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OPENSEQ.org
I_sub_last128_L_sub80
Genes: A B A+B
Length: 128 80 191
Sequences: 471 1710 276
Seq/Len: 3.68 21.38 1.45
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.01 1.29
2 0.00 0.01 1.29
5 0.00 0.01 1.29
10 0.00 0.01 1.32
20 0.00 0.01 1.33
100 0.01 0.02 1.38
∞ 0.02 0.06 1.51
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
57_V 74_F 1.46 0.83 0.09
26_E 63_E 1.43 0.82 0.09
25_P 63_E 1.37 0.78 0.07
100_I 73_A 1.34 0.76 0.07
95_Q 30_T 1.31 0.73 0.06
83_L 72_I 1.23 0.66 0.05
62_A 21_L 1.19 0.63 0.04
71_L 24_G 1.19 0.62 0.04
102_V 62_P 1.17 0.60 0.04
90_L 27_A 1.16 0.59 0.04
82_L 24_G 1.14 0.58 0.04
102_V 67_I 1.13 0.57 0.04
80_L 43_G 1.13 0.57 0.04
67_L 72_I 1.13 0.56 0.04
31_A 23_V 1.12 0.55 0.03
86_L 67_I 1.12 0.55 0.03
101_W 46_A 1.10 0.54 0.03
33_H 65_L 1.10 0.54 0.03
49_I 70_L 1.10 0.53 0.03
46_A 16_A 1.08 0.51 0.03
49_I 48_D 1.07 0.50 0.03
101_W 19_M 1.06 0.50 0.03
23_M 33_A 1.06 0.50 0.03
93_M 60_L 1.06 0.49 0.03
106_T 34_Q 1.05 0.48 0.03
22_L 60_L 1.05 0.48 0.03
105_F 56_L 1.04 0.47 0.03
92_H 61_L 1.04 0.47 0.03
37_H 62_P 1.02 0.45 0.02
18_S 58_F 1.01 0.44 0.02
66_G 65_L 1.00 0.43 0.02
100_I 46_A 1.00 0.43 0.02
121_F 43_G 0.99 0.43 0.02
55_T 62_P 0.99 0.42 0.02
124_V 21_L 0.99 0.42 0.02
81_H 62_P 0.98 0.41 0.02
110_F 47_E 0.97 0.41 0.02
33_H 33_A 0.97 0.40 0.02
21_W 24_G 0.96 0.40 0.02
72_L 74_F 0.96 0.40 0.02
90_L 29_G 0.96 0.40 0.02
61_M 73_A 0.96 0.39 0.02
51_A 62_P 0.96 0.39 0.02
47_G 64_T 0.95 0.38 0.02
28_F 63_E 0.95 0.38 0.02
75_V 14_L 0.95 0.38 0.02
96_P 43_G 0.94 0.37 0.02
33_H 63_E 0.93 0.36 0.02
102_V 46_A 0.92 0.35 0.02
83_L 24_G 0.92 0.35 0.02
74_I 76_L 0.92 0.35 0.02
101_W 73_A 0.91 0.34 0.02
95_Q 33_A 0.91 0.34 0.02
60_A 25_L 0.91 0.34 0.02
25_P 33_A 0.90 0.34 0.02
72_L 57_I 0.90 0.34 0.02
121_F 28_L 0.90 0.33 0.02
93_M 41_G 0.90 0.33 0.02
61_M 76_L 0.90 0.33 0.02
32_G 56_L 0.89 0.33 0.01
119_R 46_A 0.89 0.32 0.01
76_V 79_R 0.89 0.32 0.01
94_L 59_L 0.88 0.32 0.01
53_L 40_A 0.88 0.32 0.01
61_M 43_G 0.88 0.32 0.01
33_H 68_F 0.88 0.32 0.01
80_L 48_D 0.88 0.32 0.01
7_G 49_R 0.88 0.31 0.01
49_I 71_L 0.87 0.31 0.01
55_T 64_T 0.87 0.31 0.01
45_A 19_M 0.87 0.31 0.01
46_A 38_G 0.87 0.31 0.01
34_I 24_G 0.87 0.30 0.01
73_G 45_I 0.86 0.30 0.01
95_Q 31_G 0.86 0.30 0.01
119_R 50_S 0.86 0.30 0.01
119_R 26_A 0.86 0.30 0.01
91_G 65_L 0.86 0.30 0.01
75_V 17_V 0.85 0.29 0.01
48_G 21_L 0.85 0.29 0.01
124_V 43_G 0.85 0.29 0.01
32_G 74_F 0.85 0.29 0.01
74_I 32_V 0.84 0.28 0.01
120_P 24_G 0.83 0.28 0.01
75_V 28_L 0.83 0.28 0.01
43_V 52_F 0.83 0.28 0.01
45_A 25_L 0.83 0.27 0.01
47_G 71_L 0.83 0.27 0.01
11_F 56_L 0.82 0.27 0.01
95_Q 65_L 0.82 0.27 0.01
34_I 35_A 0.82 0.27 0.01
105_F 52_F 0.82 0.27 0.01
24_I 21_L 0.82 0.27 0.01
84_I 69_G 0.82 0.27 0.01
107_K 56_L 0.82 0.26 0.01
96_P 37_I 0.81 0.26 0.01
91_G 30_T 0.81 0.26 0.01
101_W 53_G 0.81 0.26 0.01
32_G 67_I 0.81 0.26 0.01
61_M 69_G 0.81 0.25 0.01
107_K 22_A 0.81 0.25 0.01
91_G 62_P 0.80 0.25 0.01
45_A 37_I 0.80 0.25 0.01
78_G 19_M 0.80 0.25 0.01
32_G 27_A 0.79 0.24 0.01
85_L 25_L 0.79 0.24 0.01
42_A 23_V 0.79 0.24 0.01
97_I 24_G 0.79 0.24 0.01
82_L 75_I 0.78 0.24 0.01
71_L 43_G 0.78 0.24 0.01
112_E 13_G 0.78 0.24 0.01
45_A 74_F 0.78 0.23 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)
ID Seq/Len Name Options I_Prob Status
1389 1.45 I_sub_last128_L_sub80 Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.09 Done - Shared
1388 0.35 I_sub_last128_L_sub80 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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