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OPENSEQ.org
TA_eleven
Genes: A B A+B
Length: 131 98 229
Sequences: 748 153 123
Seq/Len: 5.71 1.56 0.54
MirrorTree (Pazo et al. 2001) 0.84
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 0.54
2 0.00 0.00 0.54
5 0.01 0.00 0.54
10 0.01 0.00 0.54
20 0.01 0.00 0.54
100 0.01 0.00 0.54
∞ 0.04 0.01 0.54
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
58_K 33_D 1.74 0.75 0.01
84_T 52_S 1.64 0.69 0.01
81_L 57_S 1.36 0.48 0.01
119_V 77_T 1.35 0.47 0.01
4_P 54_F 1.34 0.46 0.01
126_L 5_T 1.34 0.46 0.01
122_K 13_V 1.31 0.44 0.01
112_S 75_L 1.23 0.38 0.00
130_I 75_L 1.21 0.36 0.00
53_F 17_V 1.21 0.36 0.00
122_K 32_A 1.20 0.35 0.00
21_T 89_D 1.17 0.34 0.00
73_F 6_P 1.17 0.34 0.00
48_E 50_S 1.17 0.33 0.00
47_K 32_A 1.16 0.33 0.00
43_S 72_R 1.16 0.32 0.00
68_T 37_L 1.15 0.32 0.00
52_A 85_T 1.15 0.32 0.00
24_G 35_L 1.14 0.32 0.00
118_R 87_I 1.14 0.31 0.00
74_I 54_F 1.14 0.31 0.00
95_G 67_W 1.12 0.30 0.00
126_L 64_H 1.12 0.30 0.00
92_F 80_V 1.12 0.30 0.00
115_K 82_L 1.10 0.29 0.00
71_P 86_V 1.10 0.28 0.00
31_G 85_T 1.08 0.27 0.00
127_L 98_K 1.07 0.27 0.00
80_K 68_Q 1.07 0.27 0.00
25_R 54_F 1.06 0.27 0.00
119_V 39_F 1.06 0.26 0.00
23_R 6_P 1.06 0.26 0.00
18_I 26_R 1.06 0.26 0.00
16_K 94_S 1.04 0.25 0.00
29_L 72_R 1.04 0.25 0.00
119_V 72_R 1.03 0.24 0.00
99_F 95_F 1.02 0.24 0.00
57_V 29_L 1.01 0.23 0.00
5_V 65_T 1.01 0.23 0.00
39_H 82_L 1.00 0.23 0.00
64_V 54_F 0.99 0.22 0.00
54_M 26_R 0.99 0.22 0.00
54_M 65_T 0.99 0.22 0.00
119_V 44_N 0.98 0.22 0.00
51_D 43_C 0.98 0.22 0.00
81_L 60_T 0.98 0.21 0.00
15_I 80_V 0.98 0.21 0.00
123_H 31_N 0.97 0.21 0.00
89_S 51_E 0.97 0.21 0.00
5_V 73_P 0.97 0.21 0.00
15_I 50_S 0.97 0.21 0.00
32_I 14_K 0.97 0.21 0.00
29_L 40_D 0.96 0.21 0.00
56_Q 29_L 0.96 0.21 0.00
118_R 47_I 0.96 0.21 0.00
75_V 18_N 0.96 0.21 0.00
114_I 31_N 0.96 0.20 0.00
40_C 49_L 0.96 0.20 0.00
12_V 40_D 0.95 0.20 0.00
95_G 58_M 0.94 0.20 0.00
20_Y 90_V 0.94 0.20 0.00
63_S 15_K 0.94 0.19 0.00
88_A 94_S 0.93 0.19 0.00
81_L 67_W 0.93 0.19 0.00
34_G 27_S 0.93 0.19 0.00
79_K 65_T 0.93 0.19 0.00
18_I 29_L 0.93 0.19 0.00
76_K 72_R 0.92 0.19 0.00
95_G 70_V 0.92 0.19 0.00
