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OPENSEQ.org
cI_J_10_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 200 263 446
Sequences: 2223 651 195
Seq/Len: 11.12 2.48 0.44
MirrorTree (Pazo et al. 2001) 0.46
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 0.02 0.00
2 0.00 0.02 0.00
5 0.01 0.02 0.00
10 0.01 0.02 0.00
20 0.01 0.02 0.01
100 0.02 0.02 0.04
∞ 0.03 0.02 0.42
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
135_L 84_Q 2.19 0.90 0.49
14_C 236_I 1.53 0.55 0.11
23_G 250_K 1.36 0.42 0.06
86_L 230_V 1.30 0.38 0.05
100_L 173_L 1.27 0.35 0.04
5_A 145_F 1.26 0.35 0.04
153_V 81_P 1.26 0.35 0.04
142_R 15_A 1.24 0.34 0.04
176_N 241_L 1.23 0.33 0.04
10_A 220_A 1.23 0.33 0.04
172_V 141_L 1.23 0.33 0.04
18_F 206_D 1.22 0.32 0.04
191_L 52_Q 1.22 0.32 0.04
199_G 112_P 1.21 0.32 0.04
105_G 240_V 1.21 0.32 0.04
21_V 224_M 1.20 0.31 0.04
78_D 69_L 1.19 0.31 0.03
102_A 94_I 1.18 0.30 0.03
54_M 42_F 1.17 0.29 0.03
150_A 99_T 1.14 0.27 0.03
153_V 44_Q 1.13 0.27 0.03
188_T 27_H 1.12 0.26 0.03
159_I 240_V 1.10 0.25 0.02
83_K 108_T 1.09 0.24 0.02
169_R 80_L 1.09 0.24 0.02
130_E 63_G 1.08 0.24 0.02
101_L 88_Y 1.08 0.24 0.02
29_S 112_P 1.08 0.24 0.02
150_A 206_D 1.08 0.24 0.02
145_L 206_D 1.07 0.23 0.02
129_V 42_F 1.06 0.23 0.02
92_L 240_V 1.05 0.23 0.02
123_A 194_Q 1.05 0.22 0.02
167_R 253_W 1.04 0.22 0.02
14_C 130_R 1.04 0.22 0.02
153_V 224_M 1.04 0.22 0.02
80_A 46_Q 1.02 0.21 0.02
107_A 152_E 1.02 0.21 0.02
151_G 219_T 1.02 0.21 0.02
47_Q 23_H 1.02 0.21 0.02
21_V 30_D 1.01 0.20 0.02
135_L 166_K 1.01 0.20 0.02
87_A 154_I 1.01 0.20 0.02
19_M 156_A 1.01 0.20 0.02
98_V 106_V 1.00 0.20 0.02
83_K 154_I 1.00 0.20 0.02
80_A 213_A 1.00 0.20 0.02
110_G 90_A 1.00 0.20 0.02
172_V 144_L 1.00 0.20 0.02
77_V 78_P 0.99 0.20 0.02
147_F 49_R 0.99 0.20 0.02
17_G 229_Q 0.99 0.19 0.01
77_V 35_F 0.99 0.19 0.01
190_E 152_E 0.99 0.19 0.01
186_A 214_A 0.98 0.19 0.01
132_T 105_R 0.98 0.19 0.01
109_S 94_I 0.98 0.19 0.01
191_L 241_L 0.98 0.19 0.01
21_V 41_K 0.97 0.19 0.01
108_F 93_D 0.97 0.18 0.01
188_T 237_F 0.97 0.18 0.01
171_D 100_E 0.96 0.18 0.01
183_R 200_G 0.96 0.18 0.01
86_L 155_H 0.96 0.18 0.01
20_V 219_T 0.96 0.18 0.01
115_D 97_P 0.96 0.18 0.01
109_S 209_A 0.96 0.18 0.01
94_L 215_F 0.96 0.18 0.01
65_A 94_I 0.96 0.18 0.01
97_G 167_E 0.96 0.18 0.01
137_L 236_I 0.96 0.18 0.01
195_K 216_L 0.95 0.18 0.01
96_I 121_P 0.95 0.17 0.01
13_A 94_I 0.94 0.17 0.01
30_V 220_A 0.94 0.17 0.01
135_L 42_F 0.94 0.17 0.01
22_I 254_Q 0.94 0.17 0.01
198_Q 254_Q 0.93 0.17 0.01
105_G 205_V 0.93 0.17 0.01
189_M 74_D 0.93 0.17 0.01
158_M 207_Q 0.93 0.17 0.01
