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OPENSEQ.org
IscSHscB
Genes: A B A+B
Length: 404 171 570
Sequences: 31466 3234 292
Seq/Len: 77.89 18.91 0.51
MirrorTree (Pazo et al. 2001) 0.75
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 0.07 0.01 0.01
2 0.09 0.01 0.03
5 0.11 0.01 0.51
10 0.12 0.02 0.55
20 0.15 0.02 0.63
100 0.25 0.03 0.99
∞ 0.29 0.05 1.75
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
383_L 152_R 1.50 0.57 0.00
174_G 165_E 1.44 0.52 0.00
377_I 45_L 1.33 0.44 0.00
71_F 152_R 1.26 0.39 0.00
71_F 69_E 1.24 0.37 0.00
58_I 56_Q 1.23 0.36 0.00
58_I 69_E 1.23 0.36 0.00
70_V 27_L 1.22 0.36 0.00
399_I 51_S 1.22 0.35 0.00
230_M 149_R 1.21 0.35 0.00
383_L 114_L 1.21 0.35 0.00
71_F 45_L 1.17 0.32 0.00
306_N 47_A 1.15 0.31 0.00
383_L 1_M 1.15 0.31 0.00
102_T 132_M 1.14 0.30 0.00
376_S 52_A 1.14 0.30 0.00
79_D 28_Q 1.13 0.30 0.00
360_F 135_Q 1.12 0.29 0.00
161_Q 132_M 1.11 0.28 0.00
196_K 63_H 1.10 0.28 0.00
391_K 140_T 1.10 0.28 0.00
63_G 31_Y 1.06 0.25 0.00
369_T 25_Q 1.06 0.25 0.00
28_T 157_L 1.06 0.25 0.00
388_E 152_R 1.06 0.25 0.00
62_V 58_W 1.05 0.25 0.00
20_A 72_L 1.02 0.23 0.00
67_R 2_D 1.00 0.22 0.00
52_D 56_Q 0.99 0.21 0.00
394_V 74_L 0.99 0.21 0.00
161_Q 136_L 0.99 0.21 0.00
383_L 56_Q 0.98 0.21 0.00
332_S 100_E 0.97 0.20 0.00
196_K 156_K 0.96 0.20 0.00
119_F 119_K 0.96 0.20 0.00
52_D 69_E 0.95 0.20 0.00
256_Y 23_R 0.93 0.18 0.00
26_F 24_F 0.93 0.18 0.00
317_L 21_S 0.93 0.18 0.00
98_I 15_L 0.92 0.18 0.00
184_S 88_D 0.92 0.18 0.00
390_Y 43_E 0.92 0.18 0.00
102_T 136_L 0.92 0.18 0.00
353_I 44_Q 0.92 0.18 0.00
360_F 25_Q 0.92 0.18 0.00
7_L 156_K 0.92 0.18 0.00
299_N 141_W 0.91 0.17 0.00
116_R 95_Q 0.91 0.17 0.00
230_M 78_D 0.90 0.17 0.00
306_N 57_A 0.90 0.17 0.00
230_M 29_R 0.90 0.17 0.00
172_A 132_M 0.90 0.17 0.00
134_L 132_M 0.90 0.17 0.00
265_T 15_L 0.89 0.17 0.00
70_V 23_R 0.89 0.17 0.00
184_S 21_S 0.89 0.17 0.00
160_V 83_Q 0.89 0.17 0.00
111_C 88_D 0.89 0.17 0.00
365_E 44_Q 0.89 0.16 0.00
203_S 157_L 0.88 0.16 0.00
377_I 145_A 0.88 0.16 0.00
152_H 88_D 0.88 0.16 0.00
197_V 35_K 0.88 0.16 0.00
28_T 72_L 0.87 0.16 0.00
379_R 73_S 0.87 0.16 0.00
377_I 24_F 0.86 0.15 0.00
171_R 91_F 0.86 0.15 0.00
159_V 136_L 0.86 0.15 0.00
224_V 41_Q 0.86 0.15 0.00
91_Q 3_Y 0.85 0.15 0.00
185_V 5_T 0.85 0.15 0.00
126_P 35_K 0.85 0.15 0.00
160_V 133_V 0.85 0.15 0.00
67_R 38_S 0.85 0.15 0.00
