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OPENSEQ.org
C2_1PH
Genes: A B A+B
Length: 96 102 184
Sequences: 8675 10251 492
Seq/Len: 90.36 100.5 2.67
MirrorTree (Pazo et al. 2001) 0.14
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 0.06 0.27
2 0.07 0.07 0.44
5 0.08 0.08 0.83
10 0.09 0.09 1.51
20 0.10 0.10 2.48
100 0.15 0.18 6.35
∞ 0.21 0.23 9.51
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
40_V 97_L 1.24 0.84 0.12
62_G 51_I 1.04 0.65 0.06
55_K 89_E 1.03 0.65 0.06
69_I 86_N 0.97 0.58 0.05
28_P 27_W 0.94 0.54 0.04
55_K 23_F 0.91 0.50 0.04
60_F 2_V 0.89 0.48 0.04
91_I 51_I 0.89 0.48 0.04
59_P 82_I 0.87 0.46 0.04
50_T 81_Y 0.85 0.43 0.03
61_Y 54_I 0.85 0.43 0.03
21_A 76_P 0.84 0.42 0.03
18_I 52_E 0.82 0.40 0.03
56_S 28_F 0.78 0.35 0.03
78_F 99_K 0.78 0.35 0.03
16_I 57_V 0.78 0.35 0.03
83_R 82_I 0.76 0.33 0.02
79_Y 66_K 0.76 0.33 0.02
41_N 29_R 0.74 0.31 0.02
18_I 34_E 0.74 0.30 0.02
42_L 11_R 0.73 0.30 0.02
78_F 86_N 0.73 0.30 0.02
21_A 62_E 0.73 0.30 0.02
35_D 96_I 0.73 0.30 0.02
61_Y 35_F 0.73 0.30 0.02
13_S 100_V 0.72 0.29 0.02
58_C 69_N 0.72 0.28 0.02
40_V 19_G 0.71 0.28 0.02
72_S 73_V 0.70 0.27 0.02
18_I 32_N 0.70 0.27 0.02
52_I 95_D 0.70 0.27 0.02
70_P 55_L 0.70 0.27 0.02
18_I 72_Q 0.70 0.27 0.02
14_V 83_Q 0.70 0.27 0.02
93_G 86_N 0.70 0.27 0.02
81_F 66_K 0.70 0.27 0.02
78_F 78_R 0.69 0.26 0.02
67_C 52_E 0.69 0.26 0.02
93_G 73_V 0.68 0.25 0.02
53_V 95_D 0.68 0.25 0.02
61_Y 25_K 0.68 0.25 0.02
51_K 88_V 0.68 0.25 0.02
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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