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OPENSEQ.org
cI_F_cIII_cyt1
Genes: A B A+B
Length: 184 263 428
Sequences: 2037 574 177
Seq/Len: 11.07 2.18 0.41
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.01 0.01 0.04
∞ 0.02 0.02 0.40
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
129_V 84_Q 1.89 0.76 0.03
17_L 206_D 1.62 0.59 0.02
13_I 236_I 1.45 0.47 0.01
144_A 99_T 1.45 0.47 0.01
79_S 46_Q 1.43 0.45 0.01
101_A 94_I 1.42 0.44 0.01
77_G 69_L 1.38 0.42 0.01
22_H 250_K 1.34 0.39 0.01
166_E 141_L 1.29 0.36 0.01
144_A 206_D 1.25 0.33 0.01
37_L 134_H 1.21 0.30 0.01
142_E 181_G 1.20 0.30 0.01
82_E 108_T 1.20 0.30 0.01
38_A 249_N 1.19 0.29 0.01
98_I 20_G 1.18 0.29 0.01
99_L 250_K 1.18 0.28 0.01
85_R 230_V 1.18 0.28 0.01
129_V 42_F 1.17 0.28 0.01
46_L 184_I 1.14 0.26 0.00
11_I 141_L 1.14 0.26 0.00
93_W 215_F 1.14 0.26 0.00
79_S 214_A 1.13 0.25 0.00
133_L 46_Q 1.12 0.25 0.00
64_M 94_I 1.12 0.25 0.00
126_A 105_R 1.12 0.25 0.00
170_N 241_L 1.11 0.25 0.00
4_A 146_N 1.11 0.25 0.00
20_I 224_M 1.10 0.24 0.00
166_E 144_L 1.09 0.23 0.00
28_A 112_P 1.08 0.23 0.00
4_A 223_K 1.08 0.23 0.00
18_R 156_A 1.08 0.23 0.00
50_F 187_A 1.08 0.23 0.00
13_I 130_R 1.07 0.23 0.00
167_V 154_I 1.07 0.23 0.00
20_I 55_T 1.07 0.22 0.00
47_G 220_A 1.06 0.22 0.00
3_F 105_R 1.06 0.22 0.00
79_S 213_A 1.05 0.21 0.00
145_S 219_T 1.05 0.21 0.00
103_M 249_N 1.04 0.21 0.00
106_V 152_E 1.04 0.21 0.00
131_I 51_L 1.03 0.20 0.00
109_Y 90_A 1.02 0.20 0.00
101_A 12_P 1.02 0.20 0.00
136_P 15_A 1.01 0.20 0.00
144_A 6_A 1.01 0.20 0.00
53_A 42_F 1.01 0.20 0.00
9_G 68_P 1.00 0.19 0.00
21_T 254_Q 1.00 0.19 0.00
177_K 200_G 0.99 0.19 0.00
57_I 154_I 0.99 0.19 0.00
101_A 63_G 0.98 0.18 0.00
163_R 191_S 0.98 0.18 0.00
4_A 145_F 0.98 0.18 0.00
44_F 213_A 0.98 0.18 0.00
97_A 106_V 0.97 0.18 0.00
83_Q 166_K 0.97 0.18 0.00
121_G 137_Y 0.96 0.17 0.00
83_Q 161_Y 0.96 0.17 0.00
19_V 219_T 0.96 0.17 0.00
16_T 243_A 0.96 0.17 0.00
4_A 147_G 0.95 0.17 0.00
11_I 198_E 0.95 0.17 0.00
127_K 240_V 0.94 0.17 0.00
40_S 46_Q 0.94 0.17 0.00
129_V 149_G 0.94 0.17 0.00
153_V 240_V 0.94 0.17 0.00
163_R 105_R 0.94 0.17 0.00
22_H 26_A 0.94 0.17 0.00
38_A 182_N 0.94 0.16 0.00
171_R 59_S 0.93 0.16 0.00
149_L 87_A 0.93 0.16 0.00
15_A 128_K 0.93 0.16 0.00
43_F 181_G 0.93 0.16 0.00
129_V 187_A 0.92 0.16 0.00
107_I 93_D 0.92 0.16 0.00
117_Q 194_Q 0.92 0.16 0.00
3_F 85_V 0.92 0.15 0.00
18_R 165_E 0.91 0.15 0.00
103_M 100_E 0.91 0.15 0.00
22_H 240_V 0.91 0.15 0.00
