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OPENSEQ.org
Consensus-DUF-consensus-N-within20
Genes: A B A+B
Length: 145 406 535
Sequences: 313 5807 151
Seq/Len: 2.16 14.3 0.28
MirrorTree (Pazo et al. 2001) 0.90
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 1.51 0.41 0.00
109_M 190_I 1.44 0.36 0.00
45_L 92_V 1.39 0.33 0.00
125_L 127_I 1.35 0.31 0.00
136_S 64_A 1.31 0.29 0.00
109_M 272_S 1.30 0.28 0.00
143_A 333_L 1.30 0.28 0.00
128_A 224_S 1.26 0.26 0.00
92_K 331_M 1.24 0.25 0.00
125_L 183_L 1.21 0.24 0.00
136_S 81_L 1.21 0.24 0.00
104_C 225_L 1.20 0.23 0.00
128_A 59_T 1.18 0.22 0.00
125_L 143_L 1.18 0.22 0.00
111_C 225_L 1.17 0.22 0.00
15_K 303_V 1.17 0.22 0.00
143_A 100_L 1.17 0.21 0.00
20_P 362_G 1.14 0.20 0.00
69_C 327_D 1.14 0.20 0.00
130_R 197_V 1.13 0.20 0.00
59_R 171_I 1.13 0.20 0.00
110_I 225_L 1.12 0.20 0.00
137_S 225_L 1.12 0.20 0.00
19_W 329_F 1.12 0.19 0.00
96_T 311_L 1.11 0.19 0.00
14_A 331_M 1.10 0.19 0.00
122_E 282_F 1.09 0.18 0.00
49_T 163_G 1.09 0.18 0.00
13_F 145_A 1.09 0.18 0.00
13_F 374_A 1.09 0.18 0.00
9_Y 82_G 1.09 0.18 0.00
139_L 240_N 1.08 0.18 0.00
98_S 246_T 1.08 0.18 0.00
75_G 103_W 1.08 0.18 0.00
13_F 221_D 1.07 0.18 0.00
55_I 97_Q 1.07 0.17 0.00
99_D 349_L 1.07 0.17 0.00
126_D 228_E 1.07 0.17 0.00
106_Q 92_V 1.07 0.17 0.00
138_K 64_A 1.06 0.17 0.00
121_F 243_L 1.06 0.17 0.00
111_C 228_E 1.06 0.17 0.00
72_L 274_A 1.06 0.17 0.00
120_R 336_V 1.06 0.17 0.00
72_L 168_A 1.05 0.17 0.00
143_A 216_H 1.05 0.17 0.00
75_G 53_L 1.05 0.17 0.00
42_L 254_G 1.05 0.17 0.00
137_S 212_I 1.04 0.16 0.00
119_V 283_L 1.04 0.16 0.00
27_P 98_N 1.03 0.16 0.00
143_A 54_T 1.03 0.16 0.00
97_V 308_A 1.03 0.16 0.00
126_D 50_N 1.03 0.16 0.00
31_C 327_D 1.03 0.16 0.00
104_C 212_I 1.02 0.16 0.00
11_Y 123_F 1.02 0.16 0.00
104_C 240_N 1.02 0.16 0.00
98_S 357_F 1.02 0.16 0.00
110_I 212_I 1.01 0.15 0.00
28_L 190_I 1.01 0.15 0.00
121_F 310_R 1.01 0.15 0.00
75_G 221_D 1.00 0.15 0.00
108_G 160_V 1.00 0.15 0.00
7_A 146_R 1.00 0.15 0.00
9_Y 183_L 1.00 0.15 0.00
96_T 373_Y 1.00 0.15 0.00
61_S 25_F 1.00 0.15 0.00
110_I 133_H 1.00 0.15 0.00
32_V 263_S 0.99 0.15 0.00
28_L 157_S 0.99 0.15 0.00
94_V 95_K 0.99 0.15 0.00
140_L 243_L 0.99 0.15 0.00
45_L 186_A 0.99 0.14 0.00
97_V 18_N 0.99 0.14 0.00
25_G 320_K 0.98 0.14 0.00
129_A 321_A 0.98 0.14 0.00
121_F 206_R 0.98 0.14 0.00
107_G 139_G 0.98 0.14 0.00
36_D 315_G 0.98 0.14 0.00
104_C 153_F 0.98 0.14 0.00
96_T 65_A 0.97 0.14 0.00
84_Q 104_H 0.97 0.14 0.00
99_D 179_L 0.97 0.14 0.00
134_R 173_I 0.97 0.14 0.00
83_Q 382_A 0.97 0.14 0.00
121_F 282_F 0.97 0.14 0.00
18_R 201_R 0.96 0.14 0.00
128_A 272_S 0.96 0.14 0.00
136_S 286_D 0.96 0.14 0.00
110_I 216_H 0.96 0.14 0.00
142_L 330_A 0.96 0.14 0.00
111_C 212_I 0.96 0.14 0.00
108_G 230_E 0.96 0.14 0.00
142_L 310_R 0.95 0.14 0.00
108_G 278_S 0.95 0.13 0.00
97_V 193_V 0.95 0.13 0.00
107_G 322_Y 0.95 0.13 0.00
132_G 64_A 0.94 0.13 0.00
135_I 332_V 0.94 0.13 0.00
104_C 228_E 0.94 0.13 0.00
71_V 39_S 0.94 0.13 0.00
142_L 291_I 0.94 0.13 0.00
128_A 240_N 0.94 0.13 0.00
52_G 291_I 0.93 0.13 0.00
93_P 330_A 0.93 0.13 0.00