179_E 193_D 0.93 0.17 0.01
116_Q 158_L 0.93 0.17 0.01
10_A 74_D 0.92 0.17 0.01
197_G 40_G 0.92 0.16 0.01
12_S 107_P 0.91 0.16 0.01
89_Y 237_F 0.91 0.16 0.01
137_L 51_L 0.91 0.16 0.01
146_M 164_E 0.91 0.16 0.01
38_L 44_Q 0.91 0.16 0.01
99_V 157_V 0.90 0.16 0.01
48_G 76_G 0.90 0.15 0.01
47_Q 184_I 0.89 0.15 0.01
5_A 223_K 0.89 0.15 0.01
183_R 53_V 0.88 0.15 0.01
176_N 100_E 0.88 0.15 0.01
17_G 36_E 0.88 0.15 0.01
188_T 254_Q 0.88 0.15 0.01
191_L 237_F 0.88 0.15 0.01
21_V 38_P 0.88 0.15 0.01
86_L 255_P 0.88 0.15 0.01
10_A 77_G 0.88 0.15 0.01
38_L 134_H 0.88 0.15 0.01
135_L 66_Y 0.88 0.15 0.01
146_M 155_H 0.87 0.15 0.01
151_G 174_Y 0.87 0.15 0.01
86_L 154_I 0.87 0.15 0.01
100_L 163_G 0.87 0.14 0.01
57_V 9_T 0.87 0.14 0.01
170_K 256_I 0.87 0.14 0.01
105_G 106_V 0.87 0.14 0.01
90_L 180_A 0.86 0.14 0.01
97_G 161_Y 0.86 0.14 0.01
169_R 81_P 0.86 0.14 0.01
32_W 145_F 0.86 0.14 0.01
163_V 244_L 0.86 0.14 0.01
15_V 47_L 0.85 0.14 0.01
28_H 80_L 0.85 0.14 0.01
77_V 143_Q 0.85 0.14 0.01
92_L 202_P 0.85 0.14 0.01
51_F 68_P 0.85 0.14 0.01
191_L 166_K 0.85 0.14 0.01
19_M 99_T 0.85 0.14 0.01
104_L 240_V 0.85 0.14 0.01
129_V 74_D 0.84 0.13 0.01
90_L 149_G 0.84 0.13 0.01
151_G 176_N 0.84 0.13 0.01
90_L 243_A 0.84 0.13 0.01
47_Q 22_S 0.84 0.13 0.01
138_V 242_A 0.84 0.13 0.01
141_D 140_G 0.84 0.13 0.01
4_F 26_A 0.83 0.13 0.01
183_R 40_G 0.83 0.13 0.01
78_D 43_D 0.83 0.13 0.01
148_Q 71_T 0.83 0.13 0.01
98_V 254_Q 0.82 0.13 0.01
186_A 9_T 0.82 0.13 0.01
61_V 157_V 0.82 0.13 0.01
83_K 59_S 0.82 0.13 0.01
79_F 43_D 0.82 0.13 0.01
160_G 146_N 0.82 0.13 0.01
38_L 141_L 0.82 0.13 0.01
102_A 14_G 0.82 0.13 0.01
116_Q 233_V 0.82 0.13 0.01
182_W 243_A 0.82 0.13 0.01
79_F 214_A 0.82 0.13 0.01
104_L 107_P 0.82 0.13 0.01
19_M 165_E 0.82 0.13 0.01
21_V 170_G 0.82 0.13 0.01
21_V 55_T 0.82 0.13 0.01
14_C 82_E 0.81 0.12 0.01
97_G 152_E 0.81 0.12 0.01
17_G 225_M 0.81 0.12 0.01
150_A 6_A 0.81 0.12 0.01
101_L 177_A 0.81 0.12 0.01
39_S 134_H 0.81 0.12 0.01
34_I 70_R 0.81 0.12 0.01
158_M 153_Y 0.81 0.12 0.01
36_A 210_T 0.81 0.12 0.01
39_S 187_A 0.81 0.12 0.01
9_F 241_L 0.81 0.12 0.01
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
2924 0.44 cI_J_10_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.49 Done - Shared
2923 0.33 cI_J_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2922 0.65 cI_J_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2921 0.41 cI_J_40_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
2920 0.44 cI_J_cIII_cyt1_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
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