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OPENSEQ.org
gerAB-SpoVAC
Genes: A B A+B
Length: 365 150 504
Sequences: 1686 557 221
Seq/Len: 4.62 3.71 0.44
MirrorTree (Pazo et al. 2001) 0.16
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 0.03 0.00 0.00
2 0.05 0.00 0.00
5 0.07 0.00 0.00
10 0.08 0.00 0.01
20 0.12 0.00 0.02
100 0.20 0.01 0.10
∞ 0.25 0.07 0.43
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
317_T 26_V 1.42 0.46 0.00
358_L 137_I 1.28 0.36 0.00
158_I 85_A 1.24 0.33 0.00
19_V 30_L 1.17 0.29 0.00
155_V 141_I 1.12 0.26 0.00
259_F 77_I 1.10 0.25 0.00
67_K 65_L 1.08 0.24 0.00
269_I 26_V 1.07 0.24 0.00
165_G 134_A 1.05 0.23 0.00
110_A 130_F 1.04 0.22 0.00
139_V 65_L 1.04 0.22 0.00
224_G 93_V 1.02 0.21 0.00
215_K 30_L 1.02 0.21 0.00
322_S 9_K 1.02 0.21 0.00
70_Q 99_S 1.01 0.21 0.00
89_I 77_I 1.00 0.20 0.00
89_I 71_L 0.98 0.19 0.00
361_R 138_V 0.98 0.19 0.00
45_W 76_G 0.98 0.19 0.00
90_I 34_L 0.96 0.18 0.00
303_F 36_C 0.96 0.18 0.00
100_G 68_I 0.96 0.18 0.00
350_F 66_I 0.96 0.18 0.00
114_K 102_S 0.96 0.18 0.00
348_L 108_K 0.95 0.18 0.00
90_I 134_A 0.94 0.17 0.00
184_L 122_K 0.94 0.17 0.00
45_W 79_D 0.93 0.17 0.00
334_Y 22_V 0.93 0.17 0.00
299_L 57_A 0.93 0.17 0.00
28_L 71_L 0.92 0.16 0.00
119_E 25_C 0.92 0.16 0.00
100_G 69_S 0.90 0.16 0.00
15_G 82_G 0.90 0.16 0.00
184_L 108_K 0.90 0.16 0.00
73_S 120_M 0.90 0.15 0.00
333_M 91_V 0.90 0.15 0.00
88_S 140_M 0.90 0.15 0.00
314_I 134_A 0.89 0.15 0.00
312_V 64_T 0.89 0.15 0.00
37_T 138_V 0.89 0.15 0.00
20_A 99_S 0.88 0.15 0.00
68_K 112_L 0.88 0.15 0.00
226_L 100_M 0.88 0.15 0.00
11_N 126_N 0.88 0.15 0.00
279_V 65_L 0.87 0.14 0.00
360_R 68_I 0.87 0.14 0.00
290_I 13_K 0.87 0.14 0.00
109_M 144_A 0.87 0.14 0.00
107_R 120_M 0.86 0.14 0.00
57_F 89_S 0.86 0.14 0.00
163_V 71_L 0.86 0.14 0.00
329_N 82_G 0.86 0.14 0.00
264_L 117_A 0.86 0.14 0.00
220_Y 81_I 0.85 0.14 0.00
7_P 140_M 0.85 0.14 0.00
135_I 46_Y 0.85 0.14 0.00
48_L 65_L 0.85 0.14 0.00
10_L 117_A 0.84 0.13 0.00
359_K 109_S 0.84 0.13 0.00
223_L 144_A 0.84 0.13 0.00
154_T 57_A 0.84 0.13 0.00
311_M 140_M 0.83 0.13 0.00
49_I 34_L 0.83 0.13 0.00
96_G 71_L 0.83 0.13 0.00
132_C 108_K 0.83 0.13 0.00
302_T 68_I 0.82 0.13 0.00
269_I 68_I 0.82 0.13 0.00
115_F 36_C 0.82 0.13 0.00
190_S 138_V 0.82 0.13 0.00
198_F 140_M 0.82 0.13 0.00
84_K 140_M 0.82 0.13 0.00
212_K 71_L 0.82 0.13 0.00
359_K 18_K 0.82 0.13 0.00
258_L 81_I 0.82 0.13 0.00
350_F 134_A 0.82 0.12 0.00
281_I 141_I 0.81 0.12 0.00
15_G 130_F 0.81 0.12 0.00
142_L 55_K 0.81 0.12 0.00
71_Y 14_T 0.81 0.12 0.00
212_K 117_A 0.81 0.12 0.00
28_L 81_I 0.81 0.12 0.00
53_F 37_A 0.80 0.12 0.00
84_K 68_I 0.80 0.12 0.00
257_S 42_L 0.80 0.12 0.00
94_I 14_T 0.80 0.12 0.00
22_T 22_V 0.80 0.12 0.00
96_G 45_F 0.80 0.12 0.00
120_R 68_I 0.80 0.12 0.00
29_L 141_I 0.80 0.12 0.00
345_L 40_Q 0.80 0.12 0.00
145_V 84_F 0.80 0.12 0.00
269_I 144_A 0.79 0.12 0.00
358_L 71_L 0.79 0.12 0.00
26_A 34_L 0.79 0.12 0.00
262_F 68_I 0.79 0.12 0.00
347_L 81_I 0.79 0.12 0.00
263_E 144_A 0.78 0.12 0.00
226_L 65_L 0.78 0.12 0.00
235_T 114_L 0.78 0.11 0.00
224_G 66_I 0.78 0.11 0.00
296_A 71_L 0.78 0.11 0.00
139_V 77_I 0.78 0.11 0.00
129_T 85_A 0.78 0.11 0.00
184_L 68_I 0.77 0.11 0.00
60_Y 71_L 0.77 0.11 0.00
291_Y 66_I 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)
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