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OPENSEQ.org
cI_A_cIII_ispB_Pnitri
Genes: A B A+B
Length: 121 195 303
Sequences: 4481 2175 575
Seq/Len: 37.03 11.15 1.9
MirrorTree (Pazo et al. 2001) 0.51
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.01
10 0.00 0.01 0.01
20 0.00 0.01 0.03
100 0.01 0.02 0.15
∞ 0.02 0.07 1.82
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
89_S 27_A 1.48 0.90 0.34
11_I 136_V 1.43 0.87 0.30
13_V 47_M 1.26 0.76 0.19
28_A 181_I 1.12 0.64 0.13
32_I 32_G 1.09 0.60 0.11
103_A 37_G 1.03 0.54 0.09
106_T 145_I 0.99 0.50 0.08
28_A 150_G 0.98 0.49 0.08
53_D 124_M 0.94 0.44 0.07
63_F 73_T 0.91 0.41 0.06
31_V 27_A 0.91 0.41 0.06
35_R 24_L 0.90 0.40 0.06
7_E 36_A 0.90 0.40 0.06
77_V 57_A 0.90 0.40 0.06
36_N 179_L 0.90 0.40 0.06
32_I 29_A 0.90 0.39 0.06
114_K 60_Q 0.89 0.39 0.06
85_V 28_T 0.88 0.37 0.05
93_V 37_G 0.88 0.37 0.05
19_S 143_V 0.87 0.37 0.05
97_G 141_G 0.87 0.37 0.05
94_A 135_G 0.87 0.36 0.05
67_S 193_K 0.86 0.36 0.05
100_V 93_A 0.86 0.36 0.05
11_I 47_M 0.86 0.36 0.05
93_V 64_S 0.86 0.36 0.05
29_A 124_M 0.85 0.35 0.05
45_Y 171_R 0.85 0.35 0.05
50_N 31_A 0.85 0.35 0.05
24_V 36_A 0.84 0.34 0.04
20_A 36_A 0.84 0.34 0.04
39_P 14_G 0.84 0.33 0.04
44_A 155_W 0.84 0.33 0.04
116_G 169_R 0.83 0.33 0.04
17_M 103_I 0.83 0.33 0.04
31_V 97_V 0.82 0.32 0.04
39_P 27_A 0.82 0.32 0.04
72_I 167_S 0.81 0.30 0.04
96_W 44_V 0.81 0.30 0.04
93_V 191_T 0.80 0.30 0.04
59_F 158_P 0.80 0.30 0.04
51_A 190_T 0.80 0.30 0.04
75_L 184_A 0.80 0.30 0.04
38_D 122_R 0.79 0.29 0.04
87_F 29_A 0.79 0.29 0.04
88_A 193_K 0.78 0.28 0.03
23_I 14_G 0.78 0.28 0.03
39_P 64_S 0.77 0.28 0.03
13_V 14_G 0.77 0.27 0.03
91_S 140_L 0.77 0.27 0.03
51_A 119_D 0.77 0.27 0.03
32_I 19_T 0.77 0.27 0.03
92_D 151_D 0.76 0.27 0.03
88_A 92_Q 0.76 0.27 0.03
103_A 148_G 0.76 0.26 0.03
29_A 52_D 0.75 0.26 0.03
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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