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t

Genes: A B A+B
Length: 274 221 432
Sequences: 2192 1051 880
Seq/Len: 8 4.76 2.04
MirrorTree (Pazo et al. 2001) 0.91
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 0.02 0.00 1.78
2 0.02 0.00 1.78
5 0.02 0.00 1.78
10 0.02 0.00 1.78
20 0.02 0.00 1.78
100 0.02 0.00 1.80
0.02 0.00 1.91
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
79_Y 153_E 1.62 0.95 0.71
69_R 130_I 1.38 0.86 0.50
135_R 157_L 1.36 0.85 0.49
79_Y 117_S 1.35 0.85 0.48
199_L 38_D 1.29 0.81 0.42
129_V 157_L 1.28 0.80 0.41
65_V 146_G 1.27 0.79 0.40
129_V 166_I 1.27 0.79 0.40
79_Y 65_R 1.26 0.78 0.39
91_S 141_R 1.25 0.77 0.38
77_A 117_S 1.22 0.75 0.35
184_P 13_I 1.22 0.75 0.35
77_A 54_G 1.21 0.74 0.34
73_F 73_S 1.21 0.74 0.34
26_I 166_I 1.18 0.71 0.31
91_S 43_I 1.18 0.71 0.31
123_D 160_L 1.17 0.71 0.31
244_L 133_R 1.17 0.71 0.31
202_L 17_L 1.16 0.70 0.30
62_L 123_V 1.16 0.70 0.30
52_L 126_E 1.13 0.67 0.28
79_Y 129_L 1.13 0.67 0.28
77_A 53_R 1.12 0.66 0.27
132_L 109_E 1.11 0.65 0.26
169_A 85_R 1.08 0.62 0.24
246_K 133_R 1.08 0.62 0.24
82_M 172_A 1.07 0.60 0.23
145_R 90_A 1.07 0.60 0.23
125_M 100_H 1.06 0.60 0.22
132_L 174_L 1.04 0.58 0.21
248_G 50_Y 1.04 0.57 0.21
132_L 48_V 1.04 0.57 0.20
201_G 130_I 1.04 0.57 0.20
266_R 97_V 1.04 0.57 0.20
42_A 127_L 1.03 0.56 0.20
208_D 165_G 1.03 0.56 0.20
236_S 138_T 1.03 0.56 0.20
52_L 12_C 1.03 0.56 0.20
125_M 103_V 1.03 0.56 0.20
169_A 168_E 1.02 0.55 0.19
101_A 121_I 1.02 0.55 0.19
52_L 175_L 1.01 0.55 0.19
183_A 13_I 1.01 0.54 0.19
163_L 155_Y 1.01 0.54 0.19
193_E 135_R 1.01 0.54 0.18
161_G 157_L 1.01 0.54 0.18
145_R 18_F 1.00 0.53 0.18
263_L 93_T 1.00 0.53 0.18
55_T 100_H 1.00 0.53 0.18
239_S 54_G 0.99 0.52 0.17
52_L 71_D 0.98 0.51 0.17
79_Y 23_P 0.98 0.51 0.17
261_I 22_E 0.98 0.51 0.17
127_K 156_G 0.98 0.50 0.16
261_I 13_I 0.97 0.50 0.16
243_E 147_T 0.97 0.50 0.16
143_F 111_V 0.97 0.50 0.16
143_F 176_E 0.97 0.49 0.16
123_D 117_S 0.96 0.48 0.15
248_G 24_L 0.95 0.48 0.15
54_I 168_E 0.95 0.47 0.15
42_A 122_D 0.95 0.47 0.15
62_L 121_I 0.95 0.47 0.15
36_H 88_K 0.94 0.46 0.14
260_D 153_E 0.94 0.46 0.14
43_R 142_P 0.94 0.46 0.14
135_R 53_R 0.93 0.45 0.14
163_L 126_E 0.93 0.45 0.14
238_L 83_P 0.93 0.45 0.14
45_Q 126_E 0.93 0.45 0.14
84_A 85_R 0.93 0.45 0.14
144_T 156_G 0.92 0.44 0.13
200_R 88_K 0.92 0.43 0.13
170_Y 168_E 0.91 0.43 0.13
81_V 31_K 0.91 0.43 0.13
56_R 111_V 0.91 0.43 0.13
165_G 87_S 0.91 0.43 0.13
249_V 22_E 0.91 0.43 0.13
239_S 145_F 0.91 0.43 0.13
81_V 53_R 0.91 0.42 0.13
55_T 11_R 0.91 0.42 0.12
93_L 171_A 0.90 0.42 0.12
221_V 190_G 0.90 0.42 0.12
64_F 146_G 0.90 0.42 0.12
128_A 9_V 0.90 0.42 0.12
143_F 18_F 0.90 0.42 0.12
170_Y 64_W 0.90 0.41 0.12
221_V 184_T 0.90 0.41 0.12
81_V 169_M 0.90 0.41 0.12
101_A 42_G 0.90 0.41 0.12
129_V 30_A 0.89 0.41 0.12
50_L 96_I 0.89 0.41 0.12
89_L 66_F 0.89 0.41 0.12
112_A 127_L 0.89 0.41 0.12
183_A 145_F 0.89 0.41 0.12
62_L 111_V 0.89 0.41 0.12
78_D 126_E 0.89 0.40 0.12
162_D 46_L 0.89 0.40 0.12
95_L 24_L 0.88 0.40 0.11
143_F 73_S 0.88 0.40 0.11
31_Y 101_Q 0.88 0.39 0.11
