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OPENSEQ.org
cI_J_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 200 263 446
Sequences: 2148 651 195
Seq/Len: 10.74 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 0.00
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 2.12 0.87 0.33
100_L 173_L 1.44 0.48 0.06
153_V 81_P 1.41 0.46 0.05
5_A 145_F 1.28 0.37 0.03
191_L 52_Q 1.26 0.35 0.03
172_V 141_L 1.26 0.35 0.03
10_A 220_A 1.23 0.33 0.03
83_K 108_T 1.23 0.33 0.03
78_D 69_L 1.21 0.32 0.03
176_N 241_L 1.21 0.31 0.03
159_I 240_V 1.20 0.31 0.03
94_L 215_F 1.19 0.30 0.02
23_G 250_K 1.18 0.30 0.02
102_A 94_I 1.18 0.30 0.02
86_L 230_V 1.17 0.29 0.02
18_F 206_D 1.15 0.28 0.02
142_R 15_A 1.13 0.27 0.02
92_L 240_V 1.13 0.27 0.02
21_V 224_M 1.13 0.27 0.02
188_T 27_H 1.12 0.26 0.02
105_G 240_V 1.11 0.26 0.02
14_C 236_I 1.11 0.26 0.02
29_S 112_P 1.11 0.25 0.02
137_L 51_L 1.10 0.25 0.02
150_A 99_T 1.10 0.25 0.02
54_M 42_F 1.10 0.25 0.02
99_V 157_V 1.09 0.25 0.02
171_D 100_E 1.07 0.23 0.01
86_L 155_H 1.06 0.23 0.01
145_L 206_D 1.06 0.23 0.01
105_G 205_V 1.06 0.23 0.01
123_A 194_Q 1.06 0.23 0.01
169_R 80_L 1.05 0.22 0.01
150_A 206_D 1.04 0.22 0.01
167_R 253_W 1.04 0.22 0.01
21_V 30_D 1.04 0.22 0.01
80_A 46_Q 1.04 0.22 0.01
20_V 219_T 1.03 0.21 0.01
77_V 35_F 1.03 0.21 0.01
10_A 74_D 1.03 0.21 0.01
101_L 88_Y 1.02 0.21 0.01
153_V 44_Q 1.02 0.21 0.01
186_A 214_A 1.02 0.21 0.01
137_L 236_I 1.02 0.21 0.01
87_A 154_I 1.02 0.21 0.01
172_V 144_L 1.01 0.21 0.01
190_E 152_E 1.01 0.20 0.01
189_M 74_D 1.01 0.20 0.01
97_G 167_E 1.00 0.20 0.01
195_K 216_L 1.00 0.20 0.01
132_T 105_R 1.00 0.20 0.01
110_G 90_A 1.00 0.20 0.01
151_G 219_T 0.99 0.20 0.01
30_V 220_A 0.99 0.19 0.01
77_V 78_P 0.99 0.19 0.01
99_V 81_P 0.99 0.19 0.01
147_F 49_R 0.99 0.19 0.01
96_I 121_P 0.98 0.19 0.01
188_T 237_F 0.98 0.19 0.01
107_A 152_E 0.97 0.19 0.01
130_E 63_G 0.97 0.19 0.01
101_L 177_A 0.97 0.18 0.01
21_V 41_K 0.97 0.18 0.01
38_L 141_L 0.96 0.18 0.01
191_L 166_K 0.95 0.18 0.01
47_Q 23_H 0.95 0.18 0.01
22_I 254_Q 0.95 0.18 0.01
38_L 44_Q 0.95 0.17 0.01
146_M 164_E 0.94 0.17 0.01
17_G 229_Q 0.94 0.17 0.01
183_R 200_G 0.94 0.17 0.01
21_V 38_P 0.94 0.17 0.01
38_L 134_H 0.94 0.17 0.01
14_C 130_R 0.94 0.17 0.01
13_A 94_I 0.93 0.17 0.01
129_V 42_F 0.93 0.17 0.01
80_A 213_A 0.93 0.17 0.01
19_M 156_A 0.93 0.17 0.01
169_R 81_P 0.93 0.17 0.01
191_L 241_L 0.93 0.17 0.01
163_V 244_L 0.92 0.16 0.01
61_V 157_V 0.91 0.16 0.01
