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OPENSEQ.org
SpoVE-SpoVD
Genes: A B A+B
Length: 366 300 652
Sequences: 4959 6040 2686
Seq/Len: 13.55 20.13 4.12
MirrorTree (Pazo et al. 2001) 0.86
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 0.02 0.05 1.58
2 0.02 0.06 1.67
5 0.02 0.06 3.78
10 0.02 0.07 3.97
20 0.02 0.08 4.03
100 0.05 0.10 4.42
∞ 0.18 0.24 5.09
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
279_T 27_D 2.89 1.00 1.00
278_G 30_L 2.44 1.00 1.00
320_M 22_V 2.19 1.00 0.99
275_F 31_G 1.95 1.00 0.98
242_L 35_F 1.79 0.99 0.97
323_I 26_I 1.58 0.98 0.94
286_S 23_F 1.57 0.98 0.94
275_F 35_F 1.38 0.96 0.87
329_L 25_I 1.37 0.95 0.87
266_F 30_L 1.29 0.93 0.83
241_G 38_G 1.29 0.93 0.82
320_M 26_I 1.18 0.88 0.75
22_I 123_E 1.18 0.88 0.74
282_L 27_D 1.13 0.85 0.70
327_T 26_I 1.13 0.85 0.70
327_T 30_L 1.06 0.80 0.63
329_L 26_I 1.05 0.79 0.61
324_G 26_I 0.99 0.73 0.55
316_A 19_G 0.98 0.72 0.54
313_S 221_T 0.92 0.64 0.45
275_F 34_Q 0.90 0.62 0.44
180_V 15_V 0.89 0.60 0.41
327_T 29_R 0.88 0.60 0.41
237_V 33_V 0.88 0.60 0.41
175_I 27_D 0.88 0.60 0.41
332_V 226_V 0.87 0.59 0.40
235_Y 41_L 0.87 0.58 0.40
232_Q 48_S 0.87 0.58 0.40
319_V 23_F 0.86 0.57 0.39
68_Y 299_I 0.85 0.56 0.38
275_F 27_D 0.85 0.56 0.38
238_G 41_L 0.82 0.52 0.34
186_A 127_I 0.81 0.50 0.32
130_L 51_R 0.80 0.49 0.32
159_M 295_T 0.80 0.48 0.30
127_A 69_K 0.79 0.48 0.30
17_L 21_I 0.79 0.48 0.30
311_I 232_R 0.78 0.46 0.29
250_S 33_V 0.78 0.46 0.29
283_L 286_V 0.78 0.46 0.29
308_A 29_R 0.78 0.46 0.28
283_L 27_D 0.78 0.46 0.28
57_V 222_V 0.76 0.44 0.27
152_F 187_E 0.76 0.44 0.27
16_T 55_F 0.76 0.44 0.27
314_M 269_P 0.75 0.43 0.26
47_K 251_M 0.74 0.41 0.24
189_V 22_V 0.74 0.41 0.24
359_N 299_I 0.73 0.40 0.24
198_G 176_L 0.73 0.40 0.24
74_W 258_I 0.73 0.40 0.24
219_P 265_P 0.73 0.39 0.23
80_V 187_E 0.73 0.39 0.23
55_I 187_E 0.72 0.39 0.23
156_L 24_L 0.72 0.39 0.23
284_L 33_V 0.72 0.39 0.23
358_L 295_T 0.71 0.38 0.22
287_V 267_F 0.71 0.38 0.22
256_Y 222_V 0.71 0.38 0.22
285_F 146_A 0.71 0.38 0.22
105_I 213_K 0.71 0.37 0.21
156_L 134_E 0.71 0.37 0.21
213_I 178_A 0.70 0.36 0.21
191_L 98_A 0.70 0.36 0.21
127_A 33_V 0.70 0.36 0.21
193_L 213_K 0.70 0.36 0.20
107_V 21_I 0.70 0.36 0.20
170_M 71_A 0.70 0.36 0.20
269_L 221_T 0.70 0.35 0.20
270_S 34_Q 0.70 0.35 0.20
29_S 202_M 0.69 0.35 0.20
