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OPENSEQ.org
prochlorococcus ssu(A) acRAF(B)
Genes: A B A+B
Length: 113 87 193
Sequences: 563 1986 67
Seq/Len: 4.98 22.83 0.35
MirrorTree (Pazo et al. 2001) 0.57
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 0.04 0.01 0.01
2 0.05 0.01 0.01
5 0.09 0.01 0.02
10 0.10 0.01 0.21
20 0.11 0.01 0.25
100 0.12 0.02 0.34
∞ 0.17 0.04 0.94
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
66_F 54_L 1.51 0.47 0.00
79_L 56_L 1.49 0.45 0.00
38_I 67_A 1.47 0.44 0.00
75_V 17_F 1.34 0.35 0.00
91_V 52_V 1.23 0.28 0.00
108_V 1_M 1.15 0.24 0.00
25_M 49_K 1.11 0.22 0.00
95_G 12_R 1.11 0.22 0.00
80_E 81_L 1.06 0.20 0.00
77_S 17_F 1.04 0.19 0.00
41_G 28_F 1.03 0.18 0.00
90_H 59_D 1.02 0.18 0.00
105_T 21_T 1.02 0.18 0.00
28_E 39_R 1.02 0.18 0.00
75_V 80_A 1.00 0.17 0.00
72_L 74_F 1.00 0.17 0.00
91_V 25_T 0.99 0.17 0.00
26_T 32_L 0.98 0.17 0.00
52_S 82_I 0.98 0.16 0.00
79_L 45_I 0.98 0.16 0.00
39_A 74_F 0.96 0.16 0.00
7_V 71_D 0.96 0.16 0.00
95_G 49_K 0.95 0.15 0.00
50_H 7_R 0.95 0.15 0.00
104_G 19_F 0.95 0.15 0.00
89_H 13_L 0.94 0.15 0.00
71_D 79_D 0.94 0.15 0.00
97_D 37_E 0.94 0.15 0.00
7_V 32_L 0.93 0.15 0.00
90_H 49_K 0.92 0.14 0.00
93_I 45_I 0.92 0.14 0.00
97_D 52_V 0.91 0.14 0.00
29_E 57_Q 0.90 0.14 0.00
93_I 82_I 0.90 0.14 0.00
34_I 77_E 0.89 0.13 0.00
107_F 37_E 0.89 0.13 0.00
30_I 42_F 0.88 0.13 0.00
7_V 44_D 0.88 0.13 0.00
28_E 11_L 0.87 0.13 0.00
15_T 14_E 0.87 0.13 0.00
57_T 17_F 0.87 0.13 0.00
84_R 22_Y 0.87 0.12 0.00
39_A 60_S 0.87 0.12 0.00
45_V 34_K 0.84 0.12 0.00
7_V 64_D 0.83 0.12 0.00
107_F 52_V 0.83 0.12 0.00
17_E 28_F 0.82 0.11 0.00
75_V 30_D 0.82 0.11 0.00
46_I 46_S 0.81 0.11 0.00
76_V 20_A 0.81 0.11 0.00
37_I 65_S 0.81 0.11 0.00
10_Y 10_P 0.81 0.11 0.00
9_D 49_K 0.81 0.11 0.00
111_Q 33_G 0.80 0.11 0.00
11_Q 8_S 0.80 0.11 0.00
98_A 69_D 0.80 0.11 0.00
21_F 24_L 0.80 0.11 0.00
79_L 48_G 0.80 0.11 0.00
14_A 32_L 0.80 0.10 0.00
93_I 40_Q 0.80 0.10 0.00
95_G 35_L 0.80 0.10 0.00
48_H 10_P 0.79 0.10 0.00
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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