95_G 95_F 0.92 0.19 0.00
95_G 68_Q 0.92 0.18 0.00
117_L 39_F 0.92 0.18 0.00
36_Y 22_V 0.91 0.18 0.00
97_N 35_L 0.91 0.18 0.00
92_F 86_V 0.91 0.18 0.00
26_K 45_V 0.90 0.18 0.00
54_M 29_L 0.90 0.18 0.00
100_S 49_L 0.90 0.18 0.00
106_N 61_Y 0.90 0.18 0.00
81_L 59_T 0.90 0.17 0.00
21_T 11_S 0.90 0.17 0.00
58_K 5_T 0.89 0.17 0.00
60_F 63_D 0.89 0.17 0.00
73_F 8_T 0.89 0.17 0.00
13_S 62_S 0.89 0.17 0.00
104_K 65_T 0.89 0.17 0.00
109_P 3_K 0.88 0.17 0.00
62_A 46_I 0.88 0.17 0.00
59_A 66_I 0.88 0.17 0.00
108_Q 44_N 0.87 0.16 0.00
31_G 46_I 0.87 0.16 0.00
53_F 37_L 0.87 0.16 0.00
122_K 15_K 0.87 0.16 0.00
42_E 56_K 0.87 0.16 0.00
52_A 60_T 0.87 0.16 0.00
75_V 8_T 0.87 0.16 0.00
27_T 14_K 0.87 0.16 0.00
94_G 70_V 0.86 0.16 0.00
25_R 19_A 0.86 0.16 0.00
42_E 80_V 0.86 0.16 0.00
57_V 33_D 0.85 0.16 0.00
7_H 94_S 0.85 0.16 0.00
57_V 30_L 0.85 0.15 0.00
49_E 92_I 0.85 0.15 0.00
52_A 7_H 0.85 0.15 0.00
53_F 42_M 0.85 0.15 0.00
6_C 49_L 0.85 0.15 0.00
83_L 64_H 0.84 0.15 0.00
7_H 15_K 0.84 0.15 0.00
37_C 49_L 0.84 0.15 0.00
97_N 94_S 0.84 0.15 0.00
127_L 60_T 0.83 0.15 0.00
43_S 26_R 0.83 0.15 0.00
30_K 77_T 0.83 0.15 0.00
80_K 7_H 0.83 0.15 0.00
106_N 80_V 0.83 0.15 0.00
47_K 66_I 0.83 0.15 0.00
43_S 55_Y 0.82 0.14 0.00
130_I 82_L 0.82 0.14 0.00
100_S 93_V 0.82 0.14 0.00
30_K 32_A 0.82 0.14 0.00
1_M 53_D 0.82 0.14 0.00
58_K 24_T 0.82 0.14 0.00
128_N 79_Q 0.82 0.14 0.00
114_I 78_G 0.82 0.14 0.00
11_M 41_G 0.81 0.14 0.00
80_K 67_W 0.81 0.14 0.00
106_N 88_H 0.81 0.14 0.00
28_V 4_R 0.81 0.14 0.00
83_L 59_T 0.81 0.14 0.00
95_G 57_S 0.81 0.14 0.00
101_R 74_R 0.81 0.14 0.00
118_R 55_Y 0.81 0.14 0.00
17_D 46_I 0.80 0.14 0.00
95_G 56_K 0.80 0.14 0.00
86_K 94_S 0.80 0.13 0.00
127_L 59_T 0.80 0.13 0.00
75_V 11_S 0.79 0.13 0.00
23_R 8_T 0.79 0.13 0.00
110_H 73_P 0.79 0.13 0.00
115_K 27_S 0.79 0.13 0.00
98_A 63_D 0.79 0.13 0.00
27_T 45_V 0.79 0.13 0.00
89_S 30_L 0.79 0.13 0.00
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
4759 0.54 TA_eleven Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
0736 0.38 3HI2_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) Killed
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