239_M 63_H 0.85 0.15 0.00
164_A 63_H 0.84 0.15 0.00
133_D 132_M 0.84 0.15 0.00
98_I 47_A 0.84 0.15 0.00
63_G 40_S 0.84 0.15 0.00
387_W 28_Q 0.84 0.15 0.00
191_D 41_Q 0.84 0.14 0.00
196_K 78_D 0.83 0.14 0.00
292_D 3_Y 0.83 0.14 0.00
396_L 15_L 0.83 0.14 0.00
165_A 5_T 0.82 0.14 0.00
196_K 7_F 0.82 0.14 0.00
396_L 107_Q 0.82 0.14 0.00
394_V 66_M 0.82 0.14 0.00
239_M 51_S 0.82 0.14 0.00
281_I 8_G 0.82 0.14 0.00
182_T 96_L 0.82 0.14 0.00
281_I 142_D 0.81 0.14 0.00
369_T 133_V 0.81 0.14 0.00
288_Y 15_L 0.81 0.14 0.00
320_L 25_Q 0.81 0.14 0.00
43_F 72_L 0.81 0.13 0.00
399_I 5_T 0.81 0.13 0.00
200_M 44_Q 0.80 0.13 0.00
383_L 45_L 0.80 0.13 0.00
52_D 50_Q 0.80 0.13 0.00
71_F 56_Q 0.80 0.13 0.00
25_Q 117_F 0.80 0.13 0.00
356_S 58_W 0.80 0.13 0.00
7_L 130_Q 0.80 0.13 0.00
404_H 63_H 0.80 0.13 0.00
174_G 23_R 0.80 0.13 0.00
320_L 54_I 0.80 0.13 0.00
177_Y 12_R 0.79 0.13 0.00
298_P 42_A 0.79 0.13 0.00
226_I 103_D 0.79 0.13 0.00
366_I 26_D 0.79 0.13 0.00
175_I 44_Q 0.79 0.13 0.00
356_S 87_R 0.79 0.13 0.00
174_G 125_F 0.78 0.12 0.00
250_V 114_L 0.78 0.12 0.00
31_G 88_D 0.78 0.12 0.00
307_Y 147_T 0.78 0.12 0.00
204_G 58_W 0.78 0.12 0.00
288_Y 44_Q 0.78 0.12 0.00
79_D 22_L 0.77 0.12 0.00
56_N 44_Q 0.77 0.12 0.00
202_F 58_W 0.77 0.12 0.00
292_D 108_A 0.77 0.12 0.00
281_I 15_L 0.77 0.12 0.00
258_I 121_V 0.77 0.12 0.00
139_A 18_Q 0.76 0.12 0.00
388_E 161_A 0.76 0.12 0.00
174_G 5_T 0.76 0.12 0.00
226_I 26_D 0.76 0.12 0.00
17_P 145_A 0.76 0.12 0.00
165_A 148_V 0.76 0.12 0.00
230_M 25_Q 0.76 0.12 0.00
63_G 39_G 0.75 0.12 0.00
388_E 40_S 0.75 0.12 0.00
230_M 85_T 0.75 0.12 0.00
224_V 105_I 0.75 0.11 0.00
399_I 43_E 0.75 0.11 0.00
184_S 50_Q 0.75 0.11 0.00
174_G 124_M 0.74 0.11 0.00
168_E 7_F 0.74 0.11 0.00
383_L 44_Q 0.74 0.11 0.00
46_Q 152_R 0.74 0.11 0.00
132_I 127_T 0.74 0.11 0.00
357_L 94_E 0.74 0.11 0.00
332_S 13_Y 0.74 0.11 0.00
379_R 13_Y 0.74 0.11 0.00
299_N 161_A 0.74 0.11 0.00
25_Q 21_S 0.74 0.11 0.00
224_V 19_A 0.74 0.11 0.00
159_V 132_M 0.74 0.11 0.00
143_D 88_D 0.74 0.11 0.00
133_D 8_G 0.73 0.11 0.00
168_E 30_Q 0.73 0.11 0.00
129_N 66_M 0.73 0.11 0.00
368_Y 70_Y 0.73 0.11 0.00
224_V 137_D 0.73 0.11 0.00
170_C 38_S 0.73 0.11 0.00
229_Q 3_Y 0.73 0.11 0.00
17_P 64_P 0.73 0.11 0.00
30_D 57_A 0.73 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)
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