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OPENSEQ.org
1A2K_lArB
Genes: A B A+B
Length: 202 121 289
Sequences: 9108 923 51
Seq/Len: 45.09 7.63 0.18
MirrorTree (Pazo et al. 2001) 0.23
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 0.04 0.05 0.02
2 0.05 0.05 0.02
5 0.06 0.05 0.06
10 0.08 0.05 0.10
20 0.10 0.05 0.16
100 0.18 0.05 0.61
∞ 0.25 0.07 1.33
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
128_A 53_L 1.51 0.30 0.00
102_D 80_S 1.47 0.28 0.00
28_G 78_I 1.42 0.26 0.00
26_L 80_S 1.35 0.23 0.00
9_V 80_S 1.30 0.21 0.00
47_F 115_M 1.25 0.19 0.00
149_N 80_S 1.24 0.19 0.00
75_Y 114_D 1.23 0.18 0.00
21_F 92_P 1.23 0.18 0.00
73_G 104_N 1.20 0.17 0.00
65_E 80_S 1.20 0.17 0.00
21_F 93_I 1.15 0.16 0.00
113_V 55_S 1.14 0.15 0.00
154_K 80_S 1.10 0.14 0.00
120_D 84_G 1.09 0.14 0.00
19_T 75_D 1.08 0.14 0.00
82_I 36_L 1.07 0.14 0.00
61_T 102_L 1.05 0.13 0.00
114_L 23_R 1.05 0.13 0.00
109_N 53_L 1.03 0.12 0.00
102_D 73_T 1.01 0.12 0.00
106_V 90_E 1.01 0.12 0.00
65_E 90_E 1.01 0.12 0.00
20_T 110_V 1.00 0.12 0.00
117_N 40_G 1.00 0.12 0.00
32_K 90_E 0.98 0.11 0.00
146_A 102_L 0.98 0.11 0.00
22_V 36_L 0.97 0.11 0.00
118_K 84_G 0.97 0.11 0.00
11_V 12_I 0.96 0.11 0.00
154_K 96_F 0.96 0.11 0.00
145_S 84_G 0.96 0.11 0.00
12_G 84_G 0.95 0.10 0.00
17_G 84_G 0.95 0.10 0.00
18_K 84_G 0.95 0.10 0.00
85_F 51_E 0.95 0.10 0.00
120_D 45_G 0.95 0.10 0.00
24_R 109_W 0.95 0.10 0.00
86_D 56_L 0.94 0.10 0.00
10_L 27_G 0.94 0.10 0.00
120_D 11_F 0.94 0.10 0.00
120_D 16_Y 0.94 0.10 0.00
154_K 26_L 0.94 0.10 0.00
115_C 98_Q 0.93 0.10 0.00
96_V 29_I 0.93 0.10 0.00
25_H 62_Q 0.93 0.10 0.00
60_D 84_G 0.93 0.10 0.00
146_A 96_F 0.93 0.10 0.00
92_T 21_N 0.92 0.10 0.00
61_T 111_C 0.91 0.10 0.00
54_I 91_D 0.91 0.10 0.00
149_N 65_I 0.91 0.10 0.00
120_D 69_D 0.90 0.10 0.00
83_I 29_I 0.90 0.09 0.00
75_Y 98_Q 0.90 0.09 0.00
93_Y 26_L 0.90 0.09 0.00
57_N 86_L 0.89 0.09 0.00
67_Y 40_G 0.89 0.09 0.00
63_G 30_Y 0.89 0.09 0.00
55_K 96_F 0.88 0.09 0.00
159_L 47_A 0.87 0.09 0.00
92_T 29_I 0.87 0.09 0.00
93_Y 32_D 0.87 0.09 0.00
56_F 72_P 0.86 0.09 0.00
126_V 65_I 0.86 0.09 0.00
92_T 101_L 0.86 0.09 0.00
145_S 117_R 0.86 0.09 0.00
115_C 117_R 0.86 0.09 0.00
114_L 110_V 0.85 0.09 0.00
96_V 18_L 0.84 0.08 0.00
46_V 10_S 0.83 0.08 0.00
115_C 90_E 0.83 0.08 0.00
121_I 68_Q 0.83 0.08 0.00
105_R 79_I 0.83 0.08 0.00
45_L 13_Q 0.82 0.08 0.00
146_A 84_G 0.82 0.08 0.00
146_A 45_G 0.82 0.08 0.00
95_N 80_S 0.81 0.08 0.00
86_D 54_S 0.81 0.08 0.00
119_V 12_I 0.81 0.08 0.00
114_L 20_D 0.81 0.08 0.00
120_D 100_F 0.81 0.08 0.00
19_T 100_F 0.81 0.08 0.00
9_V 108_A 0.81 0.08 0.00
120_D 30_Y 0.81 0.08 0.00
63_G 100_F 0.80 0.08 0.00
6_F 62_Q 0.80 0.08 0.00
153_E 68_Q 0.80 0.08 0.00
20_T 55_S 0.80 0.08 0.00
145_S 45_G 0.80 0.08 0.00
150_Y 119_A 0.80 0.08 0.00
148_S 96_F 0.80 0.07 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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