153_V 235_V 0.90 0.15 0.00
76_L 35_F 0.90 0.15 0.00
147_L 209_A 0.90 0.15 0.00
99_L 173_L 0.90 0.15 0.00
147_L 44_Q 0.90 0.15 0.00
95_G 258_H 0.89 0.14 0.00
176_A 243_A 0.89 0.14 0.00
108_V 209_A 0.89 0.14 0.00
85_R 80_L 0.88 0.14 0.00
170_N 179_F 0.88 0.14 0.00
20_I 41_K 0.88 0.14 0.00
13_I 111_F 0.88 0.14 0.00
50_F 137_Y 0.88 0.14 0.00
9_G 220_A 0.88 0.14 0.00
58_V 221_E 0.88 0.14 0.00
76_L 78_P 0.88 0.14 0.00
16_T 225_M 0.88 0.14 0.00
138_V 91_N 0.87 0.14 0.00
132_T 236_I 0.87 0.14 0.00
87_W 242_A 0.87 0.14 0.00
47_G 166_K 0.87 0.14 0.00
10_L 151_P 0.87 0.14 0.00
43_F 135_G 0.87 0.14 0.00
121_G 12_P 0.87 0.14 0.00
140_A 243_A 0.87 0.14 0.00
139_L 206_D 0.87 0.14 0.00
16_T 38_P 0.86 0.13 0.00
153_V 136_P 0.86 0.13 0.00
21_T 52_Q 0.86 0.13 0.00
144_A 46_Q 0.85 0.13 0.00
52_G 129_A 0.85 0.13 0.00
54_L 249_N 0.85 0.13 0.00
122_T 60_A 0.85 0.13 0.00
85_R 86_R 0.85 0.13 0.00
46_L 171_A 0.85 0.13 0.00
135_G 140_G 0.85 0.13 0.00
31_Y 145_F 0.85 0.13 0.00
85_R 154_I 0.85 0.13 0.00
45_S 179_F 0.85 0.13 0.00
146_M 13_A 0.85 0.13 0.00
20_I 38_P 0.84 0.13 0.00
118_G 94_I 0.84 0.13 0.00
37_L 141_L 0.84 0.13 0.00
17_L 13_A 0.84 0.13 0.00
20_I 30_D 0.84 0.13 0.00
57_I 88_Y 0.83 0.13 0.00
100_S 177_A 0.83 0.13 0.00
163_R 251_K 0.83 0.12 0.00
90_P 152_E 0.83 0.12 0.00
28_A 198_E 0.83 0.12 0.00
100_S 88_Y 0.83 0.12 0.00
10_L 59_S 0.83 0.12 0.00
173_D 193_D 0.83 0.12 0.00
47_G 174_Y 0.83 0.12 0.00
56_I 111_F 0.82 0.12 0.00
50_F 126_M 0.82 0.12 0.00
38_A 134_H 0.82 0.12 0.00
50_F 102_D 0.82 0.12 0.00
130_G 141_L 0.82 0.12 0.00
54_L 182_N 0.82 0.12 0.00
123_P 246_Y 0.82 0.12 0.00
83_Q 92_F 0.82 0.12 0.00
46_L 23_H 0.82 0.12 0.00
38_A 51_L 0.82 0.12 0.00
140_A 155_H 0.82 0.12 0.00
51_A 147_G 0.82 0.12 0.00
54_L 36_E 0.81 0.12 0.00
117_Q 113_T 0.81 0.12 0.00
108_V 47_L 0.81 0.12 0.00
164_A 55_T 0.81 0.12 0.00
78_G 214_A 0.81 0.12 0.00
18_R 99_T 0.81 0.12 0.00
136_P 143_Q 0.81 0.12 0.00
104_L 240_V 0.81 0.12 0.00
117_Q 209_A 0.81 0.12 0.00
27_H 199_D 0.81 0.12 0.00
110_A 226_D 0.80 0.12 0.00
123_P 213_A 0.80 0.12 0.00
123_P 74_D 0.80 0.12 0.00
33_I 154_I 0.80 0.12 0.00
56_I 256_I 0.80 0.12 0.00
23_T 255_P 0.80 0.12 0.00
167_V 52_Q 0.80 0.12 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
2421 0.65 cI_F_cIII_cyt1_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2293 0.41 cI_F_cIII_cyt1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.03 Done - Shared
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