15_I 300_T 0.69 0.35 0.20
267_A 166_A 0.69 0.35 0.20
298_G 222_V 0.69 0.35 0.20
96_M 235_D 0.69 0.35 0.20
18_L 162_V 0.69 0.35 0.20
236_A 238_E 0.69 0.34 0.19
209_R 291_E 0.69 0.34 0.19
179_F 14_F 0.69 0.34 0.19
267_A 138_L 0.68 0.34 0.19
55_I 98_A 0.68 0.34 0.19
239_P 41_L 0.68 0.34 0.19
282_L 23_F 0.68 0.33 0.19
336_T 194_Y 0.67 0.33 0.18
9_D 259_L 0.67 0.32 0.18
267_A 168_I 0.67 0.32 0.18
61_F 163_L 0.67 0.32 0.18
243_F 271_D 0.67 0.32 0.18
195_G 20_V 0.67 0.32 0.18
356_V 217_D 0.67 0.32 0.17
356_V 71_A 0.66 0.32 0.17
112_I 66_N 0.66 0.32 0.17
323_I 42_T 0.66 0.31 0.17
278_G 34_Q 0.66 0.31 0.17
105_I 289_T 0.66 0.31 0.17
152_F 20_V 0.66 0.31 0.17
159_M 211_P 0.66 0.30 0.17
146_P 24_L 0.66 0.30 0.17
55_I 221_T 0.65 0.30 0.16
189_V 112_T 0.65 0.30 0.16
318_Q 137_A 0.65 0.30 0.16
275_F 38_G 0.65 0.30 0.16
267_A 119_K 0.65 0.30 0.16
183_A 222_V 0.65 0.29 0.16
81_I 99_V 0.65 0.29 0.16
267_A 143_V 0.65 0.29 0.16
238_G 45_A 0.64 0.29 0.15
98_R 268_D 0.64 0.29 0.15
105_I 99_V 0.64 0.29 0.15
340_L 199_G 0.64 0.29 0.15
283_L 20_V 0.64 0.29 0.15
101_S 47_D 0.64 0.28 0.15
304_G 251_M 0.64 0.28 0.15
48_R 191_V 0.64 0.28 0.15
24_L 277_P 0.64 0.28 0.15
66_V 183_D 0.64 0.28 0.15
336_T 166_A 0.63 0.28 0.15
254_F 203_P 0.63 0.28 0.15
205_S 242_H 0.63 0.28 0.15
71_W 140_L 0.63 0.28 0.15
43_F 162_V 0.63 0.28 0.15
87_V 8_V 0.63 0.28 0.15
277_G 60_G 0.63 0.28 0.14
247_L 291_E 0.63 0.28 0.14
254_F 197_A 0.63 0.28 0.14
24_L 274_S 0.63 0.28 0.14
309_V 12_L 0.63 0.27 0.14
258_P 223_D 0.63 0.27 0.14
132_E 76_A 0.62 0.27 0.14
256_Y 67_G 0.62 0.27 0.14
174_C 145_V 0.62 0.27 0.14
158_I 272_Y 0.62 0.27 0.14
211_K 248_A 0.62 0.27 0.14
351_L 93_S 0.62 0.27 0.14
296_A 53_L 0.62 0.27 0.14
323_I 30_L 0.62 0.27 0.14
100_G 199_G 0.62 0.27 0.14
321_I 157_S 0.62 0.27 0.14
332_V 45_A 0.62 0.27 0.14
192_G 240_K 0.62 0.27 0.14
49_Q 253_P 0.61 0.26 0.13
339_F 155_F 0.61 0.26 0.13
321_I 240_K 0.61 0.26 0.13
157_I 32_Y 0.61 0.26 0.13
262_T 272_Y 0.61 0.26 0.13
30_A 169_D 0.61 0.26 0.13
129_F 176_L 0.61 0.26 0.13
107_V 123_E 0.61 0.26 0.13
189_V 47_D 0.61 0.26 0.13
169_V 79_V 0.61 0.26 0.13
270_S 70_L 0.61 0.26 0.13
356_V 233_E 0.61 0.26 0.13
156_L 29_R 0.61 0.25 0.13
235_Y 140_L 0.61 0.25 0.13
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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