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OPENSEQ.org
5194
Genes: A B A+B
Length: 76 138 208
Sequences: 1181 9173 626
Seq/Len: 15.54 66.47 3.01
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 0.04 2.93
2 0.01 0.05 2.95
5 0.02 0.08 3.01
10 0.02 0.09 3.08
20 0.02 0.10 3.19
100 0.04 0.14 3.48
∞ 0.08 0.20 4.12
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
57_D 60_H 1.61 0.97 0.86
56_A 64_V 1.57 0.97 0.84
10_G 111_I 1.22 0.84 0.56
51_L 24_L 1.01 0.66 0.35
51_L 15_I 1.01 0.66 0.34
6_I 68_C 0.94 0.58 0.28
46_T 133_L 0.93 0.56 0.27
15_I 86_T 0.91 0.54 0.25
38_I 38_V 0.91 0.54 0.25
50_F 45_S 0.90 0.53 0.24
53_Y 15_I 0.90 0.53 0.24
69_S 101_P 0.89 0.52 0.24
17_L 38_V 0.89 0.52 0.24
37_S 105_A 0.84 0.45 0.19
17_L 24_L 0.84 0.45 0.19
40_L 34_G 0.82 0.43 0.18
35_G 121_N 0.81 0.42 0.17
9_N 43_T 0.81 0.42 0.17
21_L 112_A 0.81 0.41 0.17
53_Y 64_V 0.81 0.41 0.17
58_P 4_T 0.80 0.41 0.17
50_F 63_L 0.79 0.39 0.16
4_V 128_V 0.79 0.39 0.16
15_I 113_A 0.79 0.39 0.16
57_D 56_A 0.78 0.39 0.15
58_P 95_A 0.78 0.38 0.15
17_L 113_A 0.77 0.37 0.14
35_G 124_E 0.77 0.36 0.14
20_D 111_I 0.77 0.36 0.14
56_A 18_E 0.77 0.36 0.14
27_S 135_D 0.76 0.36 0.14
69_S 114_G 0.76 0.36 0.14
23_F 97_T 0.76 0.35 0.13
3_T 97_T 0.74 0.34 0.13
36_D 7_L 0.74 0.34 0.12
7_F 118_V 0.74 0.33 0.12
27_S 133_L 0.73 0.32 0.12
19_R 51_A 0.72 0.31 0.11
61_M 135_D 0.72 0.31 0.11
57_D 77_W 0.72 0.31 0.11
50_F 67_F 0.72 0.31 0.11
7_F 5_Y 0.71 0.31 0.11
15_I 74_I 0.71 0.30 0.11
8_K 75_L 0.70 0.30 0.10
34_E 13_S 0.70 0.29 0.10
49_S 70_R 0.70 0.29 0.10
63_E 116_I 0.70 0.29 0.10
42_P 60_H 0.70 0.29 0.10
35_G 88_I 0.69 0.29 0.10
42_P 16_M 0.69 0.28 0.10
2_R 13_S 0.69 0.28 0.10
11_N 94_L 0.69 0.28 0.10
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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