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OPENSEQ.org
ecoli_chpb_seed_coevolution
Genes: A B A+B
Length: 116 85 198
Sequences: 2069 685 509
Seq/Len: 17.84 8.06 2.57
MirrorTree (Pazo et al. 2001) 0.70
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 0.01 0.00 2.50
2 0.01 0.00 2.52
5 0.01 0.00 2.53
10 0.01 0.01 2.52
20 0.02 0.02 2.53
100 0.04 0.02 2.54
∞ 0.10 0.05 2.64
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
39_A 55_D 1.81 0.99 0.93
84_R 74_W 1.69 0.98 0.90
109_L 52_Y 1.51 0.94 0.83
48_V 74_W 1.42 0.92 0.77
10_G 57_L 1.24 0.82 0.62
40_F 24_K 1.19 0.79 0.56
49_A 3_M 1.12 0.72 0.48
113_A 53_S 1.08 0.68 0.44
110_R 57_L 1.07 0.68 0.43
78_V 39_S 1.06 0.67 0.43
63_F 61_C 0.99 0.59 0.35
16_G 6_T 0.98 0.58 0.34
87_D 81_G 0.95 0.54 0.31
4_K 26_L 0.95 0.54 0.30
106_E 52_Y 0.94 0.53 0.29
111_L 32_Q 0.94 0.53 0.29
65_V 57_L 0.93 0.52 0.29
45_M 33_S 0.93 0.52 0.29
110_R 52_Y 0.92 0.51 0.28
69_C 15_G 0.92 0.50 0.27
45_M 53_S 0.91 0.49 0.26
6_E 44_I 0.88 0.46 0.23
98_L 46_T 0.87 0.45 0.23
62_G 61_C 0.86 0.44 0.22
42_Q 39_S 0.86 0.44 0.22
38_Q 54_L 0.85 0.42 0.21
16_G 18_I 0.84 0.41 0.20
39_A 58_L 0.84 0.41 0.20
112_Q 51_R 0.84 0.41 0.20
6_E 21_I 0.84 0.41 0.20
113_A 52_Y 0.82 0.38 0.18
10_G 81_G 0.81 0.38 0.18
43_L 61_C 0.81 0.38 0.18
51_I 26_L 0.81 0.37 0.17
41_N 58_L 0.80 0.37 0.17
95_R 56_E 0.80 0.37 0.17
54_G 15_G 0.80 0.36 0.17
60_Y 7_I 0.79 0.35 0.16
27_G 13_S 0.78 0.35 0.16
25_Q 10_W 0.78 0.34 0.16
22_G 83_E 0.78 0.34 0.16
46_T 15_G 0.78 0.34 0.15
85_M 16_M 0.77 0.34 0.15
24_E 83_E 0.77 0.33 0.15
33_L 34_V 0.77 0.33 0.15
81_N 67_E 0.77 0.33 0.15
78_V 33_S 0.77 0.33 0.15
60_Y 43_L 0.76 0.32 0.14
35_L 59_A 0.75 0.32 0.14
18_D 42_Q 0.75 0.32 0.14
61_A 61_C 0.75 0.31 0.14
12_I 27_N 0.75 0.31 0.14
25_Q 13_S 0.74 0.31 0.13
71_E 24_K 0.74 0.30 0.13
26_Q 57_L 0.74 0.30 0.13
36_S 22_V 0.74 0.30 0.13
98_L 25_E 0.73 0.30 0.13
86_M 6_T 0.73 0.29 0.13
97_G 74_W 0.73 0.29 0.12
96_I 28_L 0.73 0.29 0.12
74_V 23_M 0.73 0.29 0.12
9_R 82_D 0.73 0.29 0.12
46_T 4_R 0.72 0.29 0.12
81_N 17_V 0.72 0.28 0.12
63_F 54_L 0.72 0.28 0.12
12_I 21_I 0.71 0.28 0.12
66_P 49_S 0.71 0.28 0.12
70_E 27_N 0.71 0.28 0.11
13_V 12_N 0.71 0.27 0.11
53_Q 50_R 0.71 0.27 0.11
107_A 60_Q 0.71 0.27 0.11
35_L 8_K 0.70 0.27 0.11
41_N 57_L 0.70 0.27 0.11
69_C 23_M 0.70 0.26 0.11
5_S 28_L 0.69 0.26 0.10
99_A 21_I 0.69 0.26 0.10
73_D 56_E 0.69 0.26 0.10
89_R 82_D 0.69 0.25 0.10
95_R 38_V 0.69 0.25 0.10
113_A 57_L 0.69 0.25 0.10
76_G 32_Q 0.68 0.25 0.10
15_V 25_E 0.68 0.25 0.10
16_G 22_V 0.68 0.24 0.10
80_V 67_E 0.68 0.24 0.10
81_N 10_W 0.68 0.24 0.10
105_E 4_R 0.67 0.24 0.09
62_G 58_L 0.67 0.24 0.09
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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