62_S 280_L 0.93 0.13 0.00
73_Y 402_E 0.93 0.13 0.00
69_C 250_D 0.93 0.13 0.00
69_C 253_T 0.93 0.13 0.00
69_C 258_R 0.93 0.13 0.00
69_C 284_D 0.93 0.13 0.00
69_C 292_N 0.93 0.13 0.00
69_C 296_G 0.93 0.13 0.00
69_C 300_G 0.93 0.13 0.00
69_C 301_D 0.93 0.13 0.00
69_C 304_L 0.93 0.13 0.00
69_C 323_R 0.93 0.13 0.00
69_C 372_G 0.93 0.13 0.00
110_I 145_A 0.93 0.13 0.00
91_G 164_C 0.93 0.13 0.00
13_F 126_P 0.92 0.12 0.00
19_W 327_D 0.92 0.12 0.00
86_L 58_M 0.92 0.12 0.00
75_G 201_R 0.92 0.12 0.00
20_P 155_W 0.92 0.12 0.00
33_L 218_F 0.92 0.12 0.00
121_F 327_D 0.92 0.12 0.00
109_M 186_A 0.91 0.12 0.00
144_R 24_I 0.91 0.12 0.00
111_C 153_F 0.91 0.12 0.00
137_S 57_T 0.91 0.12 0.00
72_L 175_L 0.91 0.12 0.00
111_C 53_L 0.91 0.12 0.00
96_T 256_A 0.91 0.12 0.00
61_S 272_S 0.90 0.12 0.00
111_C 50_N 0.90 0.12 0.00
55_I 188_K 0.90 0.12 0.00
86_L 311_L 0.90 0.12 0.00
80_A 59_T 0.90 0.12 0.00
116_G 38_T 0.90 0.12 0.00
133_L 126_P 0.90 0.12 0.00
21_A 141_V 0.90 0.12 0.00
110_I 153_F 0.90 0.12 0.00
136_S 285_G 0.90 0.12 0.00
8_A 357_F 0.90 0.12 0.00
14_A 40_V 0.90 0.12 0.00
81_Q 191_T 0.89 0.12 0.00
14_A 121_W 0.89 0.12 0.00
123_I 311_L 0.89 0.12 0.00
34_G 224_S 0.89 0.12 0.00
123_I 230_E 0.89 0.12 0.00
111_C 240_N 0.89 0.12 0.00
63_A 87_F 0.89 0.12 0.00
141_R 42_T 0.89 0.12 0.00
85_L 197_V 0.89 0.12 0.00
107_G 347_S 0.89 0.12 0.00
108_G 153_F 0.89 0.12 0.00
141_R 377_I 0.89 0.12 0.00
144_R 171_I 0.88 0.12 0.00
108_G 345_I 0.88 0.12 0.00
121_F 261_F 0.88 0.12 0.00
121_F 325_G 0.88 0.12 0.00
130_R 50_N 0.88 0.12 0.00
110_I 285_G 0.88 0.11 0.00
135_I 93_R 0.88 0.11 0.00
18_R 63_E 0.88 0.11 0.00
73_Y 103_W 0.87 0.11 0.00
85_L 105_Y 0.87 0.11 0.00
136_S 34_L 0.87 0.11 0.00
29_R 11_T 0.87 0.11 0.00
110_I 402_E 0.87 0.11 0.00
119_V 64_A 0.87 0.11 0.00
111_C 221_D 0.87 0.11 0.00
111_C 145_A 0.87 0.11 0.00
107_G 265_I 0.87 0.11 0.00
110_I 228_E 0.87 0.11 0.00
16_F 356_P 0.87 0.11 0.00
112_L 394_Y 0.87 0.11 0.00
52_G 105_Y 0.86 0.11 0.00
124_N 299_T 0.86 0.11 0.00
56_R 354_N 0.86 0.11 0.00
122_E 186_A 0.86 0.11 0.00
48_K 112_D 0.86 0.11 0.00
9_Y 402_E 0.86 0.11 0.00
110_I 164_C 0.86 0.11 0.00
143_A 270_N 0.86 0.11 0.00
20_P 74_A 0.86 0.11 0.00
9_Y 365_T 0.86 0.11 0.00
9_Y 285_G 0.86 0.11 0.00
108_G 369_L 0.86 0.11 0.00
140_L 250_D 0.86 0.11 0.00
140_L 253_T 0.86 0.11 0.00
140_L 258_R 0.86 0.11 0.00
140_L 284_D 0.86 0.11 0.00
140_L 292_N 0.86 0.11 0.00
140_L 296_G 0.86 0.11 0.00
140_L 300_G 0.86 0.11 0.00
140_L 301_D 0.86 0.11 0.00
140_L 304_L 0.86 0.11 0.00
140_L 323_R 0.86 0.11 0.00
140_L 372_G 0.86 0.11 0.00
97_V 341_E 0.86 0.11 0.00
36_D 109_D 0.85 0.11 0.00
99_D 240_N 0.85 0.11 0.00
18_R 177_R 0.85 0.11 0.00
59_R 141_V 0.85 0.11 0.00
141_R 180_H 0.85 0.11 0.00
38_F 43_L 0.85 0.11 0.00
124_N 254_G 0.85 0.11 0.00
104_C 53_L 0.85 0.11 0.00
102_G 332_V 0.85 0.10 0.00
120_R 145_A 0.85 0.10 0.00
55_I 283_L 0.85 0.10 0.00
133_L 67_V 0.84 0.10 0.00
8_A 20_S 0.84 0.10 0.00
55_I 307_I 0.84 0.10 0.00
141_R 332_V 0.84 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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