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OPENSEQ.org
cIV_B_40_cI_J_40_Pdenitr
Genes: A B A+B
Length: 252 200 442
Sequences: 2518 733 406
Seq/Len: 9.99 3.67 0.92
MirrorTree (Pazo et al. 2001) 0.49
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 0.04
2 0.00 0.00 0.08
5 0.00 0.00 0.17
10 0.00 0.00 0.31
20 0.00 0.00 0.37
100 0.00 0.00 0.44
∞ 0.00 0.00 0.90
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
237_E 40_A 1.59 0.80 0.04
172_V 77_V 1.54 0.77 0.03
233_A 166_M 1.40 0.67 0.02
143_A 12_S 1.40 0.67 0.02
97_L 32_W 1.39 0.67 0.02
34_L 76_D 1.34 0.62 0.02
170_V 159_I 1.31 0.60 0.02
176_A 41_A 1.30 0.58 0.02
56_C 135_L 1.26 0.55 0.01
20_F 195_K 1.24 0.53 0.01
92_I 27_V 1.24 0.53 0.01
97_L 44_F 1.22 0.52 0.01
231_V 153_V 1.22 0.51 0.01
116_A 143_Y 1.22 0.51 0.01
153_E 57_V 1.18 0.48 0.01
129_N 94_L 1.16 0.46 0.01
20_F 12_S 1.14 0.45 0.01
213_F 17_G 1.14 0.44 0.01
80_I 82_L 1.14 0.44 0.01
44_A 41_A 1.11 0.41 0.01
190_V 97_G 1.10 0.40 0.01
164_V 166_M 1.09 0.40 0.01
187_A 149_L 1.08 0.39 0.01
212_Y 186_A 1.08 0.39 0.01
45_V 101_L 1.08 0.39 0.01
41_I 36_A 1.08 0.39 0.01
11_G 36_A 1.07 0.38 0.01
129_N 133_L 1.05 0.36 0.01
161_P 52_V 1.05 0.36 0.01
241_A 92_L 1.05 0.36 0.01
162_V 138_V 1.05 0.36 0.01
174_V 12_S 1.05 0.36 0.01
98_P 56_L 1.04 0.36 0.01
50_C 157_A 1.04 0.36 0.01
239_Y 36_A 1.04 0.35 0.01
20_F 47_Q 1.03 0.35 0.01
209_E 166_M 1.03 0.34 0.01
174_V 84_G 1.03 0.34 0.01
180_I 176_N 1.02 0.34 0.01
72_T 7_Y 1.02 0.34 0.01
188_F 151_G 1.01 0.33 0.01
133_A 72_V 1.01 0.33 0.01
53_L 159_I 1.01 0.33 0.01
180_I 56_L 1.01 0.33 0.01
112_L 173_K 1.01 0.33 0.01
79_V 28_H 1.00 0.33 0.01
153_E 59_V 1.00 0.32 0.01
205_S 29_S 0.99 0.32 0.01
202_L 153_V 0.99 0.32 0.01
170_V 145_L 0.99 0.31 0.01
187_A 52_V 0.99 0.31 0.01
57_I 147_F 0.99 0.31 0.01
176_A 129_V 0.99 0.31 0.01
45_V 51_F 0.99 0.31 0.01
245_G 150_A 0.99 0.31 0.01
236_Q 124_P 0.98 0.31 0.01
99_I 16_A 0.98 0.31 0.01
138_M 74_M 0.98 0.30 0.01
87_L 55_L 0.97 0.30 0.01
128_P 64_V 0.97 0.30 0.01
68_P 41_A 0.97 0.30 0.01
166_V 48_G 0.97 0.30 0.01
114_I 14_C 0.97 0.30 0.01
213_F 20_V 0.96 0.29 0.01
119_H 55_L 0.96 0.29 0.01
170_V 20_V 0.95 0.29 0.01
235_S 173_K 0.95 0.28 0.01
80_I 135_L 0.94 0.28 0.01
49_V 69_L 0.94 0.28 0.01
164_V 153_V 0.94 0.28 0.01
92_I 81_E 0.94 0.28 0.01
163_V 150_A 0.94 0.28 0.01
246_A 21_V 0.94 0.28 0.01
95_F 39_S 0.94 0.27 0.01
170_V 4_F 0.93 0.27 0.01
