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OPENSEQ.org
cIV_A_20_B_20_pn
Genes: A B A+B
Length: 538 252 750
Sequences: 4187 4606 3177
Seq/Len: 7.78 18.28 4.24
MirrorTree (Pazo et al. 2001) 0.89
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 0.00 3.34
2 0.01 0.00 3.42
5 0.02 0.00 3.59
10 0.02 0.01 3.78
20 0.03 0.01 3.84
100 0.04 0.02 3.88
∞ 0.08 0.04 4.02
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
249_V 195_V 3.25 1.00 1.00
388_D 218_E 2.58 1.00 1.00
466_F 13_P 1.88 1.00 0.98
388_D 191_K 1.79 1.00 0.97
388_D 193_D 1.74 0.99 0.97
453_Q 17_G 1.71 0.99 0.96
460_I 225_A 1.70 0.99 0.96
353_F 57_I 1.51 0.98 0.92
372_V 46_T 1.46 0.97 0.91
459_Y 225_A 1.45 0.97 0.90
338_K 78_E 1.44 0.97 0.90
361_F 53_L 1.41 0.96 0.89
247_D 198_R 1.31 0.94 0.84
468_Y 16_G 1.28 0.93 0.82
352_E 62_R 1.17 0.88 0.74
154_L 219_L 1.17 0.88 0.74
252_Q 180_I 1.15 0.87 0.73
313_T 182_A 1.13 0.86 0.71
343_I 52_L 1.11 0.84 0.68
314_A 200_A 1.08 0.82 0.65
348_G 60_F 1.06 0.81 0.64
287_F 82_T 1.06 0.80 0.63
372_V 42_I 1.03 0.77 0.59
299_I 78_E 0.98 0.72 0.54
114_L 233_A 0.96 0.70 0.52
330_T 86_V 0.94 0.69 0.50
391_Y 35_D 0.93 0.67 0.47
333_V 49_V 0.92 0.66 0.47
514_L 52_L 0.91 0.65 0.45
376_V 38_V 0.91 0.64 0.45
314_A 195_V 0.90 0.63 0.44
68_G 223_N 0.89 0.62 0.43
347_W 56_C 0.88 0.61 0.42
456_P 216_C 0.86 0.58 0.39
358_L 47_I 0.86 0.58 0.39
75_I 219_L 0.85 0.57 0.38
447_Q 25_S 0.85 0.57 0.38
359_W 225_A 0.84 0.56 0.37
68_G 225_A 0.84 0.55 0.36
379_Q 96_S 0.84 0.55 0.36
368_T 49_V 0.84 0.55 0.36
220_P 121_W 0.83 0.55 0.36
365_F 50_C 0.82 0.52 0.34
388_D 182_A 0.81 0.52 0.33
388_D 217_S 0.81 0.51 0.32
343_I 56_C 0.80 0.50 0.32
378_S 92_I 0.80 0.49 0.31
191_M 18_M 0.79 0.49 0.31
194_P 174_V 0.79 0.48 0.30
175_A 45_V 0.78 0.47 0.29
333_V 60_F 0.78 0.47 0.29
531_P 76_P 0.78 0.47 0.29
385_V 20_F 0.78 0.46 0.29
419_M 87_L 0.77 0.46 0.29
315_G 200_A 0.76 0.44 0.27
449_F 89_L 0.76 0.44 0.27
326_L 97_L 0.75 0.43 0.26
384_R 103_S 0.74 0.42 0.25
350_S 62_R 0.74 0.42 0.25
99_F 77_I 0.74 0.42 0.25
7_F 233_A 0.74 0.41 0.25
29_I 166_V 0.73 0.41 0.24
72_N 219_L 0.73 0.41 0.24
382_L 38_V 0.73 0.41 0.24
335_T 78_E 0.72 0.40 0.23
365_F 53_L 0.72 0.40 0.23
253_H 191_K 0.72 0.39 0.23
271_F 78_E 0.72 0.39 0.23
287_F 78_E 0.72 0.39 0.23
225_A 211_V 0.71 0.38 0.22
175_A 172_V 0.71 0.38 0.22
382_L 91_A 0.71 0.38 0.22
385_V 184_T 0.71 0.38 0.22
37_M 71_F 0.70 0.37 0.21
357_M 188_F 0.70 0.37 0.21
75_I 114_I 0.70 0.36 0.21
155_S 174_V 0.70 0.36 0.21
164_D 214_G 0.69 0.36 0.20
335_T 85_P 0.69 0.36 0.20
465_E 13_P 0.69 0.35 0.20
461_D 226_Y 0.69 0.35 0.20
242_P 172_V 0.69 0.35 0.20
312_Y 153_E 0.69 0.35 0.20
289_Y 14_V 0.68 0.34 0.19
459_Y 215_Q 0.67 0.33 0.18
73_V 92_I 0.67 0.33 0.18
483_S 106_M 0.67 0.33 0.18
71_W 225_A 0.67 0.33 0.18
252_Q 218_E 0.67 0.33 0.18
308_A 82_T 0.67 0.33 0.18
481_F 183_W 0.66 0.32 0.17
479_I 129_N 0.66 0.32 0.17
190_N 219_L 0.66 0.32 0.17
485_L 116_A 0.66 0.32 0.17
456_P 220_C 0.66 0.32 0.17
351_I 60_F 0.66 0.31 0.17
114_L 19_N 0.66 0.31 0.17
198_L 177_T 0.65 0.31 0.17
348_G 66_P 0.65 0.30 0.16
297_A 58_V 0.65 0.30 0.16
335_T 125_Y 0.65 0.30 0.16
489_G 166_V 0.65 0.30 0.16
283_K 225_A 0.65 0.30 0.16
312_Y 212_Y 0.65 0.30 0.16
456_P 224_H 0.64 0.30 0.16
392_V 193_D 0.64 0.30 0.16
270_G 182_A 0.64 0.29 0.16
389_T 217_S 0.64 0.29 0.16
75_I 174_V 0.64 0.29 0.16
341_S 78_E 0.64 0.29 0.15
402_L 216_C 0.64 0.29 0.15
486_F 91_A 0.64 0.29 0.15
241_D 176_A 0.63 0.29 0.15
527_F 92_I 0.63 0.28 0.15
500_R 238_K 0.63 0.28 0.15
381_P 99_I 0.63 0.28 0.15
474_S 237_E 0.63 0.28 0.15
303_G 239_Y 0.63 0.28 0.15
368_T 174_V 0.63 0.28 0.15
98_Y 114_I 0.63 0.28 0.15
343_I 53_L 0.63 0.28 0.14
332_A 78_E 0.63 0.28 0.14
376_V 39_L 0.63 0.28 0.14
108_D 85_P 0.62 0.28 0.14
361_F 57_I 0.62 0.28 0.14
252_Q 193_D 0.62 0.28 0.14
350_S 188_F 0.62 0.27 0.14
242_P 196_P 0.62 0.27 0.14
378_S 238_K 0.62 0.27 0.14
369_V 46_T 0.62 0.27 0.14
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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