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OPENSEQ.org
DI1210003_2A7U
Genes: A B A+B
Length: 30 134 163
Sequences: 495 8376 1360
Seq/Len: 16.5 62.51 8.34
MirrorTree (Pazo et al. 2001) 0.72
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 8.34
2 0.00 0.00 8.29
5 0.00 0.00 8.29
10 0.00 0.00 8.29
20 0.00 0.00 8.29
100 0.00 0.00 8.29
∞ 0.00 0.00 8.29
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
19_F 114_A 1.56 1.00 0.90
26_H 131_R 1.46 0.99 0.86
13_K 20_E 1.44 0.99 0.85
15_R 14_A 1.30 0.98 0.77
5_S 50_A 1.16 0.96 0.65
6_T 28_Q 1.15 0.96 0.65
28_E 110_V 1.02 0.91 0.51
27_N 108_V 1.01 0.90 0.49
9_S 50_A 0.96 0.87 0.43
10_E 71_N 0.90 0.82 0.37
11_L 75_L 0.90 0.82 0.37
17_A 21_H 0.89 0.81 0.35
5_S 49_G 0.88 0.80 0.34
23_S 128_M 0.88 0.80 0.34
10_E 82_N 0.85 0.77 0.31
12_I 11_A 0.84 0.76 0.30
18_Q 70_E 0.84 0.75 0.30
19_F 77_R 0.82 0.73 0.28
2_Q 3_F 0.82 0.73 0.28
12_I 51_L 0.82 0.72 0.27
15_R 127_A 0.80 0.71 0.26
27_N 2_E 0.80 0.71 0.26
20_N 12_K 0.79 0.68 0.24
27_N 134_R 0.79 0.68 0.24
28_E 104_A 0.78 0.68 0.24
23_S 124_I 0.76 0.64 0.21
17_A 78_V 0.75 0.63 0.21
4_N 82_N 0.75 0.62 0.21
11_L 132_L 0.74 0.62 0.20
28_E 42_Q 0.72 0.59 0.19
6_T 50_A 0.72 0.58 0.18
15_R 17_F 0.70 0.56 0.17
12_I 131_R 0.70 0.56 0.17
12_I 112_S 0.70 0.56 0.17
26_H 59_S 0.70 0.56 0.17
27_N 96_I 0.70 0.55 0.17
10_E 105_T 0.69 0.54 0.16
16_I 82_N 0.69 0.53 0.16
15_R 106_A 0.68 0.53 0.16
20_N 83_G 0.68 0.52 0.15
19_F 53_P 0.68 0.52 0.15
6_T 96_I 0.68 0.52 0.15
9_S 114_A 0.68 0.52 0.15
10_E 121_L 0.67 0.50 0.14
28_E 133_S 0.67 0.50 0.14
21_V 41_E 0.66 0.49 0.14
13_K 130_K 0.66 0.49 0.14
19_F 33_F 0.66 0.48 0.14
6_T 27_W 0.66 0.48 0.14
24_E 114_A 0.66 0.48 0.14
15_R 92_L 0.66 0.48 0.14
10_E 22_Q 0.65 0.47 0.13
4_N 57_A 0.65 0.47 0.13
2_Q 82_N 0.65 0.47 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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