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OPENSEQ.org
TA_ten
Genes: A B A+B
Length: 138 58 192
Sequences: 489 1807 168
Seq/Len: 3.54 31.16 0.88
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.86
2 0.00 0.01 0.86
5 0.01 0.02 0.89
10 0.01 0.03 0.89
20 0.01 0.04 0.90
100 0.02 0.05 0.94
∞ 0.03 0.09 1.17
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_Q 44_K 1.60 0.79 0.03
14_G 44_K 1.59 0.79 0.03
89_S 57_L 1.47 0.71 0.02
18_S 48_R 1.41 0.67 0.02
26_L 43_I 1.34 0.61 0.02
55_E 32_R 1.23 0.51 0.01
16_M 44_K 1.23 0.51 0.01
9_P 44_K 1.21 0.49 0.01
119_I 2_K 1.21 0.49 0.01
48_D 25_K 1.18 0.46 0.01
45_T 34_V 1.12 0.41 0.01
79_K 55_L 1.08 0.38 0.01
25_A 54_Q 1.06 0.36 0.01
110_L 39_P 1.06 0.36 0.01
135_L 18_A 1.04 0.35 0.01
27_T 54_Q 1.02 0.33 0.01
46_A 34_V 1.02 0.33 0.01
47_F 22_N 1.01 0.32 0.01
49_F 25_K 1.00 0.31 0.01
135_L 31_R 1.00 0.31 0.01
57_I 35_M 0.99 0.31 0.01
36_M 19_N 0.99 0.30 0.01
7_L 34_V 0.99 0.30 0.01
2_R 47_L 0.97 0.29 0.01
45_T 25_K 0.97 0.29 0.01
111_F 19_N 0.97 0.29 0.01
55_E 25_K 0.96 0.28 0.01
53_D 30_G 0.95 0.28 0.01
4_P 4_S 0.92 0.25 0.00
7_L 44_K 0.92 0.25 0.00
101_G 56_G 0.92 0.25 0.00
66_H 49_K 0.91 0.25 0.00
120_D 35_M 0.91 0.25 0.00
28_Q 35_M 0.91 0.25 0.00
50_Y 25_K 0.91 0.25 0.00
89_S 52_L 0.90 0.24 0.00
65_S 12_S 0.90 0.24 0.00
24_E 33_S 0.90 0.24 0.00
99_R 11_E 0.89 0.23 0.00
100_I 21_S 0.89 0.23 0.00
29_G 1_M 0.88 0.23 0.00
12_E 44_K 0.88 0.23 0.00
18_S 43_I 0.88 0.23 0.00
111_F 15_V 0.88 0.23 0.00
18_S 45_E 0.87 0.22 0.00
6_T 16_D 0.86 0.21 0.00
65_S 49_K 0.85 0.21 0.00
82_L 14_G 0.84 0.21 0.00
49_F 32_R 0.84 0.20 0.00
59_L 54_Q 0.84 0.20 0.00
42_A 34_V 0.84 0.20 0.00
115_H 55_L 0.84 0.20 0.00
43_L 27_R 0.83 0.20 0.00
106_E 39_P 0.83 0.20 0.00
82_L 41_D 0.83 0.20 0.00
92_T 16_D 0.82 0.20 0.00
97_A 56_G 0.82 0.20 0.00
40_K 35_M 0.82 0.19 0.00
77_A 29_H 0.82 0.19 0.00
34_E 50_A 0.82 0.19 0.00
33_A 8_R 0.81 0.19 0.00
16_M 47_L 0.81 0.18 0.00
117_T 39_P 0.80 0.18 0.00
15_Y 20_G 0.80 0.18 0.00
5_V 24_L 0.80 0.18 0.00
121_A 43_I 0.80 0.18 0.00
25_A 34_V 0.79 0.18 0.00
112_N 54_Q 0.79 0.18 0.00
105_Q 36_P 0.79 0.17 0.00
1_M 22_N 0.78 0.17 0.00
25_A 47_L 0.78 0.17 0.00
113_L 11_E 0.77 0.17 0.00
46_A 33_S 0.77 0.17 0.00
106_E 3_Q 0.77 0.17 0.00
84_N 53_K 0.77 0.16 0.00
75_S 37_R 0.76 0.16 0.00
60_P 40_C 0.76 0.16 0.00
30_E 41_D 0.76 0.16 0.00
41_D 12_S 0.75 0.16 0.00
34_E 14_G 0.75 0.16 0.00
119_I 37_R 0.75 0.15 0.00
107_I 28_F 0.74 0.15 0.00
127_K 12_S 0.74 0.15 0.00
25_A 25_K 0.74 0.15 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)
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