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OPENSEQ.org
cIV_B_80_C_80_pn
Genes: A B A+B
Length: 252 273 495
Sequences: 2165 2296 2026
Seq/Len: 8.59 8.41 4.09
MirrorTree (Pazo et al. 2001) 0.90
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 0.16
2 0.00 0.00 0.34
5 0.00 0.00 3.58
10 0.00 0.00 3.72
20 0.00 0.00 3.78
100 0.00 0.00 3.84
∞ 0.00 0.00 3.86
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
53_L 265_F 1.35 0.95 0.56
203_W 8_Y 1.11 0.83 0.34
170_V 232_I 1.10 0.82 0.33
151_E 135_F 1.09 0.82 0.32
176_A 99_M 1.05 0.79 0.29
15_N 240_T 1.03 0.77 0.27
52_L 174_G 1.03 0.77 0.27
243_L 227_L 1.02 0.76 0.27
137_L 272_G 1.01 0.75 0.26
105_E 110_K 1.00 0.74 0.25
239_Y 270_I 0.98 0.72 0.23
167_G 158_A 0.98 0.72 0.23
77_I 140_L 0.94 0.66 0.20
223_N 71_N 0.92 0.64 0.19
51_L 161_A 0.91 0.64 0.18
177_T 109_I 0.91 0.63 0.18
92_I 6_H 0.90 0.63 0.18
30_D 140_L 0.90 0.62 0.17
53_L 108_F 0.89 0.61 0.17
226_Y 252_W 0.89 0.60 0.17
116_A 53_I 0.88 0.60 0.17
151_E 153_V 0.88 0.59 0.16
134_F 208_A 0.87 0.59 0.16
243_L 167_D 0.87 0.58 0.16
73_H 99_M 0.86 0.57 0.15
92_I 135_F 0.86 0.57 0.15
222_I 227_L 0.85 0.55 0.14
195_V 8_Y 0.84 0.55 0.14
101_F 11_L 0.84 0.54 0.14
56_C 162_F 0.84 0.54 0.14
175_T 179_V 0.84 0.54 0.14
114_I 199_G 0.83 0.52 0.13
190_V 70_V 0.82 0.52 0.13
90_V 53_I 0.82 0.52 0.13
204_F 186_T 0.82 0.52 0.13
32_Q 58_V 0.82 0.52 0.13
105_E 206_A 0.79 0.48 0.12
35_D 178_A 0.79 0.48 0.12
230_V 54_G 0.79 0.48 0.12
158_T 21_A 0.79 0.47 0.11
154_Y 15_I 0.79 0.47 0.11
29_H 201_A 0.79 0.47 0.11
90_V 69_V 0.79 0.47 0.11
212_Y 102_V 0.79 0.47 0.11
77_I 177_V 0.78 0.46 0.11
194_A 24_A 0.78 0.46 0.11
70_R 265_F 0.78 0.46 0.11
126_E 124_D 0.77 0.45 0.11
116_A 237_G 0.77 0.45 0.11
204_F 74_E 0.77 0.45 0.10
86_V 154_A 0.77 0.44 0.10
67_V 161_A 0.77 0.44 0.10
116_A 243_Q 0.76 0.44 0.10
48_F 227_L 0.76 0.43 0.10
189_A 152_G 0.76 0.43 0.10
180_I 237_G 0.76 0.43 0.10
47_I 186_T 0.76 0.43 0.10
129_N 36_K 0.76 0.43 0.10
42_I 140_L 0.75 0.42 0.10
152_D 150_L 0.75 0.42 0.10
71_F 10_I 0.75 0.42 0.10
98_P 265_F 0.75 0.42 0.10
133_A 21_A 0.74 0.41 0.09
114_I 126_V 0.74 0.41 0.09
21_Q 35_M 0.74 0.41 0.09
104_Q 28_L 0.74 0.41 0.09
83_L 84_I 0.74 0.41 0.09
23_A 23_G 0.74 0.41 0.09
192_Q 73_G 0.74 0.40 0.09
28_A 66_W 0.73 0.40 0.09
