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OPENSEQ.org
L2-S6 coevolution
Genes: A B A+B
Length: 273 135 400
Sequences: 2094 1051 533
Seq/Len: 7.67 7.79 1.33
MirrorTree (Pazo et al. 2001) 0.73
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.16
∞ 0.00 0.00 1.31
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
123_A 76_T 1.90 0.96 0.81
123_A 73_E 1.68 0.91 0.67
163_Q 61_L 1.29 0.69 0.32
133_R 79_R 1.26 0.66 0.30
125_K 73_E 1.17 0.57 0.23
123_A 25_Y 1.11 0.52 0.19
228_V 74_L 1.07 0.48 0.16
88_S 78_F 1.05 0.46 0.15
106_A 42_W 1.01 0.42 0.13
200_H 29_I 1.01 0.42 0.13
266_F 35_K 1.01 0.41 0.13
130_L 30_T 1.00 0.41 0.13
161_Y 82_D 0.99 0.40 0.12
139_S 67_P 0.99 0.40 0.12
247_P 13_D 0.98 0.39 0.12
263_T 10_V 0.97 0.38 0.11
112_A 9_M 0.95 0.36 0.10
64_I 84_V 0.94 0.35 0.10
167_R 17_Q 0.94 0.35 0.10
175_R 6_I 0.94 0.35 0.10
268_V 2_R 0.92 0.33 0.09
105_L 69_E 0.92 0.33 0.09
160_T 88_M 0.90 0.32 0.08
6_C 30_T 0.89 0.31 0.08
123_A 77_T 0.89 0.31 0.08
129_T 30_T 0.89 0.30 0.08
177_R 57_A 0.88 0.30 0.08
176_L 61_L 0.88 0.30 0.08
164_I 88_M 0.87 0.29 0.07
154_L 1_M 0.87 0.29 0.07
255_K 102_M 0.87 0.29 0.07
106_A 85_I 0.86 0.28 0.07
167_R 8_F 0.86 0.28 0.07
146_M 32_A 0.85 0.28 0.07
232_H 13_D 0.84 0.27 0.06
152_G 17_Q 0.84 0.27 0.06
88_S 93_K 0.84 0.26 0.06
125_K 88_M 0.83 0.26 0.06
176_L 85_I 0.83 0.26 0.06
94_V 109_R 0.83 0.26 0.06
175_R 89_V 0.83 0.26 0.06
238_R 75_E 0.81 0.24 0.06
116_I 26_T 0.81 0.24 0.06
167_R 104_K 0.81 0.24 0.06
222_G 53_K 0.81 0.24 0.05
196_G 112_R 0.81 0.24 0.05
195_V 61_L 0.80 0.23 0.05
19_V 64_V 0.80 0.23 0.05
16_V 86_R 0.80 0.23 0.05
143_N 76_T 0.80 0.23 0.05
270_R 6_I 0.79 0.23 0.05
165_V 91_R 0.79 0.23 0.05
245_V 13_D 0.79 0.23 0.05
162_V 46_Q 0.79 0.23 0.05
144_V 26_T 0.79 0.23 0.05
232_H 63_N 0.79 0.23 0.05
118_S 75_E 0.78 0.22 0.05
256_K 108_E 0.77 0.22 0.05
77_V 84_V 0.77 0.21 0.04
270_R 48_A 0.76 0.21 0.04
88_S 118_N 0.76 0.21 0.04
174_L 31_G 0.76 0.21 0.04
246_T 111_E 0.76 0.21 0.04
118_S 23_E 0.76 0.21 0.04
220_V 59_Y 0.75 0.20 0.04
247_P 99_A 0.75 0.20 0.04
146_M 29_I 0.75 0.20 0.04
111_K 36_I 0.75 0.20 0.04
80_R 100_S 0.75 0.20 0.04
15_H 78_F 0.74 0.20 0.04
169_G 74_L 0.74 0.20 0.04
40_S 33_E 0.74 0.20 0.04
116_I 31_G 0.73 0.19 0.04
105_L 50_P 0.73 0.19 0.04
17_V 90_M 0.73 0.19 0.04
162_V 64_V 0.72 0.19 0.04
121_D 53_K 0.72 0.19 0.04
165_V 52_N 0.72 0.19 0.04
152_G 109_R 0.72 0.18 0.04
192_L 71_I 0.72 0.18 0.03
181_M 95_A 0.71 0.18 0.03
181_M 106_K 0.71 0.18 0.03
88_S 104_K 0.71 0.18 0.03
15_H 61_L 0.71 0.18 0.03
40_S 87_S 0.71 0.18 0.03
110_L 110_R 0.71 0.18 0.03
139_S 117_A 0.71 0.18 0.03
124_I 73_E 0.71 0.18 0.03
183_K 62_M 0.71 0.18 0.03
232_H 83_A 0.71 0.17 0.03
157_S 72_D 0.70 0.17 0.03
205_L 87_S 0.70 0.17 0.03
202_L 54_L 0.70 0.17 0.03
152_G 6_I 0.70 0.17 0.03
90_N 46_Q 0.70 0.17 0.03
80_R 56_K 0.70 0.17 0.03
77_V 28_A 0.70 0.17 0.03
9_T 73_E 0.70 0.17 0.03
76_A 9_M 0.70 0.17 0.03
3_V 116_F 0.69 0.17 0.03
177_R 46_Q 0.69 0.17 0.03
246_T 8_F 0.69 0.17 0.03
16_V 80_F 0.69 0.17 0.03
31_A 82_D 0.69 0.17 0.03
184_V 67_P 0.69 0.17 0.03
53_H 55_H 0.69 0.17 0.03
181_M 92_T 0.69 0.17 0.03
247_P 56_K 0.69 0.17 0.03
174_L 60_V 0.68 0.16 0.03
174_L 51_I 0.68 0.16 0.03
232_H 64_V 0.68 0.16 0.03
25_H 46_Q 0.68 0.16 0.03
79_E 40_E 0.68 0.16 0.03
132_M 26_T 0.68 0.16 0.03
245_V 80_F 0.68 0.16 0.03
115_Q 35_K 0.68 0.16 0.03
266_F 20_G 0.68 0.16 0.03
139_S 9_M 0.68 0.16 0.03
20_V 2_R 0.67 0.16 0.03
253_K 56_K 0.67 0.16 0.03
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
1916 1.33 L2-S6 coevolution Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.81 Done
1457 0.01 L2-S6 coevolution Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 2) msa: Jackhmmer (2014_03) Killed - Shared
1453 0.01 L2-S6 coevolution Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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