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OPENSEQ.org
Consensus-DUF-consensus-N-within1
Genes: A B A+B
Length: 145 406 534
Sequences: 313 5807 146
Seq/Len: 2.16 14.3 0.27
MirrorTree (Pazo et al. 2001) 0.91
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 0.26
2 0.00 0.01 0.27
5 0.00 0.02 0.27
10 0.00 0.02 0.27
20 0.00 0.03 0.27
100 0.00 0.07 0.30
∞ 0.01 0.15 0.41
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
71_V 368_T 1.64 0.48 0.00
45_L 92_V 1.57 0.43 0.00
97_V 308_A 1.46 0.37 0.00
122_E 282_F 1.40 0.33 0.00
128_A 224_S 1.37 0.31 0.00
136_S 64_A 1.35 0.30 0.00
55_I 97_Q 1.34 0.29 0.00
109_M 190_I 1.33 0.29 0.00
104_C 225_L 1.30 0.28 0.00
136_S 81_L 1.30 0.27 0.00
128_A 59_T 1.29 0.27 0.00
13_F 374_A 1.29 0.27 0.00
109_M 272_S 1.28 0.26 0.00
69_C 327_D 1.26 0.26 0.00
137_S 225_L 1.26 0.25 0.00
111_C 225_L 1.26 0.25 0.00
125_L 183_L 1.22 0.23 0.00
125_L 143_L 1.20 0.23 0.00
110_I 225_L 1.20 0.23 0.00
15_K 303_V 1.19 0.22 0.00
31_C 327_D 1.16 0.20 0.00
59_R 171_I 1.15 0.20 0.00
121_F 243_L 1.14 0.20 0.00
20_P 362_G 1.14 0.20 0.00
92_K 331_M 1.14 0.20 0.00
13_F 145_A 1.13 0.20 0.00
130_R 197_V 1.13 0.19 0.00
125_L 127_I 1.12 0.19 0.00
82_L 303_V 1.11 0.19 0.00
7_A 146_R 1.10 0.18 0.00
72_L 168_A 1.10 0.18 0.00
45_L 186_A 1.09 0.18 0.00
132_G 64_A 1.09 0.18 0.00
49_T 163_G 1.09 0.18 0.00
107_G 322_Y 1.08 0.18 0.00
138_K 64_A 1.08 0.17 0.00
143_A 333_L 1.07 0.17 0.00
13_F 221_D 1.06 0.17 0.00
143_A 216_H 1.06 0.17 0.00
119_V 283_L 1.05 0.17 0.00
121_F 206_R 1.05 0.17 0.00
133_L 126_P 1.05 0.16 0.00
9_Y 82_G 1.04 0.16 0.00
71_V 39_S 1.04 0.16 0.00
72_L 274_A 1.03 0.16 0.00
94_V 95_K 1.03 0.16 0.00
28_L 190_I 1.03 0.16 0.00
33_L 380_A 1.02 0.15 0.00
91_G 164_C 1.02 0.15 0.00
104_C 153_F 1.02 0.15 0.00
126_D 50_N 1.02 0.15 0.00
111_C 50_N 1.02 0.15 0.00
135_I 99_I 1.01 0.15 0.00
18_R 201_R 1.01 0.15 0.00
129_A 321_A 1.01 0.15 0.00
9_Y 183_L 1.01 0.15 0.00
134_R 173_I 1.01 0.15 0.00
11_Y 123_F 1.00 0.15 0.00
61_S 25_F 1.00 0.15 0.00
136_S 286_D 0.99 0.14 0.00
96_T 256_A 0.99 0.14 0.00
135_I 352_I 0.99 0.14 0.00
122_E 166_L 0.99 0.14 0.00
143_A 100_L 0.99 0.14 0.00
108_G 278_S 0.99 0.14 0.00
14_A 331_M 0.99 0.14 0.00
34_G 224_S 0.99 0.14 0.00
28_L 157_S 0.99 0.14 0.00
104_C 212_I 0.99 0.14 0.00
140_L 243_L 0.98 0.14 0.00
111_C 53_L 0.98 0.14 0.00
98_S 246_T 0.98 0.14 0.00
110_I 133_H 0.98 0.14 0.00
81_Q 191_T 0.98 0.14 0.00
110_I 212_I 0.98 0.14 0.00
126_D 228_E 0.98 0.14 0.00
108_G 160_V 0.98 0.14 0.00
36_D 315_G 0.97 0.14 0.00
142_L 291_I 0.97 0.14 0.00
130_R 298_A 0.97 0.14 0.00
106_Q 92_V 0.97 0.14 0.00
70_H 281_L 0.97 0.14 0.00
143_A 54_T 0.97 0.14 0.00
110_I 153_F 0.97 0.14 0.00
139_L 240_N 0.97 0.14 0.00
73_Y 103_W 0.96 0.14 0.00
75_G 221_D 0.96 0.14 0.00
63_A 87_F 0.96 0.14 0.00
84_Q 104_H 0.96 0.14 0.00
52_G 291_I 0.96 0.13 0.00
56_R 354_N 0.96 0.13 0.00
59_R 141_V 0.95 0.13 0.00
88_K 97_Q 0.95 0.13 0.00
96_T 311_L 0.95 0.13 0.00
32_V 263_S 0.94 0.13 0.00
14_A 40_V 0.94 0.13 0.00
75_G 53_L 0.94 0.13 0.00