173_Q 90_F 0.73 0.40 0.09
69_A 240_T 0.73 0.40 0.09
183_W 188_L 0.73 0.40 0.09
143_A 47_G 0.73 0.40 0.09
235_S 47_G 0.73 0.39 0.09
122_Y 7_D 0.73 0.39 0.09
111_D 265_F 0.73 0.39 0.09
20_F 138_W 0.72 0.39 0.09
92_I 99_M 0.72 0.39 0.09
243_L 22_I 0.72 0.38 0.09
100_L 153_V 0.72 0.38 0.08
103_S 85_G 0.72 0.38 0.08
168_K 200_L 0.72 0.38 0.08
223_N 104_W 0.71 0.37 0.08
238_K 229_V 0.71 0.37 0.08
180_I 20_G 0.71 0.37 0.08
223_N 252_W 0.71 0.37 0.08
27_L 251_A 0.71 0.37 0.08
206_V 259_V 0.71 0.36 0.08
154_Y 198_F 0.70 0.36 0.08
163_V 232_I 0.70 0.36 0.08
98_P 69_V 0.70 0.36 0.08
87_L 38_I 0.70 0.35 0.08
187_A 47_G 0.70 0.35 0.07
38_V 34_W 0.70 0.35 0.07
114_I 75_T 0.70 0.35 0.07
72_T 10_I 0.69 0.35 0.07
77_I 158_A 0.69 0.35 0.07
101_F 67_A 0.69 0.35 0.07
102_R 99_M 0.69 0.35 0.07
231_V 56_V 0.69 0.35 0.07
183_W 140_L 0.69 0.35 0.07
157_A 29_T 0.69 0.35 0.07
182_A 71_N 0.69 0.35 0.07
198_R 9_Q 0.69 0.34 0.07
74_N 117_G 0.69 0.34 0.07
133_A 162_F 0.69 0.34 0.07
115_K 270_I 0.69 0.34 0.07
184_T 150_L 0.69 0.34 0.07
49_V 272_G 0.69 0.34 0.07
50_C 83_R 0.69 0.34 0.07
117_I 22_I 0.69 0.34 0.07
202_L 25_F 0.68 0.34 0.07
92_I 191_Y 0.68 0.34 0.07
33_W 103_A 0.68 0.34 0.07
219_L 140_L 0.68 0.34 0.07
151_E 240_T 0.68 0.33 0.07
223_N 270_I 0.68 0.33 0.07
204_F 265_F 0.68 0.33 0.07
64_A 21_A 0.68 0.33 0.07
35_D 238_Q 0.68 0.33 0.07
52_L 27_M 0.68 0.33 0.07
30_D 20_G 0.68 0.33 0.07
13_P 234_L 0.67 0.33 0.07
44_A 187_G 0.67 0.32 0.07
21_Q 131_G 0.67 0.32 0.07
154_Y 11_L 0.67 0.32 0.07
77_I 102_V 0.67 0.32 0.07
213_F 57_G 0.67 0.32 0.07
25_S 195_H 0.67 0.32 0.07
98_P 188_L 0.67 0.32 0.07
138_M 123_K 0.67 0.32 0.07
187_A 9_Q 0.67 0.32 0.07
127_Y 149_L 0.67 0.32 0.07
190_V 222_I 0.67 0.32 0.07
105_E 115_P 0.67 0.32 0.07
143_A 107_A 0.67 0.32 0.07
231_V 236_K 0.67 0.32 0.07
203_W 102_V 0.67 0.32 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
5103 4.09 cIV_B_80_C_80_pn Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
5102 4.68 cIV_B_60_C_60_pn Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.52 Done - Shared
5005 5.58 cIV_B_4_C_4_pn Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
5004 5.13 cIV_B_20_C_20_pn Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
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