96_S 160_G 0.93 0.27 0.01
42_I 100_L 0.93 0.27 0.01
27_L 17_G 0.93 0.27 0.01
68_P 72_V 0.93 0.27 0.01
20_F 15_V 0.93 0.27 0.01
180_I 45_V 0.93 0.27 0.01
39_L 142_R 0.93 0.27 0.01
212_Y 92_L 0.92 0.27 0.01
212_Y 148_Q 0.92 0.27 0.01
66_P 92_L 0.92 0.26 0.01
230_V 147_F 0.92 0.26 0.01
235_S 84_G 0.92 0.26 0.01
28_A 22_I 0.92 0.26 0.01
177_T 106_I 0.91 0.26 0.01
64_A 28_H 0.91 0.26 0.01
240_E 148_Q 0.91 0.25 0.01
151_E 195_K 0.90 0.25 0.01
55_I 64_V 0.90 0.25 0.01
243_L 92_L 0.90 0.24 0.01
114_I 127_A 0.89 0.24 0.01
68_P 136_G 0.89 0.24 0.01
174_V 9_F 0.89 0.24 0.01
199_I 198_Q 0.89 0.24 0.01
170_V 77_V 0.89 0.24 0.01
180_I 145_L 0.89 0.24 0.01
18_M 4_F 0.89 0.24 0.01
60_F 13_A 0.89 0.24 0.01
187_A 153_V 0.88 0.24 0.01
111_D 21_V 0.88 0.24 0.01
162_V 189_M 0.88 0.24 0.01
19_N 93_A 0.88 0.23 0.00
151_E 11_I 0.88 0.23 0.00
98_P 8_L 0.88 0.23 0.00
134_F 193_D 0.87 0.23 0.00
19_N 27_V 0.87 0.23 0.00
66_P 34_I 0.87 0.23 0.00
243_L 150_A 0.87 0.23 0.00
201_Q 167_R 0.87 0.23 0.00
187_A 40_A 0.87 0.23 0.00
13_P 48_G 0.87 0.23 0.00
239_Y 166_M 0.87 0.23 0.00
203_W 44_F 0.87 0.23 0.00
83_L 41_A 0.86 0.23 0.00
225_A 44_F 0.86 0.23 0.00
176_A 95_V 0.86 0.23 0.00
92_I 42_G 0.86 0.23 0.00
173_Q 61_V 0.86 0.22 0.00
64_A 156_V 0.86 0.22 0.00
101_F 185_P 0.86 0.22 0.00
114_I 46_L 0.86 0.22 0.00
99_I 160_G 0.86 0.22 0.00
230_V 158_M 0.86 0.22 0.00
189_A 32_W 0.86 0.22 0.00
79_V 139_L 0.85 0.22 0.00
202_L 27_V 0.85 0.22 0.00
79_V 55_L 0.85 0.22 0.00
243_L 135_L 0.85 0.22 0.00
170_V 139_L 0.85 0.22 0.00
29_H 181_M 0.85 0.21 0.00
62_R 169_R 0.85 0.21 0.00
132_V 126_D 0.85 0.21 0.00
38_V 151_G 0.85 0.21 0.00
96_S 183_R 0.85 0.21 0.00
170_V 16_A 0.85 0.21 0.00
30_D 181_M 0.85 0.21 0.00
72_T 49_A 0.84 0.21 0.00
117_I 31_L 0.84 0.21 0.00
116_A 145_L 0.84 0.21 0.00
80_I 35_L 0.84 0.21 0.00
100_L 139_L 0.84 0.21 0.00
23_A 14_C 0.84 0.21 0.00
203_W 148_Q 0.84 0.21 0.00
75_T 163_V 0.84 0.21 0.00
112_L 177_V 0.83 0.21 0.00
212_Y 142_R 0.83 0.21 0.00
52_L 44_F 0.83 0.21 0.00
112_L 125_V 0.83 0.21 0.00
59_R 99_V 0.83 0.20 0.00
231_V 74_M 0.83 0.20 0.00
239_Y 153_V 0.83 0.20 0.00
68_P 144_V 0.83 0.20 0.00
40_Y 95_V 0.83 0.20 0.00
53_L 177_V 0.83 0.20 0.00
213_F 197_G 0.83 0.20 0.00
219_L 167_R 0.83 0.20 0.00
173_Q 147_F 0.83 0.20 0.00
185_I 135_L 0.83 0.20 0.00
38_V 169_R 0.83 0.20 0.00
141_K 76_D 0.82 0.20 0.00
206_V 27_V 0.82 0.20 0.00
72_T 135_L 0.82 0.20 0.00
