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OPENSEQ.org
Consensus-DUF-consensus-N-same-genome
Genes: A B A+B
Length: 145 406 546
Sequences: 253 765 153
Seq/Len: 1.74 1.88 0.28
MirrorTree (Pazo et al. 2001) 0.78
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.23
2 0.00 0.00 0.23
5 0.00 0.00 0.23
10 0.00 0.00 0.23
20 0.00 0.00 0.23
100 0.00 0.01 0.23
∞ 0.01 0.10 0.28
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
53_R 229_M 1.24 0.25 0.00
42_L 130_P 1.23 0.24 0.00
72_L 83_Q 1.22 0.24 0.00
109_M 27_T 1.22 0.24 0.00
69_C 329_F 1.17 0.22 0.00
130_R 197_V 1.17 0.21 0.00
16_F 356_P 1.16 0.21 0.00
132_G 221_D 1.15 0.21 0.00
125_L 143_L 1.15 0.21 0.00
122_E 186_A 1.11 0.19 0.00
16_F 163_G 1.10 0.19 0.00
5_L 385_L 1.10 0.19 0.00
141_R 180_H 1.09 0.18 0.00
96_T 263_S 1.09 0.18 0.00
97_V 12_F 1.07 0.18 0.00
73_Y 183_L 1.07 0.18 0.00
142_L 172_A 1.06 0.17 0.00
66_A 371_I 1.06 0.17 0.00
105_R 283_L 1.05 0.17 0.00
135_I 171_I 1.05 0.17 0.00
56_R 162_T 1.05 0.17 0.00
69_C 258_R 1.05 0.17 0.00
69_C 323_R 1.05 0.17 0.00
111_C 225_L 1.04 0.17 0.00
12_N 282_F 1.04 0.16 0.00
42_L 35_L 1.03 0.16 0.00
50_V 90_A 1.03 0.16 0.00
128_A 224_S 1.02 0.16 0.00
96_T 256_A 1.02 0.16 0.00
104_C 225_L 1.02 0.16 0.00
20_P 304_L 1.01 0.15 0.00
32_V 281_L 1.01 0.15 0.00
47_G 331_M 1.01 0.15 0.00
144_R 307_I 1.00 0.15 0.00
123_I 368_T 1.00 0.15 0.00
137_S 225_L 1.00 0.15 0.00
119_V 283_L 0.99 0.15 0.00
5_L 362_G 0.98 0.14 0.00
140_L 243_L 0.98 0.14 0.00
128_A 59_T 0.98 0.14 0.00
116_G 93_R 0.97 0.14 0.00
144_R 24_I 0.97 0.14 0.00
143_A 244_L 0.96 0.14 0.00
131_S 247_A 0.96 0.14 0.00
7_A 228_E 0.96 0.14 0.00
89_L 317_L 0.96 0.14 0.00
110_I 50_N 0.96 0.14 0.00
112_L 294_T 0.95 0.14 0.00
123_I 143_L 0.95 0.14 0.00
140_L 261_F 0.95 0.14 0.00
73_Y 50_N 0.95 0.13 0.00
138_K 280_L 0.95 0.13 0.00
137_S 103_W 0.94 0.13 0.00
75_G 201_R 0.94 0.13 0.00
110_I 145_A 0.94 0.13 0.00
41_A 315_G 0.94 0.13 0.00
94_V 86_Q 0.94 0.13 0.00
71_V 347_S 0.93 0.13 0.00
109_M 312_A 0.93 0.13 0.00
124_N 47_A 0.93 0.13 0.00
73_Y 92_V 0.93 0.13 0.00
99_D 179_L 0.93 0.13 0.00
69_C 301_D 0.93 0.13 0.00
25_G 381_S 0.93 0.13 0.00
63_A 155_W 0.93 0.13 0.00
69_C 296_G 0.92 0.12 0.00
71_V 368_T 0.92 0.12 0.00
110_I 225_L 0.92 0.12 0.00
6_K 53_L 0.92 0.12 0.00
69_C 257_N 0.92 0.12 0.00
69_C 250_D 0.92 0.12 0.00
55_I 131_I 0.92 0.12 0.00
98_S 76_E 0.92 0.12 0.00
16_F 330_A 0.92 0.12 0.00
143_A 66_V 0.91 0.12 0.00
39_A 187_L 0.91 0.12 0.00
130_R 164_C 0.91 0.12 0.00
107_G 92_V 0.91 0.12 0.00
32_V 110_P 0.90 0.12 0.00
19_W 257_N 0.90 0.12 0.00
139_L 50_N 0.90 0.12 0.00
14_A 368_T 0.89 0.12 0.00
59_R 264_G 0.89 0.12 0.00
127_A 307_I 0.89 0.12 0.00
130_R 362_G 0.88 0.12 0.00
94_V 186_A 0.88 0.11 0.00
113_V 256_A 0.88 0.11 0.00
