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OPENSEQ.org
GatBC_truncated
Genes: A B A+B
Length: 280 100 375
Sequences: 2036 2469 1587
Seq/Len: 7.27 24.69 4.23
MirrorTree (Pazo et al. 2001) 0.58
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 0.00 0.00 0.07
2 0.00 0.00 2.75
5 0.00 0.00 3.14
10 0.00 0.00 3.26
20 0.00 0.00 3.29
100 0.01 0.00 3.39
∞ 0.03 0.00 4.18
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
53_K 65_E 4.25 1.00 1.00
42_L 77_A 1.92 1.00 0.98
24_P 69_I 1.62 0.99 0.95
20_S 68_A 1.56 0.98 0.94
19_D 67_K 1.56 0.98 0.94
137_S 94_I 1.53 0.98 0.93
130_S 94_I 1.49 0.98 0.92
26_P 71_G 1.32 0.95 0.85
24_P 64_R 1.23 0.91 0.79
42_L 89_F 1.14 0.87 0.72
131_T 88_Q 1.11 0.84 0.69
19_D 68_A 1.06 0.81 0.64
136_Y 90_K 1.05 0.80 0.63
35_S 74_Q 1.03 0.78 0.60
42_L 72_I 1.01 0.75 0.57
82_F 16_A 0.99 0.74 0.56
24_P 71_G 0.99 0.73 0.55
138_L 88_Q 0.95 0.70 0.51
32_E 74_Q 0.91 0.64 0.45
268_R 15_L 0.88 0.61 0.42
25_S 71_G 0.88 0.61 0.42
278_L 63_L 0.88 0.60 0.41
127_A 92_P 0.86 0.58 0.39
26_P 68_A 0.84 0.55 0.36
279_Y 60_Q 0.81 0.50 0.32
276_V 61_N 0.78 0.47 0.29
32_E 87_G 0.78 0.47 0.29
23_S 69_I 0.72 0.40 0.23
39_V 71_G 0.72 0.39 0.22
274_D 16_A 0.71 0.38 0.22
23_S 71_G 0.71 0.38 0.22
248_F 38_F 0.71 0.38 0.22
264_S 13_A 0.69 0.36 0.20
197_L 95_M 0.69 0.35 0.20
136_Y 83_E 0.69 0.35 0.20
271_P 15_L 0.68 0.34 0.19
180_S 14_N 0.68 0.34 0.19
270_F 15_L 0.67 0.33 0.18
209_A 55_H 0.67 0.33 0.18
263_G 42_N 0.66 0.32 0.17
24_P 68_A 0.66 0.31 0.17
35_S 87_G 0.65 0.30 0.16
12_V 16_A 0.65 0.30 0.16
105_I 41_Q 0.65 0.30 0.16
20_S 5_T 0.65 0.30 0.16
272_E 90_K 0.64 0.29 0.15
218_N 69_I 0.64 0.29 0.15
41_D 71_G 0.63 0.28 0.15
56_V 63_L 0.63 0.28 0.15
99_I 48_E 0.62 0.28 0.14
138_L 90_K 0.62 0.27 0.14
89_A 94_I 0.62 0.27 0.14
37_T 78_L 0.62 0.27 0.14
82_F 14_N 0.62 0.27 0.14
65_A 47_T 0.62 0.27 0.14
87_P 92_P 0.62 0.27 0.14
64_M 33_E 0.61 0.26 0.14
263_G 11_H 0.60 0.25 0.13
149_I 56_V 0.59 0.24 0.12
44_Y 51_E 0.59 0.24 0.12
71_A 55_H 0.59 0.24 0.12
71_A 61_N 0.58 0.23 0.11
60_M 19_Q 0.58 0.23 0.11
228_E 53_T 0.57 0.22 0.10
274_D 15_L 0.57 0.22 0.10
262_E 15_L 0.56 0.21 0.10
12_V 91_V 0.56 0.21 0.10
156_D 16_A 0.56 0.21 0.10
218_N 17_R 0.55 0.21 0.10
116_I 28_M 0.55 0.21 0.10
237_N 48_E 0.55 0.20 0.10
87_P 91_V 0.55 0.20 0.09
114_K 95_M 0.55 0.20 0.09
197_L 32_L 0.55 0.20 0.09
38_N 71_G 0.55 0.20 0.09
128_G 15_L 0.54 0.20 0.09
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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