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OPENSEQ.org
MinDZ
Genes: A B A+B
Length: 383 270 630
Sequences: 2759 13894 133
Seq/Len: 7.2 51.46 0.21
MirrorTree (Pazo et al. 2001) 0.35
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 0.01 0.03 0.02
2 0.01 0.04 0.02
5 0.01 0.05 0.04
10 0.01 0.07 0.08
20 0.01 0.08 0.20
100 0.02 0.12 0.95
∞ 0.04 0.17 2.91
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
94_G 34_T 1.32 0.24 0.00
215_T 239_Y 1.31 0.24 0.00
86_D 141_I 1.16 0.18 0.00
284_A 242_T 1.16 0.17 0.00
218_S 247_L 1.14 0.17 0.00
180_D 117_I 1.11 0.16 0.00
262_V 28_A 1.11 0.16 0.00
129_A 232_N 1.09 0.15 0.00
373_D 7_V 1.09 0.15 0.00
308_V 242_T 1.07 0.15 0.00
141_K 27_L 1.06 0.14 0.00
102_A 145_P 1.06 0.14 0.00
217_M 217_V 1.04 0.14 0.00
206_M 29_Q 1.04 0.14 0.00
143_M 119_C 1.04 0.14 0.00
100_I 37_I 1.04 0.14 0.00
206_M 87_P 1.02 0.13 0.00
38_E 214_D 1.01 0.13 0.00
60_I 155_R 1.00 0.13 0.00
299_D 33_K 0.99 0.12 0.00
208_V 170_G 0.98 0.12 0.00
40_F 50_M 0.97 0.12 0.00
115_V 34_T 0.97 0.12 0.00
244_I 70_L 0.96 0.12 0.00
100_I 106_L 0.96 0.12 0.00
90_A 180_L 0.96 0.12 0.00
294_I 19_S 0.94 0.11 0.00
289_N 7_V 0.93 0.11 0.00
100_I 32_K 0.93 0.11 0.00
265_T 224_G 0.92 0.11 0.00
306_L 33_K 0.92 0.11 0.00
171_V 243_V 0.92 0.11 0.00
78_R 199_V 0.91 0.10 0.00
121_K 217_V 0.91 0.10 0.00
11_A 167_A 0.90 0.10 0.00
240_A 106_L 0.90 0.10 0.00
40_F 116_F 0.90 0.10 0.00
21_G 87_P 0.89 0.10 0.00
167_K 119_C 0.89 0.10 0.00
208_V 204_R 0.89 0.10 0.00
303_N 196_M 0.89 0.10 0.00
88_L 243_V 0.88 0.10 0.00
21_G 216_S 0.88 0.10 0.00
88_L 200_L 0.87 0.10 0.00
306_L 186_G 0.87 0.10 0.00
343_G 85_I 0.87 0.10 0.00
245_S 146_E 0.86 0.10 0.00
150_I 74_L 0.86 0.09 0.00
101_A 21_A 0.85 0.09 0.00
64_I 238_A 0.84 0.09 0.00
155_K 25_T 0.84 0.09 0.00
224_M 227_V 0.84 0.09 0.00
52_T 140_I 0.84 0.09 0.00
76_V 60_F 0.84 0.09 0.00
155_K 4_I 0.84 0.09 0.00
155_K 37_I 0.84 0.09 0.00
270_L 68_A 0.83 0.09 0.00
277_T 249_E 0.83 0.09 0.00
159_S 17_T 0.83 0.09 0.00
234_D 117_I 0.83 0.09 0.00
40_F 60_F 0.83 0.09 0.00
31_R 19_S 0.83 0.09 0.00
129_A 221_S 0.82 0.09 0.00
44_T 40_D 0.82 0.09 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)
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