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OPENSEQ.org
NorrinIMD-ARCandFz4SMC-EEVPLP2
Genes: A B A+B
Length: 133 120 237
Sequences: 534 723 64
Seq/Len: 4.02 6.03 0.27
MirrorTree (Pazo et al. 2001) 0.01
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 0.06 0.04 0.00
2 0.06 0.04 0.00
5 0.07 0.04 0.01
10 0.08 0.04 0.02
20 0.09 0.05 0.04
100 0.10 0.05 0.11
∞ 0.12 0.07 0.25
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
65_C 40_C 1.23 0.24 0.00
65_C 49_C 1.23 0.24 0.00
65_C 54_P 1.23 0.24 0.00
65_C 56_C 1.23 0.24 0.00
65_C 71_C 1.23 0.24 0.00
65_C 78_C 1.23 0.24 0.00
65_C 95_C 1.23 0.24 0.00
67_G 40_C 1.23 0.24 0.00
67_G 49_C 1.23 0.24 0.00
67_G 54_P 1.23 0.24 0.00
67_G 56_C 1.23 0.24 0.00
67_G 71_C 1.23 0.24 0.00
67_G 78_C 1.23 0.24 0.00
67_G 95_C 1.23 0.24 0.00
69_C 40_C 1.23 0.24 0.00
69_C 49_C 1.23 0.24 0.00
69_C 54_P 1.23 0.24 0.00
69_C 56_C 1.23 0.24 0.00
69_C 71_C 1.23 0.24 0.00
69_C 78_C 1.23 0.24 0.00
69_C 95_C 1.23 0.24 0.00
126_C 40_C 1.23 0.24 0.00
126_C 49_C 1.23 0.24 0.00
126_C 54_P 1.23 0.24 0.00
126_C 56_C 1.23 0.24 0.00
126_C 71_C 1.23 0.24 0.00
126_C 78_C 1.23 0.24 0.00
126_C 95_C 1.23 0.24 0.00
128_C 40_C 1.23 0.24 0.00
128_C 49_C 1.23 0.24 0.00
128_C 54_P 1.23 0.24 0.00
128_C 56_C 1.23 0.24 0.00
128_C 71_C 1.23 0.24 0.00
128_C 78_C 1.23 0.24 0.00
128_C 95_C 1.23 0.24 0.00
96_C 40_C 1.03 0.16 0.00
96_C 49_C 1.03 0.16 0.00
96_C 54_P 1.03 0.16 0.00
96_C 56_C 1.03 0.16 0.00
96_C 71_C 1.03 0.16 0.00
96_C 78_C 1.03 0.16 0.00
96_C 95_C 1.03 0.16 0.00
42_H 75_K 0.97 0.14 0.00
43_H 82_L 0.95 0.13 0.00
50_H 10_V 0.94 0.13 0.00
45_V 16_L 0.91 0.12 0.00
65_C 3_C 0.91 0.12 0.00
67_G 3_C 0.91 0.12 0.00
69_C 3_C 0.91 0.12 0.00
126_C 3_C 0.91 0.12 0.00
128_C 3_C 0.91 0.12 0.00
107_R 98_F 0.89 0.11 0.00
54_K 44_L 0.89 0.11 0.00
48_I 97_K 0.87 0.11 0.00
92_S 63_P 0.85 0.10 0.00
49_S 58_E 0.85 0.10 0.00
39_C 40_C 0.84 0.10 0.00
39_C 49_C 0.84 0.10 0.00
39_C 54_P 0.84 0.10 0.00
39_C 56_C 0.84 0.10 0.00
39_C 71_C 0.84 0.10 0.00
39_C 78_C 0.84 0.10 0.00
39_C 95_C 0.84 0.10 0.00
61_L 109_M 0.84 0.10 0.00
25_K 36_I 0.83 0.10 0.00
68_H 98_F 0.83 0.10 0.00
105_A 11_T 0.82 0.10 0.00
99_Q 29_L 0.82 0.10 0.00
96_C 35_L 0.81 0.09 0.00
44_Y 86_G 0.80 0.09 0.00
98_P 32_F 0.79 0.09 0.00
23_D 25_A 0.79 0.09 0.00
65_C 108_C 0.78 0.09 0.00
67_G 108_C 0.78 0.09 0.00
69_C 108_C 0.78 0.09 0.00
126_C 108_C 0.78 0.09 0.00
128_C 108_C 0.78 0.09 0.00
48_I 12_K 0.77 0.09 0.00
71_Q 13_M 0.77 0.09 0.00
45_V 62_I 0.76 0.09 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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