112_L 303_V 0.94 0.13 0.00
97_V 18_N 0.94 0.13 0.00
8_A 357_F 0.94 0.13 0.00
111_C 153_F 0.94 0.13 0.00
108_G 369_L 0.93 0.13 0.00
109_M 186_A 0.93 0.13 0.00
104_C 240_N 0.93 0.13 0.00
142_L 310_R 0.93 0.13 0.00
121_F 261_F 0.93 0.13 0.00
143_A 270_N 0.93 0.12 0.00
27_P 98_N 0.93 0.12 0.00
108_G 230_E 0.93 0.12 0.00
29_R 11_T 0.93 0.12 0.00
130_R 50_N 0.93 0.12 0.00
111_C 228_E 0.92 0.12 0.00
132_G 176_T 0.92 0.12 0.00
75_G 103_W 0.92 0.12 0.00
20_P 155_W 0.92 0.12 0.00
12_N 282_F 0.92 0.12 0.00
95_L 331_M 0.92 0.12 0.00
104_C 53_L 0.92 0.12 0.00
12_N 225_L 0.92 0.12 0.00
135_I 93_R 0.91 0.12 0.00
111_C 212_I 0.91 0.12 0.00
137_S 212_I 0.91 0.12 0.00
116_G 38_T 0.91 0.12 0.00
143_A 30_L 0.91 0.12 0.00
33_L 218_F 0.91 0.12 0.00
110_I 145_A 0.91 0.12 0.00
48_K 112_D 0.91 0.12 0.00
140_L 393_M 0.91 0.12 0.00
137_S 57_T 0.91 0.12 0.00
28_L 291_I 0.91 0.12 0.00
86_L 311_L 0.90 0.12 0.00
104_C 228_E 0.90 0.12 0.00
21_A 141_V 0.90 0.12 0.00
128_A 272_S 0.90 0.12 0.00
42_L 130_P 0.90 0.12 0.00
110_I 216_H 0.90 0.12 0.00
80_A 59_T 0.90 0.12 0.00
25_G 320_K 0.89 0.12 0.00
55_I 283_L 0.89 0.12 0.00
125_L 64_A 0.89 0.12 0.00
38_F 43_L 0.89 0.11 0.00
93_P 41_L 0.89 0.11 0.00
8_A 20_S 0.88 0.11 0.00
143_A 340_S 0.88 0.11 0.00
144_R 24_I 0.88 0.11 0.00
104_C 46_Y 0.88 0.11 0.00
119_V 64_A 0.88 0.11 0.00
14_A 121_W 0.88 0.11 0.00
78_E 294_T 0.88 0.11 0.00
19_W 250_D 0.88 0.11 0.00
19_W 253_T 0.88 0.11 0.00
19_W 258_R 0.88 0.11 0.00
19_W 284_D 0.88 0.11 0.00
19_W 292_N 0.88 0.11 0.00
19_W 296_G 0.88 0.11 0.00
19_W 297_H 0.88 0.11 0.00
19_W 300_G 0.88 0.11 0.00
19_W 301_D 0.88 0.11 0.00
19_W 304_L 0.88 0.11 0.00
19_W 323_R 0.88 0.11 0.00
19_W 326_G 0.88 0.11 0.00
19_W 328_E 0.88 0.11 0.00
19_W 329_F 0.88 0.11 0.00
19_W 372_G 0.88 0.11 0.00
19_W 390_D 0.88 0.11 0.00
64_D 291_I 0.88 0.11 0.00
128_A 240_N 0.88 0.11 0.00
116_G 134_N 0.88 0.11 0.00
111_C 145_A 0.88 0.11 0.00
76_S 58_M 0.88 0.11 0.00
13_F 126_P 0.88 0.11 0.00
70_H 254_G 0.88 0.11 0.00
107_G 139_G 0.88 0.11 0.00
34_G 141_V 0.88 0.11 0.00
43_S 146_R 0.88 0.11 0.00
12_N 203_F 0.87 0.11 0.00
18_R 63_E 0.87 0.11 0.00
16_F 151_S 0.87 0.11 0.00
141_R 332_V 0.87 0.11 0.00
49_T 256_A 0.87 0.11 0.00
55_I 165_I 0.87 0.11 0.00
141_R 42_T 0.87 0.11 0.00
104_C 50_N 0.87 0.11 0.00
133_L 240_N 0.87 0.11 0.00
74_I 161_L 0.87 0.11 0.00
117_G 315_G 0.87 0.11 0.00
126_D 53_L 0.87 0.11 0.00
142_L 90_A 0.87 0.11 0.00
120_R 150_I 0.87 0.11 0.00
69_C 250_D 0.87 0.11 0.00
69_C 253_T 0.87 0.11 0.00
69_C 258_R 0.87 0.11 0.00
69_C 284_D 0.87 0.11 0.00
69_C 292_N 0.87 0.11 0.00
69_C 296_G 0.87 0.11 0.00
69_C 297_H 0.87 0.11 0.00
69_C 300_G 0.87 0.11 0.00
69_C 301_D 0.87 0.11 0.00
69_C 304_L 0.87 0.11 0.00
69_C 323_R 0.87 0.11 0.00
69_C 326_G 0.87 0.11 0.00
69_C 328_E 0.87 0.11 0.00
69_C 329_F 0.87 0.11 0.00
69_C 372_G 0.87 0.11 0.00
69_C 390_D 0.87 0.11 0.00
139_L 50_N 0.86 0.11 0.00
84_Q 339_E 0.86 0.11 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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