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OPENSEQ.org
Consensus-DUF-consensus-N-same-genome-Jackhmmer
Genes: A B A+B
Length: 145 406 539
Sequences: 313 5807 224
Seq/Len: 2.16 14.3 0.42
MirrorTree (Pazo et al. 2001) 0.73
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
143_A 333_L 1.37 0.41 0.00
109_M 272_S 1.35 0.40 0.00
94_V 95_K 1.30 0.36 0.00
96_T 311_L 1.21 0.31 0.00
17_T 318_R 1.19 0.30 0.00
55_I 154_I 1.12 0.26 0.00
128_A 240_N 1.11 0.25 0.00
71_V 368_T 1.10 0.24 0.00
19_W 329_F 1.10 0.24 0.00
16_F 229_M 1.08 0.23 0.00
107_G 322_Y 1.07 0.23 0.00
72_L 274_A 1.03 0.21 0.00
99_D 261_F 1.02 0.20 0.00
143_A 216_H 1.01 0.20 0.00
30_L 347_S 1.00 0.19 0.00
114_L 332_V 0.99 0.19 0.00
131_S 94_D 0.98 0.19 0.00
44_R 280_L 0.98 0.18 0.00
23_A 402_E 0.97 0.18 0.00
128_A 224_S 0.97 0.18 0.00
16_F 177_R 0.97 0.18 0.00
127_A 48_Q 0.95 0.17 0.00
125_L 127_I 0.95 0.17 0.00
72_L 128_I 0.95 0.17 0.00
127_A 92_V 0.94 0.17 0.00
10_L 235_R 0.94 0.17 0.00
105_R 92_V 0.94 0.17 0.00
125_L 78_L 0.94 0.17 0.00
127_A 316_G 0.93 0.16 0.00
76_S 58_M 0.93 0.16 0.00
143_A 100_L 0.93 0.16 0.00
59_R 171_I 0.92 0.16 0.00
49_T 163_G 0.92 0.16 0.00
17_T 198_R 0.92 0.16 0.00
30_L 308_A 0.91 0.16 0.00
86_L 364_Q 0.91 0.15 0.00
99_D 349_L 0.91 0.15 0.00
4_Q 310_R 0.91 0.15 0.00
16_F 102_S 0.90 0.15 0.00
128_A 219_A 0.90 0.15 0.00
8_A 246_T 0.89 0.15 0.00
73_Y 389_A 0.89 0.15 0.00
116_G 311_L 0.89 0.15 0.00
133_L 184_V 0.89 0.15 0.00
14_A 331_M 0.89 0.15 0.00
20_P 362_G 0.89 0.15 0.00
109_M 93_R 0.88 0.14 0.00
83_Q 385_L 0.88 0.14 0.00
69_C 296_G 0.88 0.14 0.00
93_P 58_M 0.88 0.14 0.00
112_L 281_L 0.87 0.14 0.00
109_M 377_I 0.86 0.14 0.00
48_K 112_D 0.86 0.14 0.00
125_L 215_F 0.86 0.14 0.00
75_G 401_A 0.86 0.14 0.00
40_S 162_T 0.86 0.14 0.00
16_F 149_S 0.86 0.14 0.00
142_L 291_I 0.86 0.14 0.00
72_L 168_A 0.86 0.14 0.00
115_E 118_I 0.85 0.14 0.00
128_A 59_T 0.85 0.14 0.00
134_R 51_L 0.85 0.14 0.00
85_L 356_P 0.85 0.14 0.00
13_F 145_A 0.85 0.13 0.00
7_A 347_S 0.84 0.13 0.00
72_L 375_M 0.84 0.13 0.00
72_L 209_E 0.84 0.13 0.00
40_S 94_D 0.84 0.13 0.00
96_T 256_A 0.84 0.13 0.00
117_G 381_S 0.84 0.13 0.00
95_L 329_F 0.84 0.13 0.00
99_D 240_N 0.84 0.13 0.00
142_L 236_L 0.84 0.13 0.00
74_I 348_A 0.83 0.13 0.00
112_L 330_A 0.83 0.13 0.00
16_F 67_V 0.83 0.13 0.00
16_F 233_Q 0.83 0.13 0.00
70_H 283_L 0.83 0.13 0.00
102_G 100_L 0.83 0.13 0.00
123_I 311_L 0.83 0.13 0.00
141_R 21_M 0.82 0.12 0.00
111_C 228_E 0.82 0.12 0.00
31_C 323_R 0.82 0.12 0.00
70_H 320_K 0.82 0.12 0.00
13_F 221_D 0.82 0.12 0.00
122_E 191_T 0.82 0.12 0.00
108_G 237_Q 0.82 0.12 0.00
13_F 74_A 0.81 0.12 0.00
120_R 336_V 0.81 0.12 0.00
135_I 352_I 0.81 0.12 0.00
55_I 97_Q 0.81 0.12 0.00
111_C 50_N 0.81 0.12 0.00
136_S 147_D 0.81 0.12 0.00
50_V 234_L 0.81 0.12 0.00
33_L 380_A 0.81 0.12 0.00
85_L 215_F 0.81 0.12 0.00
134_R 173_I 0.80 0.12 0.00
53_R 368_T 0.80 0.12 0.00
96_T 125_A 0.80 0.12 0.00
16_F 12_F 0.80 0.12 0.00
138_K 62_L 0.80 0.12 0.00
108_G 149_S 0.80 0.12 0.00
93_P 318_R 0.80 0.12 0.00
62_S 168_A 0.80 0.12 0.00
72_L 354_N 0.80 0.12 0.00
54_P 19_I 0.79 0.12 0.00
49_T 256_A 0.79 0.12 0.00
79_P 117_F 0.79 0.12 0.00
124_N 214_E 0.79 0.12 0.00
50_V 368_T 0.79 0.12 0.00
9_Y 365_T 0.79 0.12 0.00
104_C 164_C 0.79 0.11 0.00
138_K 64_A 0.79 0.11 0.00
74_I 28_M 0.79 0.11 0.00
95_L 298_A 0.79 0.11 0.00
143_A 54_T 0.79 0.11 0.00
119_V 404_L 0.79 0.11 0.00
35_D 78_L 0.79 0.11 0.00
107_G 265_I 0.79 0.11 0.00
123_I 374_A 0.79 0.11 0.00
140_L 296_G 0.78 0.11 0.00
144_R 366_T 0.78 0.11 0.00
52_G 242_Q 0.78 0.11 0.00
129_A 44_K 0.78 0.11 0.00
137_S 18_N 0.78 0.11 0.00
60_L 391_H 0.78 0.11 0.00
140_L 380_A 0.78 0.11 0.00
143_A 383_E 0.77 0.11 0.00
28_L 127_I 0.77 0.11 0.00
16_F 341_E 0.77 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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