 207_C 0.89 0.78 0.47
26_L 19_V 0.89 0.78 0.46
33_G 27_T 0.87 0.76 0.44
76_V 236_L 0.87 0.76 0.44
107_I 316_T 0.87 0.76 0.44
19_F 99_A 0.87 0.76 0.44
103_A 313_L 0.86 0.75 0.43
16_F 112_L 0.86 0.75 0.43
31_L 88_M 0.86 0.75 0.43
92_I 118_F 0.86 0.75 0.42
80_V 72_D 0.86 0.74 0.42
61_R 79_D 0.86 0.74 0.42
111_L 311_I 0.85 0.74 0.42
124_D 164_L 0.85 0.74 0.41
68_F 256_F 0.85 0.73 0.41
97_W 321_L 0.84 0.72 0.40
37_L 69_F 0.83 0.72 0.40
77_I 202_A 0.83 0.72 0.39
92_I 321_L 0.83 0.71 0.39
54_I 226_H 0.83 0.71 0.39
24_I 88_M 0.83 0.71 0.39
28_C 88_M 0.81 0.69 0.36
123_L 248_I 0.81 0.68 0.36
35_W 72_D 0.81 0.68 0.36
18_I 97_A 0.80 0.68 0.35
93_R 320_I 0.80 0.68 0.35
23_A 18_A 0.80 0.67 0.35
50_F 215_P 0.80 0.67 0.35
121_G 260_W 0.80 0.67 0.35
69_Y 215_P 0.80 0.66 0.34
27_C 236_L 0.79 0.66 0.34
68_F 30_A 0.79 0.66 0.34
125_W 298_M 0.79 0.65 0.34
86_F 116_I 0.78 0.65 0.33
20_L 92_T 0.78 0.64 0.33
60_A 143_L 0.78 0.64 0.33
79_D 141_Y 0.77 0.63 0.32
33_G 68_F 0.77 0.63 0.32
30_M 64_M 0.77 0.62 0.31
91_S 201_I 0.76 0.61 0.30
120_I 246_V 0.76 0.61 0.30
83_L 161_G 0.76 0.61 0.30
69_Y 282_F 0.76 0.61 0.30
34_G 232_M 0.76 0.61 0.30
23_A 22_L 0.76 0.61 0.30
49_P 77_F 0.75 0.60 0.29
99_G 192_Q 0.73 0.57 0.27
80_V 301_G 0.73 0.57 0.27
73_M 24_V 0.72 0.55 0.26
29_L 13_L 0.72 0.55 0.25
49_P 132_F 0.72 0.55 0.25
84_Y 279_M 0.72 0.54 0.25
28_C 85_L 0.72 0.54 0.25
104_A 281_M 0.71 0.54 0.25
88_W 277_F 0.71 0.54 0.25
121_G 207_C 0.71 0.54 0.25
69_Y 235_G 0.71 0.54 0.25
68_F 221_L 0.71 0.53 0.24
61_R 30_A 0.71 0.53 0.24
68_F 47_Y 0.71 0.53 0.24
52_S 192_Q 0.71 0.53 0.24
28_C 178_D 0.70 0.52 0.24
106_F 212_F 0.70 0.52 0.24
34_G 246_V 0.70 0.52 0.24
38_G 233_K 0.70 0.52 0.23
74_F 283_I 0.70 0.52 0.23
56_S 162_L 0.70 0.52 0.23
80_V 296_Q 0.69 0.51 0.23
113_G 205_A 0.69 0.51 0.23
69_Y 217_A 0.69 0.50 0.22
23_A 92_T 0.69 0.50 0.22
14_W 115_G 0.69 0.50 0.22
65_S 131_L 0.68 0.49 0.22
82_A 210_H 0.68 0.49 0.22
16_F 96_L 0.68 0.49 0.22
116_Y 123_A 0.68 0.49 0.22
68_F 155_S 0.68 0.49 0.22
21_I 181_N 0.68 0.49 0.21
117_L 294_Y 0.68 0.48 0.21
82_A 67_M 0.68 0.48 0.21
67_K 298_M 0.67 0.47 0.21
94_E 314_L 0.67 0.47 0.21
52_S 209_R 0.67 0.47 0.21
47_N 76_K 0.67 0.47 0.21
49_P 243_I 0.67 0.47 0.20
22_V 22_L 0.67 0.46 0.20
57_V 116_I 0.66 0.46 0.20
56_S 145_G 0.66 0.46 0.20
54_I 98_F 0.66 0.45 0.20
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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