35_L 109_E 0.87 0.39 0.11
201_G 97_V 0.87 0.39 0.11
118_R 60_V 0.87 0.38 0.11
248_G 20_A 0.87 0.38 0.11
236_S 119_G 0.87 0.38 0.11
193_E 18_F 0.86 0.38 0.10
115_L 147_T 0.86 0.38 0.10
68_A 69_A 0.86 0.37 0.10
173_Q 127_L 0.86 0.37 0.10
44_S 18_F 0.86 0.37 0.10
220_R 184_T 0.86 0.37 0.10
44_S 160_L 0.86 0.37 0.10
156_S 43_I 0.86 0.37 0.10
110_E 141_R 0.85 0.37 0.10
44_S 104_T 0.85 0.37 0.10
247_E 66_F 0.85 0.36 0.10
43_R 155_Y 0.85 0.36 0.10
192_L 57_L 0.84 0.36 0.10
256_E 93_T 0.84 0.36 0.10
46_K 165_G 0.84 0.35 0.10
44_S 130_I 0.84 0.35 0.10
241_S 41_A 0.84 0.35 0.10
32_E 160_L 0.84 0.35 0.10
145_R 64_W 0.84 0.35 0.10
174_R 103_V 0.84 0.35 0.09
238_L 91_Q 0.84 0.35 0.09
35_L 107_E 0.84 0.35 0.09
246_K 123_V 0.83 0.35 0.09
51_Q 127_L 0.83 0.35 0.09
29_D 29_L 0.83 0.35 0.09
229_S 96_I 0.83 0.35 0.09
91_S 109_E 0.83 0.35 0.09
75_L 34_P 0.83 0.35 0.09
72_R 70_A 0.83 0.34 0.09
126_R 103_V 0.83 0.34 0.09
211_V 130_I 0.83 0.34 0.09
258_F 96_I 0.83 0.34 0.09
129_V 73_S 0.83 0.34 0.09
150_A 17_L 0.83 0.34 0.09
243_E 152_M 0.83 0.34 0.09
47_V 105_R 0.83 0.34 0.09
139_K 73_S 0.83 0.34 0.09
200_R 25_S 0.83 0.34 0.09
215_V 9_V 0.82 0.34 0.09
178_H 134_G 0.82 0.34 0.09
133_K 71_D 0.82 0.34 0.09
135_R 145_F 0.82 0.34 0.09
237_T 53_R 0.82 0.34 0.09
128_A 89_A 0.82 0.33 0.09
264_R 84_R 0.82 0.33 0.09
147_D 16_L 0.82 0.33 0.09
118_R 33_L 0.82 0.33 0.09
200_R 121_I 0.82 0.33 0.09
237_T 155_Y 0.82 0.33 0.09
97_K 44_D 0.82 0.33 0.09
125_M 116_A 0.81 0.33 0.09
78_D 161_A 0.81 0.33 0.09
31_Y 160_L 0.81 0.33 0.09
82_M 109_E 0.81 0.33 0.09
52_L 149_D 0.81 0.32 0.08
220_R 183_F 0.81 0.32 0.08
219_D 186_P 0.81 0.32 0.08
245_V 59_C 0.81 0.32 0.08
221_V 186_P 0.80 0.32 0.08
229_S 108_I 0.80 0.32 0.08
76_A 173_G 0.80 0.32 0.08
53_S 107_E 0.80 0.31 0.08
118_R 136_R 0.80 0.31 0.08
221_V 180_P 0.80 0.31 0.08
263_L 43_I 0.80 0.31 0.08
234_L 161_A 0.80 0.31 0.08
176_R 109_E 0.80 0.31 0.08
118_R 7_L 0.80 0.31 0.08
35_L 136_R 0.80 0.31 0.08
176_R 108_I 0.80 0.31 0.08
91_S 151_F 0.80 0.31 0.08
105_E 76_M 0.79 0.31 0.08
123_D 67_Q 0.79 0.31 0.08
202_L 71_D 0.79 0.31 0.08
259_Q 87_S 0.79 0.31 0.08
19_E 97_V 0.79 0.31 0.08
108_A 148_T 0.79 0.30 0.08
63_A 45_A 0.79 0.30 0.08
143_F 46_L 0.79 0.30 0.08
239_S 20_A 0.79 0.30 0.08
160_E 77_T 0.79 0.30 0.07
208_D 51_E 0.79 0.30 0.07
184_P 77_T 0.79 0.30 0.07
162_D 85_R 0.79 0.30 0.07
163_L 162_D 0.79 0.30 0.07
82_M 107_E 0.79 0.30 0.07
171_I 95_A 0.78 0.30 0.07
235_A 100_H 0.78 0.30 0.07
268_E 97_V 0.78 0.30 0.07
199_L 6_P 0.78 0.30 0.07
56_R 26_D 0.78 0.30 0.07
239_S 153_E 0.78 0.29 0.07
219_D 185_V 0.78 0.29 0.07
79_Y 120_T 0.78 0.29 0.07
203_L 63_R 0.78 0.29 0.07
96_P 57_L 0.78 0.29 0.07
195_A 135_R 0.78 0.29 0.07
62_L 31_K 0.78 0.29 0.07
221_V 181_P 0.78 0.29 0.07
214_S 44_D 0.78 0.29 0.07
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
6885 2.04 t Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.71 Done - Shared
2846 3.58 CC_scpA-scpB_complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared

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