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OPENSEQ.org
cI_J_cIII_cyt1_40_Pdenitr
Genes: A B A+B
Length: 200 263 444
Sequences: 2148 570 147
Seq/Len: 10.74 2.17 0.33
MirrorTree (Pazo et al. 2001) 0.41
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 0.03
∞ 0.03 0.02 0.32
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
80_A 46_Q 1.43 0.40 0.00
14_C 130_R 1.38 0.36 0.00
47_Q 184_I 1.36 0.35 0.00
135_L 84_Q 1.35 0.34 0.00
23_G 250_K 1.34 0.34 0.00
172_V 141_L 1.34 0.34 0.00
102_A 94_I 1.31 0.32 0.00
39_S 249_N 1.29 0.30 0.00
77_V 77_G 1.27 0.29 0.00
188_T 27_H 1.27 0.29 0.00
17_G 225_M 1.27 0.29 0.00
78_D 69_L 1.26 0.29 0.00
137_L 51_L 1.22 0.27 0.00
18_F 206_D 1.22 0.27 0.00
21_V 224_M 1.22 0.27 0.00
155_L 87_A 1.19 0.25 0.00
10_A 74_D 1.18 0.24 0.00
29_S 112_P 1.17 0.24 0.00
105_G 205_V 1.16 0.23 0.00
23_G 240_V 1.15 0.23 0.00
54_M 42_F 1.14 0.23 0.00
57_V 111_F 1.12 0.22 0.00
100_L 173_L 1.11 0.21 0.00
101_L 88_Y 1.11 0.21 0.00
153_V 44_Q 1.11 0.21 0.00
190_E 152_E 1.10 0.21 0.00
110_G 90_A 1.10 0.21 0.00
83_K 108_T 1.09 0.20 0.00
80_A 213_A 1.09 0.20 0.00
86_L 230_V 1.09 0.20 0.00
171_D 100_E 1.07 0.20 0.00
132_T 105_R 1.07 0.19 0.00
5_A 36_E 1.06 0.19 0.00
139_L 144_L 1.06 0.19 0.00
84_G 166_K 1.06 0.19 0.00
197_G 38_P 1.05 0.19 0.00
38_L 134_H 1.05 0.18 0.00
39_S 182_N 1.04 0.18 0.00
38_L 144_L 1.04 0.18 0.00
150_A 46_Q 1.03 0.18 0.00
80_A 214_A 1.03 0.18 0.00
8_L 212_V 1.02 0.17 0.00
44_F 181_G 1.02 0.17 0.00
153_V 224_M 1.02 0.17 0.00
88_R 207_Q 1.02 0.17 0.00
148_Q 181_G 1.02 0.17 0.00
14_C 236_I 1.01 0.17 0.00
11_I 59_S 1.00 0.17 0.00
5_A 223_K 0.99 0.16 0.00
41_A 46_Q 0.98 0.16 0.00
130_E 104_P 0.98 0.16 0.00
83_K 145_F 0.98 0.16 0.00
187_K 85_V 0.98 0.16 0.00
142_R 15_A 0.98 0.16 0.00
139_L 190_L 0.98 0.16 0.00
159_I 240_V 0.98 0.16 0.00
169_R 191_S 0.97 0.16 0.00
159_I 82_E 0.97 0.16 0.00
21_V 30_D 0.97 0.16 0.00
170_K 59_S 0.97 0.16 0.00
52_V 143_Q 0.97 0.15 0.00
150_A 99_T 0.97 0.15 0.00
77_V 78_P 0.97 0.15 0.00
44_F 135_G 0.96 0.15 0.00
15_V 47_L 0.96 0.15 0.00
185_P 143_Q 0.96 0.15 0.00
190_E 246_Y 0.96 0.15 0.00
57_V 8_G 0.95 0.15 0.00
99_V 157_V 0.95 0.15 0.00
109_S 47_L 0.95 0.15 0.00
19_M 99_T 0.95 0.15 0.00
146_M 155_H 0.95 0.15 0.00
104_L 249_N 0.95 0.15 0.00
196_P 196_T 0.95 0.15 0.00
19_M 156_A 0.95 0.15 0.00
32_W 33_F 0.95 0.15 0.00
153_V 157_V 0.95 0.15 0.00
189_M 64_L 0.95 0.15 0.00
173_K 154_I 0.94 0.14 0.00
89_Y 232_F 0.94 0.14 0.00
57_V 245_L 0.94 0.14 0.00
58_V 154_I 0.94 0.14 0.00
39_S 134_H 0.93 0.14 0.00
186_A 209_A 0.93 0.14 0.00
5_A 142_S 0.93 0.14 0.00
100_L 53_V 0.93 0.14 0.00
188_T 254_Q 0.93 0.14 0.00
22_I 52_Q 0.93 0.14 0.00
48_G 174_Y 0.92 0.14 0.00
97_G 93_D 0.92 0.14 0.00
4_F 228_K 0.92 0.14 0.00
153_V 247_L 0.92 0.14 0.00
168_H 130_R 0.92 0.14 0.00
182_W 33_F 0.92 0.14 0.00
97_G 161_Y 0.91 0.14 0.00
191_L 107_P 0.91 0.14 0.00