229_I 17_G 0.82 0.20 0.00
77_I 72_V 0.82 0.20 0.00
231_V 57_V 0.82 0.20 0.00
155_L 71_V 0.82 0.20 0.00
232_K 5_A 0.82 0.20 0.00
133_A 135_L 0.82 0.20 0.00
48_F 175_Q 0.81 0.20 0.00
57_I 107_A 0.81 0.20 0.00
231_V 128_A 0.81 0.20 0.00
107_P 49_A 0.81 0.19 0.00
79_V 93_A 0.81 0.19 0.00
74_N 112_T 0.81 0.19 0.00
29_H 196_P 0.81 0.19 0.00
83_L 25_N 0.81 0.19 0.00
138_M 151_G 0.81 0.19 0.00
163_V 165_T 0.81 0.19 0.00
114_I 157_A 0.81 0.19 0.00
239_Y 182_W 0.81 0.19 0.00
115_K 71_V 0.81 0.19 0.00
183_W 110_G 0.81 0.19 0.00
97_L 20_V 0.81 0.19 0.00
20_F 105_G 0.81 0.19 0.00
111_D 146_M 0.81 0.19 0.00
173_Q 44_F 0.81 0.19 0.00
180_I 66_V 0.81 0.19 0.00
96_S 44_F 0.81 0.19 0.00
185_I 126_D 0.80 0.19 0.00
114_I 8_L 0.80 0.19 0.00
87_L 14_C 0.80 0.19 0.00
69_A 163_V 0.80 0.19 0.00
231_V 137_L 0.80 0.19 0.00
42_I 10_A 0.80 0.19 0.00
112_L 167_R 0.80 0.19 0.00
217_S 151_G 0.80 0.19 0.00
22_P 195_K 0.80 0.19 0.00
132_V 98_V 0.80 0.19 0.00
13_P 40_A 0.80 0.19 0.00
143_A 57_V 0.80 0.19 0.00
226_Y 162_I 0.80 0.18 0.00
31_Q 142_R 0.80 0.18 0.00
231_V 123_A 0.80 0.18 0.00
241_A 57_V 0.80 0.18 0.00
87_L 26_P 0.79 0.18 0.00
20_F 14_C 0.79 0.18 0.00
77_I 135_L 0.79 0.18 0.00
81_W 33_L 0.79 0.18 0.00
26_P 162_I 0.79 0.18 0.00
96_S 158_M 0.79 0.18 0.00
161_P 191_L 0.79 0.18 0.00
161_P 132_T 0.79 0.18 0.00
133_A 9_F 0.79 0.18 0.00
158_T 17_G 0.79 0.18 0.00
114_I 120_L 0.79 0.18 0.00
98_P 184_D 0.79 0.18 0.00
142_E 181_M 0.79 0.18 0.00
112_L 149_L 0.79 0.18 0.00
152_D 87_A 0.79 0.18 0.00
73_H 48_G 0.78 0.18 0.00
131_G 36_A 0.78 0.18 0.00
198_R 160_G 0.78 0.18 0.00
161_P 31_L 0.78 0.18 0.00
41_I 45_V 0.78 0.18 0.00
93_G 184_D 0.78 0.18 0.00
83_L 106_I 0.78 0.17 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)
ID Seq/Len Name Options I_Prob Status
3238 0.58 cIV_B_40_cI_J_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3237 0.92 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3236 0.99 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
3235 2.02 cIV_B_40_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.13 Done - Shared
3234 2 cIV_B_40_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3233 1.1 cIV_B_20_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3232 2.3 cIV_B_20_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3231 2.3 cIV_B_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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