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OPENSEQ.org
cI_K_H_Ecoli
Genes: A B A+B
Length: 100 325 417
Sequences: 1292 4760 1394
Seq/Len: 12.92 14.65 3.34
MirrorTree (Pazo et al. 2001) 0.63
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 0.10
2 0.00 0.00 0.36
5 0.00 0.00 2.99
10 0.01 0.01 3.04
20 0.01 0.01 3.16
100 0.02 0.02 3.21
∞ 0.03 0.05 3.28
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
2_I 34_F 1.07 0.75 0.03
79_L 240_G 1.02 0.70 0.02
10_L 196_F 0.99 0.67 0.02
60_V 174_F 0.98 0.66 0.02
11_A 41_G 0.98 0.65 0.02
34_G 93_S 0.97 0.65 0.02
65_A 124_G 0.96 0.64 0.02
32_L 239_V 0.96 0.63 0.02
44_L 254_T 0.93 0.59 0.02
32_L 247_T 0.92 0.59 0.02
40_N 233_K 0.91 0.56 0.02
26_R 62_A 0.90 0.56 0.02
45_A 128_Y 0.90 0.56 0.02
26_R 215_P 0.90 0.56 0.02
27_N 62_A 0.88 0.54 0.02
79_L 239_V 0.88 0.54 0.02
8_L 103_V 0.88 0.53 0.01
79_L 65_I 0.87 0.52 0.01
76_G 54_W 0.87 0.52 0.01
43_A 301_G 0.86 0.51 0.01
29_L 132_F 0.86 0.51 0.01
66_I 260_W 0.84 0.48 0.01
66_I 161_G 0.84 0.48 0.01
8_L 115_G 0.83 0.47 0.01
49_A 280_M 0.82 0.46 0.01
68_L 283_I 0.82 0.46 0.01
16_V 83_F 0.82 0.46 0.01
37_I 43_F 0.81 0.45 0.01
38_M 145_G 0.81 0.44 0.01
11_A 203_G 0.80 0.43 0.01
83_L 285_I 0.80 0.43 0.01
80_L 251_L 0.80 0.43 0.01
31_M 217_A 0.79 0.42 0.01
7_G 317_A 0.79 0.42 0.01
1_M 297_V 0.79 0.42 0.01
89_N 173_S 0.79 0.41 0.01
25_R 128_Y 0.78 0.41 0.01
37_I 180_V 0.78 0.41 0.01
40_N 194_F 0.78 0.41 0.01
30_F 294_Y 0.78 0.41 0.01
62_Y 164_L 0.78 0.40 0.01
95_V 122_M 0.78 0.40 0.01
32_L 234_F 0.77 0.40 0.01
79_L 238_F 0.77 0.40 0.01
34_G 240_G 0.77 0.40 0.01
99_R 230_S 0.77 0.39 0.01
97_E 136_S 0.76 0.38 0.01
58_G 256_F 0.75 0.37 0.01
44_L 197_I 0.75 0.37 0.01
46_F 208_H 0.75 0.37 0.01
20_T 131_L 0.75 0.37 0.01
32_L 106_G 0.75 0.37 0.01
62_Y 60_L 0.75 0.36 0.01
79_L 150_S 0.74 0.36 0.01
99_R 80_R 0.74 0.36 0.01
44_L 308_L 0.74 0.36 0.01
33_I 52_V 0.74 0.35 0.01
67_S 306_L 0.73 0.35 0.01
89_N 113_N 0.73 0.35 0.01
74_S 33_S 0.73 0.34 0.01
45_A 159_F 0.73 0.34 0.01
40_N 195_G 0.73 0.34 0.01
31_M 60_L 0.72 0.34 0.01
66_I 131_L 0.72 0.33 0.01
29_L 314_L 0.72 0.33 0.01
48_V 221_L 0.72 0.33 0.01
65_A 23_L 0.71 0.33 0.01
84_H 22_L 0.71 0.33 0.01
52_Y 265_L 0.71 0.33 0.01
46_F 238_F 0.71 0.32 0.01
82_Q 83_F 0.71 0.32 0.01
16_V 313_L 0.71 0.32 0.01
46_F 97_A 0.71 0.32 0.01
60_V 141_Y 0.71 0.32 0.01
98_M 248_I 0.70 0.32 0.01
62_Y 31_F 0.70 0.32 0.01
34_G 319_V 0.70 0.32 0.01
45_A 132_F 0.70 0.32 0.01
63_I 79_D 0.70 0.31 0.01
66_I 72_D 0.70 0.31 0.01
66_I 139_N 0.70 0.31 0.01
40_N 192_Q 0.70 0.31 0.01
25_R 313_L 0.69 0.31 0.01
29_L 23_L 0.69 0.31 0.01
89_N 252_M 0.69 0.31 0.01
38_M 262_G 0.69 0.30 0.01
81_L 207_C 0.69 0.30 0.01
79_L 159_F 0.69 0.30 0.01
65_A 253_V 0.69 0.30 0.01
4_L 182_S 0.68 0.29 0.01
67_S 298_M 0.68 0.29 0.01
98_M 271_F 0.68 0.29 0.01
54_G 23_L 0.68 0.29 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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