65_A 94_I 0.91 0.16 0.01
10_A 196_T 0.91 0.16 0.01
123_A 94_I 0.91 0.16 0.01
127_A 12_P 0.91 0.16 0.01
32_W 145_F 0.91 0.16 0.01
95_V 86_R 0.91 0.16 0.01
135_L 166_K 0.91 0.16 0.01
158_M 207_Q 0.91 0.16 0.01
146_M 155_H 0.90 0.16 0.01
51_F 180_A 0.90 0.16 0.01
187_K 35_F 0.90 0.16 0.01
122_A 42_F 0.90 0.15 0.01
39_S 249_N 0.90 0.15 0.01
176_N 100_E 0.90 0.15 0.01
47_Q 184_I 0.89 0.15 0.01
100_L 250_K 0.89 0.15 0.01
98_V 106_V 0.89 0.15 0.01
109_S 244_L 0.89 0.15 0.01
17_G 225_M 0.89 0.15 0.01
148_Q 71_T 0.89 0.15 0.01
183_R 53_V 0.89 0.15 0.01
8_L 212_V 0.89 0.15 0.01
19_M 99_T 0.89 0.15 0.01
90_L 149_G 0.88 0.15 0.01
39_S 187_A 0.88 0.15 0.01
115_D 243_A 0.88 0.15 0.01
153_V 224_M 0.88 0.15 0.01
20_V 142_S 0.88 0.15 0.01
129_V 10_T 0.88 0.15 0.01
86_L 255_P 0.87 0.15 0.01
188_T 254_Q 0.87 0.15 0.01
195_K 154_I 0.87 0.14 0.01
149_L 215_F 0.87 0.14 0.01
141_D 140_G 0.87 0.14 0.01
53_A 250_K 0.87 0.14 0.01
135_L 42_F 0.87 0.14 0.01
104_L 249_N 0.86 0.14 0.01
170_K 256_I 0.86 0.14 0.01
179_E 193_D 0.86 0.14 0.01
23_G 240_V 0.86 0.14 0.01
135_L 66_Y 0.86 0.14 0.01
57_V 111_F 0.86 0.14 0.01
12_S 107_P 0.86 0.14 0.01
57_V 9_T 0.86 0.14 0.01
183_R 40_G 0.86 0.14 0.01
114_S 17_Q 0.85 0.14 0.01
182_W 33_F 0.85 0.14 0.01
12_S 38_P 0.85 0.14 0.01
94_L 166_K 0.85 0.14 0.01
77_V 143_Q 0.85 0.14 0.01
192_K 152_E 0.85 0.14 0.01
83_K 59_S 0.85 0.14 0.01
129_V 74_D 0.85 0.14 0.01
78_D 43_D 0.84 0.13 0.01
186_A 209_A 0.84 0.13 0.01
157_A 154_I 0.84 0.13 0.01
89_Y 237_F 0.84 0.13 0.01
17_G 36_E 0.84 0.13 0.01
79_F 214_A 0.84 0.13 0.01
79_F 43_D 0.84 0.13 0.01
159_I 188_A 0.84 0.13 0.01
66_V 244_L 0.84 0.13 0.01
149_L 45_H 0.83 0.13 0.01
151_G 174_Y 0.83 0.13 0.01
104_L 197_Y 0.83 0.13 0.01
196_P 196_T 0.83 0.13 0.01
10_A 68_P 0.83 0.13 0.01
105_G 156_A 0.83 0.13 0.01
83_K 154_I 0.83 0.13 0.01
21_V 170_G 0.83 0.13 0.01
186_A 9_T 0.83 0.13 0.01
10_A 77_G 0.82 0.13 0.01
151_G 176_N 0.82 0.13 0.01
21_V 55_T 0.82 0.13 0.01
15_V 47_L 0.82 0.13 0.01
92_L 82_E 0.82 0.13 0.01
5_A 36_E 0.82 0.13 0.01
102_A 12_P 0.82 0.13 0.01
170_K 55_T 0.82 0.13 0.01
46_L 235_V 0.82 0.13 0.01
163_V 219_T 0.82 0.13 0.01
184_D 96_D 0.82 0.13 0.01
10_A 92_F 0.82 0.12 0.01
176_N 179_F 0.81 0.12 0.01
5_A 147_G 0.81 0.12 0.01
4_F 36_E 0.81 0.12 0.01
34_I 70_R 0.81 0.12 0.01
84_G 161_Y 0.81 0.12 0.01
183_R 186_M 0.81 0.12 0.01
105_G 106_V 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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