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OPENSEQ.org
MFD_BACSU_495-625_RPOB_BACSU_21-131
Genes: A B A+B
Length: 131 111 240
Sequences: 4682 3147 1356
Seq/Len: 35.74 28.35 5.65
MirrorTree (Pazo et al. 2001) 0.65
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.03
10 0.00 0.00 0.06
20 0.00 0.00 0.15
100 0.00 0.00 1.03
∞ 0.00 0.00 5.60
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
28_L 77_R 1.83 1.00 0.97
46_D 89_Q 1.77 1.00 0.96
28_L 86_V 1.56 0.99 0.93
122_F 17_Y 1.46 0.98 0.90
22_Y 18_Q 1.45 0.98 0.89
59_Q 17_Y 1.38 0.98 0.86
28_L 47_I 1.24 0.95 0.78
49_Y 88_D 1.19 0.94 0.74
119_Q 110_A 1.15 0.92 0.70
37_Y 86_V 1.08 0.88 0.63
47_K 88_D 1.06 0.87 0.61
36_D 29_F 1.04 0.86 0.59
96_D 93_M 1.03 0.85 0.58
62_V 96_F 1.02 0.84 0.57
55_I 10_I 1.01 0.83 0.56
22_Y 110_A 1.00 0.82 0.54
113_S 107_I 0.99 0.81 0.53
13_V 104_T 0.98 0.81 0.52
49_Y 61_S 0.97 0.80 0.51
30_I 79_I 0.97 0.80 0.51
92_D 8_N 0.96 0.79 0.50
3_Y 29_F 0.96 0.78 0.49
47_K 51_L 0.95 0.77 0.48
71_L 12_I 0.94 0.76 0.47
97_L 103_G 0.91 0.73 0.43
5_E 23_E 0.88 0.70 0.40
94_A 49_Y 0.88 0.69 0.40
27_T 53_E 0.88 0.69 0.40
74_L 87_K 0.88 0.69 0.39
55_I 65_D 0.88 0.69 0.39
99_K 107_I 0.86 0.66 0.37
66_G 89_Q 0.85 0.66 0.36
36_D 17_Y 0.85 0.66 0.36
127_P 74_V 0.85 0.66 0.36
124_S 61_S 0.84 0.65 0.35
67_K 102_T 0.84 0.64 0.35
22_Y 67_T 0.82 0.61 0.32
52_V 33_S 0.81 0.60 0.32
71_L 9_L 0.81 0.60 0.32
86_V 11_E 0.81 0.60 0.32
102_A 93_M 0.81 0.60 0.32
98_I 69_S 0.81 0.60 0.32
50_V 75_K 0.81 0.60 0.32
93_I 28_M 0.81 0.59 0.31
60_K 56_Y 0.81 0.59 0.31
113_S 101_D 0.80 0.59 0.30
24_G 75_K 0.80 0.58 0.30
60_K 28_M 0.80 0.58 0.30
72_Y 110_A 0.79 0.58 0.29
12_V 69_S 0.79 0.57 0.29
32_G 5_E 0.79 0.57 0.29
19_I 29_F 0.79 0.57 0.29
119_Q 42_L 0.79 0.57 0.29
48_L 64_R 0.79 0.56 0.28
122_F 31_D 0.78 0.56 0.28
27_T 91_V 0.78 0.56 0.28
72_Y 75_K 0.78 0.56 0.28
81_R 36_E 0.78 0.56 0.28
13_V 9_L 0.78 0.56 0.28
93_I 91_V 0.78 0.55 0.28
122_F 46_F 0.77 0.55 0.27
43_Q 92_F 0.77 0.54 0.27
38_L 84_G 0.77 0.54 0.27
59_Q 76_V 0.77 0.54 0.27
71_L 61_S 0.77 0.54 0.27
22_Y 102_T 0.77 0.54 0.27
89_S 76_V 0.77 0.54 0.27
31_N 43_S 0.77 0.54 0.26
81_R 48_D 0.77 0.53 0.26
76_G 4_L 0.76 0.53 0.26
37_Y 84_G 0.76 0.53 0.26
58_V 47_I 0.76 0.52 0.26
127_P 86_V 0.76 0.52 0.25
119_Q 83_T 0.75 0.52 0.25
17_H 37_D 0.75 0.51 0.25
4_S 61_S 0.75 0.51 0.25
103_E 36_E 0.75 0.51 0.25
19_I 45_E 0.74 0.50 0.24
112_F 96_F 0.74 0.50 0.24
107_S 67_T 0.74 0.50 0.24
46_D 41_N 0.73 0.49 0.23
30_I 86_V 0.73 0.49 0.23
54_Q 85_E 0.73 0.49 0.23
31_N 30_Q 0.73 0.49 0.23
21_K 10_I 0.73 0.49 0.23
36_D 8_N 0.73 0.48 0.23
24_G 78_L 0.73 0.48 0.23
50_V 96_F 0.73 0.48 0.23
37_Y 76_V 0.73 0.48 0.23
57_Q 93_M 0.73 0.48 0.22
19_I 46_F 0.73 0.48 0.22
30_I 5_E 0.72 0.47 0.22
116_H 15_S 0.72 0.47 0.22
21_K 67_T 0.72 0.47 0.22
5_E 77_R 0.72 0.47 0.22
107_S 21_L 0.71 0.46 0.21
103_E 71_P 0.71 0.46 0.21
91_Q 58_V 0.71 0.45 0.21
122_F 28_M 0.71 0.45 0.21
101_Y 76_V 0.71 0.45 0.21
78_E 48_D 0.71 0.45 0.21
99_K 28_M 0.71 0.45 0.21
39_N 52_G 0.71 0.45 0.20
74_L 72_L 0.70 0.45 0.20
63_G 76_V 0.70 0.44 0.20
36_D 31_D 0.70 0.44 0.20
42_Y 14_T 0.70 0.44 0.20
89_S 46_F 0.70 0.44 0.20
27_T 64_R 0.70 0.43 0.20
48_L 87_K 0.70 0.43 0.20
54_Q 84_G 0.70 0.43 0.20
33_I 32_I 0.70 0.43 0.20
91_Q 93_M 0.69 0.43 0.19
76_G 75_K 0.69 0.43 0.19
51_P 87_K 0.69 0.43 0.19
105_E 12_I 0.69 0.43 0.19
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)
ID Seq/Len Name Options I_Prob Status
8457 0.15 MFD_BACSU_495-625_RPOB_BACSU_21-131 Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
7314 5.65 MFD_BACSU_495-625_RPOB_BACSU_21-131 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.97 Done - Shared
7306 0.15 MFD_BACSU_495-625_RPOB_BACSU_21-131 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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