21_V 38_P 0.91 0.14 0.00
170_K 55_T 0.91 0.14 0.00
40_A 15_A 0.91 0.14 0.00
79_F 214_A 0.91 0.13 0.00
90_L 106_V 0.91 0.13 0.00
179_E 193_D 0.91 0.13 0.00
57_V 9_T 0.91 0.13 0.00
182_W 243_A 0.91 0.13 0.00
51_F 187_A 0.91 0.13 0.00
188_T 237_F 0.90 0.13 0.00
150_A 205_V 0.90 0.13 0.00
10_A 68_P 0.90 0.13 0.00
176_N 100_E 0.89 0.13 0.00
98_V 106_V 0.89 0.13 0.00
129_V 74_D 0.89 0.13 0.00
161_A 244_L 0.89 0.13 0.00
150_A 112_P 0.89 0.13 0.00
123_A 194_Q 0.89 0.13 0.00
135_L 42_F 0.89 0.13 0.00
142_R 204_T 0.88 0.13 0.00
21_V 41_K 0.88 0.13 0.00
101_L 177_A 0.88 0.13 0.00
174_R 96_D 0.88 0.12 0.00
80_A 67_V 0.88 0.12 0.00
20_V 219_T 0.88 0.12 0.00
169_R 69_L 0.87 0.12 0.00
142_R 102_D 0.87 0.12 0.00
102_A 63_G 0.87 0.12 0.00
13_A 94_I 0.87 0.12 0.00
159_I 161_Y 0.87 0.12 0.00
101_L 242_A 0.86 0.12 0.00
98_V 10_T 0.86 0.12 0.00
102_A 12_P 0.86 0.12 0.00
103_Q 249_N 0.86 0.12 0.00
21_V 55_T 0.86 0.12 0.00
123_A 209_A 0.86 0.12 0.00
119_S 193_D 0.86 0.12 0.00
92_L 240_V 0.86 0.12 0.00
133_L 134_H 0.86 0.12 0.00
5_A 146_N 0.86 0.12 0.00
22_I 254_Q 0.85 0.12 0.00
52_V 228_K 0.85 0.12 0.00
176_N 179_F 0.85 0.12 0.00
141_D 138_G 0.85 0.12 0.00
125_V 93_D 0.85 0.12 0.00
45_V 77_G 0.85 0.12 0.00
137_L 236_I 0.85 0.12 0.00
65_A 94_I 0.84 0.12 0.00
115_D 42_F 0.84 0.12 0.00
57_V 242_A 0.84 0.11 0.00
139_L 206_D 0.84 0.11 0.00
89_Y 112_P 0.84 0.11 0.00
99_V 81_P 0.84 0.11 0.00
150_A 206_D 0.84 0.11 0.00
94_L 234_S 0.84 0.11 0.00
191_L 203_A 0.84 0.11 0.00
4_F 105_R 0.84 0.11 0.00
5_A 208_M 0.83 0.11 0.00
95_V 101_E 0.83 0.11 0.00
189_M 11_A 0.83 0.11 0.00
48_G 166_K 0.83 0.11 0.00
167_R 253_W 0.83 0.11 0.00
100_L 65_R 0.82 0.11 0.00
5_A 249_N 0.82 0.11 0.00
101_L 34_S 0.82 0.11 0.00
10_A 196_T 0.82 0.11 0.00
141_D 114_V 0.82 0.11 0.00
111_W 251_K 0.82 0.11 0.00
189_M 74_D 0.82 0.11 0.00
32_W 154_I 0.82 0.11 0.00
169_R 251_K 0.82 0.11 0.00
102_A 204_T 0.82 0.11 0.00
144_V 91_N 0.82 0.11 0.00
127_A 166_K 0.82 0.11 0.00
145_L 206_D 0.82 0.11 0.00
196_P 168_E 0.82 0.11 0.00
77_V 232_F 0.82 0.11 0.00
129_V 42_F 0.82 0.11 0.00
133_L 59_S 0.81 0.11 0.00
100_L 250_K 0.81 0.11 0.00
77_V 35_F 0.81 0.11 0.00
123_A 94_I 0.81 0.11 0.00
191_L 250_K 0.81 0.11 0.00
12_S 107_P 0.81 0.11 0.00
99_V 20_G 0.81 0.11 0.00
150_A 224_M 0.81 0.11 0.00
171_D 67_V 0.81 0.11 0.00
122_A 42_F 0.81 0.11 0.00
135_L 149_G 0.81 0.11 0.00
29_S 224_M 0.81 0.10 0.00
15_V 67_V 0.81 0.10 0.00
159_I 52_Q 0.80 0.10 0.00
150_A 32_S 0.80 0.10 0.00
39_S 51_L 0.80 0.10 0.00
100_L 95_T 0.80 0.10 0.00
8_L 57_V 0.80 0.10 0.00
115_D 243_A 0.80 0.10 0.00
135_L 96_D 0.80 0.10 0.00
86_L 155_H 0.80 0.10 0.00
176_N 203_A 0.80 0.10 0.00
139_L 209_A 0.80 0.10 0.00
14_C 116_G 0.80 0.10 0.00
185_P 63_G 0.80 0.10 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
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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