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OPENSEQ.org
SecY_YchJ
Genes: A B A+B
Length: 443 152 567
Sequences: 2570 613 193
Seq/Len: 5.8 4.03 0.34
MirrorTree (Pazo et al. 2001) 0.35
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.05 0.00
2 0.01 0.05 0.00
5 0.01 0.05 0.00
10 0.01 0.05 0.00
20 0.01 0.05 0.00
100 0.02 0.05 0.02
∞ 0.03 0.05 0.32
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
422_T 55_P 1.73 0.61 0.00
217_F 80_V 1.65 0.55 0.00
307_S 41_F 1.40 0.38 0.00
82_I 36_S 1.31 0.33 0.00
310_L 49_L 1.22 0.27 0.00
401_F 127_G 1.22 0.27 0.00
77_I 21_V 1.20 0.26 0.00
132_S 80_V 1.18 0.25 0.00
102_L 77_G 1.17 0.25 0.00
353_V 18_H 1.15 0.23 0.00
162_V 47_D 1.14 0.23 0.00
115_K 124_Y 1.14 0.23 0.00
65_N 113_S 1.12 0.22 0.00
393_D 70_F 1.09 0.21 0.00
366_I 39_C 1.09 0.21 0.00
384_I 70_F 1.08 0.20 0.00
37_S 39_C 1.08 0.20 0.00
189_I 151_G 1.08 0.20 0.00
132_S 49_L 1.07 0.20 0.00
223_V 52_T 1.06 0.19 0.00
305_T 146_F 1.05 0.19 0.00
125_L 39_C 1.04 0.19 0.00
109_G 49_L 1.03 0.18 0.00
431_S 83_H 1.03 0.18 0.00
98_V 92_G 1.02 0.18 0.00
321_Y 95_S 1.02 0.18 0.00
215_L 148_K 1.01 0.17 0.00
111_S 42_V 1.00 0.17 0.00
162_V 116_L 1.00 0.17 0.00
11_S 80_V 0.99 0.17 0.00
232_F 52_T 0.99 0.16 0.00
378_A 80_V 0.99 0.16 0.00
190_I 132_F 0.98 0.16 0.00
118_Q 135_N 0.97 0.16 0.00
147_G 85_W 0.97 0.16 0.00
341_E 53_W 0.96 0.15 0.00
118_Q 134_R 0.96 0.15 0.00
118_Q 124_Y 0.96 0.15 0.00
283_I 38_Y 0.95 0.15 0.00
264_H 52_T 0.95 0.15 0.00
82_I 82_E 0.95 0.15 0.00
392_R 30_P 0.94 0.15 0.00
430_E 86_Q 0.94 0.15 0.00
63_M 117_K 0.93 0.14 0.00
426_S 49_L 0.93 0.14 0.00
27_I 50_I 0.93 0.14 0.00
95_L 82_E 0.92 0.14 0.00
76_S 99_R 0.92 0.14 0.00
249_A 27_A 0.92 0.14 0.00
319_L 69_G 0.92 0.14 0.00
339_P 31_E 0.92 0.14 0.00
375_L 44_Q 0.92 0.14 0.00
430_E 144_K 0.91 0.14 0.00
154_F 116_L 0.90 0.13 0.00
378_A 18_H 0.90 0.13 0.00
39_I 25_K 0.90 0.13 0.00
252_Q 80_V 0.89 0.13 0.00
269_V 30_P 0.89 0.13 0.00
356_I 49_L 0.89 0.13 0.00
391_M 117_K 0.89 0.13 0.00
95_L 25_K 0.88 0.13 0.00
32_V 80_V 0.88 0.13 0.00
179_T 124_Y 0.88 0.13 0.00
171_L 54_H 0.88 0.13 0.00
232_F 29_D 0.88 0.13 0.00
132_S 14_S 0.87 0.12 0.00
256_R 48_Y 0.87 0.12 0.00
23_L 14_S 0.87 0.12 0.00
38_F 123_Y 0.86 0.12 0.00
296_G 39_C 0.86 0.12 0.00
31_I 22_S 0.86 0.12 0.00
82_I 52_T 0.86 0.12 0.00
154_F 36_S 0.85 0.12 0.00
158_F 100_F 0.85 0.12 0.00
26_V 91_I 0.85 0.12 0.00
283_I 114_R 0.85 0.12 0.00
323_S 32_H 0.84 0.12 0.00
95_L 49_L 0.84 0.12 0.00
101_T 82_E 0.84 0.12 0.00
148_L 91_I 0.84 0.12 0.00
163_S 39_C 0.84 0.12 0.00
28_G 91_I 0.84 0.11 0.00
53_L 135_N 0.83 0.11 0.00
363_A 70_F 0.83 0.11 0.00
102_L 43_M 0.83 0.11 0.00
139_L 126_D 0.83 0.11 0.00
128_A 55_P 0.83 0.11 0.00
237_V 29_D 0.82 0.11 0.00
158_F 41_F 0.82 0.11 0.00
30_L 102_E 0.82 0.11 0.00
73_S 125_I 0.82 0.11 0.00
92_I 74_E 0.82 0.11 0.00
344_D 101_T 0.82 0.11 0.00
78_F 55_P 0.82 0.11 0.00
23_L 116_L 0.82 0.11 0.00
129_I 144_K 0.82 0.11 0.00
324_A 30_P 0.82 0.11 0.00
118_Q 49_L 0.81 0.11 0.00
363_A 139_P 0.81 0.11 0.00
128_A 58_G 0.81 0.11 0.00
379_L 100_F 0.81 0.11 0.00
39_I 141_G 0.81 0.11 0.00
335_L 80_V 0.80 0.10 0.00
63_M 148_K 0.80 0.10 0.00
202_A 134_R 0.80 0.10 0.00
319_L 114_R 0.80 0.10 0.00
45_D 99_R 0.80 0.10 0.00
165_V 20_Y 0.80 0.10 0.00
420_V 45_D 0.80 0.10 0.00
314_Q 52_T 0.80 0.10 0.00
146_Q 49_L 0.80 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)
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