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OPENSEQ.org
ssa1 and ydj1 (A, 379-508) (B, 1-60)
Genes: A B A+B
Length: 130 60 180
Sequences: 2335 8979 805
Seq/Len: 17.96 149.65 4.47
MirrorTree (Pazo et al. 2001) 0.41
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 0.07 0.05 3.24
2 0.07 0.05 3.76
5 0.07 0.05 3.96
10 0.08 0.06 4.07
20 0.08 0.07 4.24
100 0.08 0.10 5.43
∞ 0.13 0.18 8.55
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
35_R 31_L 1.47 0.98 0.80
58_L 37_K 1.38 0.96 0.74
22_I 24_K 1.12 0.86 0.49
105_L 45_E 1.09 0.84 0.46
43_K 51_S 1.08 0.84 0.46
51_A 49_E 1.00 0.76 0.37
55_P 28_K 0.99 0.75 0.36
45_E 46_K 0.95 0.70 0.32
19_S 18_T 0.93 0.69 0.30
31_K 29_C 0.93 0.68 0.30
58_L 31_L 0.92 0.67 0.29
13_L 30_A 0.92 0.67 0.29
112_K 20_V 0.92 0.67 0.28
41_T 23_K 0.91 0.67 0.28
48_S 37_K 0.91 0.66 0.28
79_E 37_K 0.90 0.65 0.27
85_P 57_L 0.90 0.64 0.27
79_E 31_L 0.89 0.63 0.26
48_S 57_L 0.88 0.62 0.25
60_Q 7_F 0.86 0.60 0.23
45_E 32_K 0.85 0.58 0.22
106_N 19_D 0.85 0.58 0.22
93_I 21_E 0.83 0.55 0.21
74_L 13_V 0.82 0.54 0.20
114_T 4_E 0.82 0.54 0.20
105_L 31_L 0.81 0.53 0.19
50_Y 6_K 0.81 0.52 0.19
113_G 27_R 0.81 0.52 0.19
25_A 9_D 0.80 0.52 0.19
39_I 48_K 0.80 0.52 0.19
96_T 46_K 0.80 0.51 0.18
102_N 27_R 0.80 0.51 0.18
58_L 32_K 0.80 0.51 0.18
93_I 32_K 0.77 0.47 0.16
82_G 25_A 0.77 0.47 0.16
67_A 30_A 0.76 0.46 0.16
32_L 15_V 0.76 0.46 0.16
34_P 10_I 0.74 0.43 0.14
105_L 37_K 0.73 0.42 0.14
21_G 57_L 0.73 0.42 0.14
45_E 31_L 0.73 0.41 0.14
112_K 26_Y 0.72 0.41 0.13
22_I 15_V 0.72 0.40 0.13
45_E 5_T 0.71 0.40 0.13
68_K 60_S 0.71 0.40 0.13
88_R 38_N 0.71 0.39 0.13
46_I 55_E 0.70 0.38 0.12
59_I 16_T 0.70 0.38 0.12
35_R 51_S 0.70 0.38 0.12
119_K 21_E 0.69 0.37 0.12
25_A 13_V 0.69 0.37 0.12
53_N 57_L 0.69 0.36 0.11
8_Q 41_E 0.69 0.36 0.11
94_E 49_E 0.68 0.36 0.11
58_L 14_S 0.68 0.35 0.11
46_I 16_T 0.68 0.35 0.11
56_G 59_D 0.68 0.35 0.11
74_L 15_V 0.68 0.35 0.11
74_L 7_F 0.68 0.35 0.11
38_T 39_P 0.67 0.34 0.10
41_T 52_A 0.67 0.34 0.10
69_T 13_V 0.67 0.34 0.10
41_T 37_K 0.67 0.33 0.10
29_M 22_I 0.66 0.33 0.10
56_G 31_L 0.66 0.32 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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