31_C 329_F 0.88 0.11 0.00
129_A 321_A 0.88 0.11 0.00
10_L 265_I 0.88 0.11 0.00
84_Q 236_L 0.88 0.11 0.00
136_S 397_K 0.88 0.11 0.00
74_I 92_V 0.88 0.11 0.00
112_L 359_L 0.88 0.11 0.00
21_A 14_R 0.87 0.11 0.00
29_R 370_S 0.87 0.11 0.00
16_F 341_E 0.87 0.11 0.00
36_D 166_L 0.86 0.11 0.00
107_G 139_G 0.86 0.11 0.00
96_T 190_I 0.86 0.11 0.00
139_L 240_N 0.86 0.11 0.00
97_V 18_N 0.86 0.11 0.00
30_L 199_S 0.86 0.11 0.00
98_S 311_L 0.86 0.11 0.00
104_C 50_N 0.86 0.11 0.00
10_L 12_F 0.86 0.11 0.00
7_A 151_S 0.85 0.11 0.00
137_S 61_S 0.85 0.11 0.00
52_G 55_A 0.85 0.11 0.00
12_N 285_G 0.85 0.11 0.00
123_I 141_V 0.85 0.11 0.00
120_R 145_A 0.85 0.11 0.00
73_Y 64_A 0.85 0.11 0.00
15_K 367_M 0.85 0.11 0.00
84_Q 104_H 0.85 0.11 0.00
54_P 21_M 0.85 0.10 0.00
16_F 381_S 0.85 0.10 0.00
99_D 161_L 0.85 0.10 0.00
27_P 100_L 0.85 0.10 0.00
102_G 273_D 0.84 0.10 0.00
16_F 104_H 0.84 0.10 0.00
135_I 225_L 0.84 0.10 0.00
104_C 67_V 0.84 0.10 0.00
13_F 400_R 0.84 0.10 0.00
136_S 81_L 0.84 0.10 0.00
114_L 143_L 0.84 0.10 0.00
97_V 225_L 0.84 0.10 0.00
18_R 63_E 0.84 0.10 0.00
73_Y 401_A 0.84 0.10 0.00
101_E 11_T 0.84 0.10 0.00
97_V 213_A 0.84 0.10 0.00
52_G 374_A 0.84 0.10 0.00
44_R 283_L 0.84 0.10 0.00
83_Q 345_I 0.84 0.10 0.00
32_V 263_S 0.83 0.10 0.00
16_F 43_L 0.83 0.10 0.00
69_C 253_T 0.83 0.10 0.00
110_I 353_F 0.83 0.10 0.00
13_F 145_A 0.83 0.10 0.00
55_I 188_K 0.83 0.10 0.00
52_G 342_V 0.83 0.10 0.00
39_A 147_D 0.83 0.10 0.00
16_F 193_V 0.83 0.10 0.00
134_R 173_I 0.83 0.10 0.00
85_L 167_L 0.83 0.10 0.00
142_L 243_L 0.82 0.10 0.00
107_G 322_Y 0.82 0.10 0.00
109_M 92_V 0.82 0.10 0.00
26_A 98_N 0.82 0.10 0.00
11_Y 315_G 0.82 0.10 0.00
137_S 195_H 0.82 0.10 0.00
122_E 282_F 0.82 0.10 0.00
134_R 207_V 0.82 0.10 0.00
96_T 271_N 0.82 0.10 0.00
42_L 237_Q 0.82 0.10 0.00
119_V 77_T 0.81 0.10 0.00
66_A 171_I 0.81 0.10 0.00
141_R 215_F 0.81 0.10 0.00
107_G 131_I 0.81 0.10 0.00
99_D 240_N 0.81 0.10 0.00
113_V 203_F 0.81 0.10 0.00
124_N 66_V 0.81 0.10 0.00
96_T 22_T 0.81 0.10 0.00
89_L 94_D 0.81 0.10 0.00
32_V 78_L 0.81 0.10 0.00
101_E 306_E 0.81 0.10 0.00
143_A 175_L 0.81 0.10 0.00
123_I 230_E 0.80 0.10 0.00
17_T 311_L 0.80 0.10 0.00
64_D 264_G 0.80 0.10 0.00
70_H 345_I 0.80 0.10 0.00
17_T 71_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
1245 0.27 Consensus-DUF-consensus-N-within1 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1244 0.28 Consensus-DUF-consensus-N-within20 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1238 0.42 Consensus-DUF-consensus-N-same-genome-Jackhmmer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1237 0.28 Consensus-DUF-consensus-N-same-genome Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
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