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OPENSEQ.org
Ftype_a_c_sub_real
Genes: A B A+B
Length: 72 226 289
Sequences: 1674 5369 2473
Seq/Len: 23.25 23.76 8.56
MirrorTree (Pazo et al. 2001) 0.70
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 7.56
2 0.00 0.00 7.72
5 0.00 0.00 7.93
10 0.00 0.00 8.19
20 0.00 0.00 8.30
100 0.00 0.00 8.42
∞ 0.01 0.00 8.48
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
61_L 162_A 2.42 1.00 1.00
67_A 97_Q 1.14 0.96 0.74
20_S 166_A 1.04 0.92 0.65
62_F 155_A 1.03 0.92 0.63
55_L 209_I 1.01 0.91 0.61
50_I 213_V 0.95 0.87 0.54
22_A 26_F 0.90 0.82 0.47
68_F 176_G 0.89 0.82 0.47
60_G 104_M 0.89 0.82 0.47
58_A 221_Y 0.88 0.81 0.45
24_I 203_E 0.87 0.80 0.44
17_V 201_I 0.86 0.79 0.43
61_L 158_V 0.86 0.79 0.43
38_N 153_P 0.85 0.77 0.41
47_S 212_Y 0.82 0.74 0.37
58_A 155_A 0.82 0.73 0.37
42_K 68_W 0.80 0.71 0.35
27_V 73_M 0.80 0.71 0.35
30_S 202_L 0.79 0.70 0.34
6_K 213_V 0.77 0.67 0.32
30_S 36_R 0.77 0.67 0.31
16_G 221_Y 0.76 0.65 0.30
38_N 102_L 0.76 0.65 0.30
55_L 155_A 0.76 0.65 0.29
62_F 206_V 0.73 0.61 0.27
24_I 145_E 0.73 0.61 0.27
49_A 50_L 0.73 0.60 0.26
59_M 145_E 0.72 0.60 0.26
54_A 213_V 0.72 0.60 0.26
33_I 14_I 0.72 0.60 0.26
24_I 149_L 0.71 0.58 0.24
7_F 15_L 0.71 0.57 0.24
58_A 141_L 0.70 0.57 0.24
45_L 51_Q 0.70 0.56 0.24
51_L 105_A 0.70 0.56 0.24
46_F 216_L 0.68 0.52 0.21
52_G 173_L 0.67 0.52 0.21
50_I 220_L 0.67 0.51 0.20
49_A 126_A 0.67 0.51 0.20
8_I 27_P 0.66 0.49 0.20
68_F 174_I 0.65 0.48 0.19
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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