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OPENSEQ.org
MA-NC
Genes: A B A+B
Length: 99 55 154
Sequences: 10854 4762 595
Seq/Len: 109.64 86.58 3.86
MirrorTree (Pazo et al. 2001) 0.92
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 0.02 2.84
2 0.01 0.02 3.05
5 0.02 0.03 3.25
10 0.03 0.03 3.40
20 0.03 0.03 3.86
100 0.04 0.03 4.71
∞ 0.06 0.04 6.34
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
84_I 32_P 1.29 0.92 0.39
33_L 47_M 1.12 0.83 0.25
64_I 12_K 1.11 0.82 0.25
2_Q 47_M 1.07 0.79 0.22
62_I 26_A 1.05 0.77 0.21
33_L 2_M 0.98 0.70 0.17
47_I 48_K 0.97 0.69 0.16
85_I 38_W 0.97 0.69 0.16
76_L 23_G 0.95 0.66 0.15
90_L 30_R 0.94 0.65 0.14
50_I 21_K 0.94 0.65 0.14
94_G 20_G 0.93 0.64 0.14
56_V 41_G 0.92 0.63 0.14
13_I 30_R 0.90 0.60 0.13
95_C 53_R 0.88 0.58 0.12
18_Q 27_R 0.86 0.56 0.11
26_T 48_K 0.86 0.55 0.11
77_V 52_E 0.85 0.54 0.10
90_L 23_G 0.85 0.53 0.10
27_G 19_C 0.84 0.52 0.10
70_K 23_G 0.84 0.52 0.10
65_E 12_K 0.83 0.52 0.10
10_L 12_K 0.83 0.51 0.10
25_D 37_C 0.83 0.51 0.10
15_I 2_M 0.83 0.51 0.10
71_A 8_K 0.82 0.50 0.09
68_G 13_F 0.82 0.50 0.09
42_W 30_R 0.82 0.50 0.09
88_N 25_I 0.82 0.49 0.09
47_I 23_G 0.82 0.49 0.09
68_G 34_K 0.81 0.49 0.09
20_K 52_E 0.81 0.48 0.09
90_L 22_E 0.79 0.46 0.08
75_V 30_R 0.79 0.46 0.08
85_I 44_G 0.79 0.45 0.08
29_D 21_K 0.78 0.45 0.08
77_V 55_A 0.78 0.45 0.08
94_G 11_R 0.78 0.44 0.08
49_G 32_P 0.77 0.44 0.08
31_T 51_T 0.76 0.42 0.07
77_V 40_C 0.76 0.42 0.07
92_Q 51_T 0.76 0.42 0.07
22_A 44_G 0.76 0.42 0.07
43_K 35_K 0.76 0.42 0.07
57_R 21_K 0.76 0.42 0.07
15_I 20_G 0.76 0.41 0.07
83_N 54_Q 0.75 0.40 0.07
72_I 32_P 0.74 0.40 0.07
63_L 8_K 0.74 0.40 0.07
82_V 22_E 0.74 0.40 0.07
36_M 30_R 0.74 0.39 0.07
81_P 20_G 0.74 0.39 0.07
16_G 13_F 0.74 0.39 0.07
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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