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OPENSEQ.org
msrATrxC
Genes: A B A+B
Length: 182 116 263
Sequences: 4709 15797 214
Seq/Len: 25.87 136.18 0.81
MirrorTree (Pazo et al. 2001) 0.37
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 0.03 0.02 0.10
2 0.03 0.03 0.14
5 0.04 0.03 0.23
10 0.04 0.03 0.42
20 0.04 0.04 0.72
100 0.06 0.09 2.83
∞ 0.12 0.19 8.23
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
6_K 66_D 1.37 0.61 0.00
62_V 92_V 1.27 0.52 0.00
34_Y 47_L 1.13 0.40 0.00
68_L 99_K 1.12 0.40 0.00
24_Q 58_L 1.10 0.38 0.00
58_F 88_D 1.05 0.34 0.00
8_I 30_V 0.98 0.28 0.00
62_V 77_V 0.98 0.28 0.00
64_D 21_V 0.98 0.28 0.00
69_L 34_A 0.95 0.26 0.00
100_D 64_D 0.93 0.25 0.00
124_V 94_R 0.93 0.25 0.00
45_R 100_G 0.92 0.24 0.00
59_D 72_A 0.90 0.23 0.00
45_R 28_V 0.89 0.22 0.00
54_V 47_L 0.88 0.22 0.00
100_D 109_S 0.87 0.21 0.00
96_I 94_R 0.87 0.21 0.00
41_N 63_L 0.86 0.21 0.00
56_I 61_A 0.86 0.21 0.00
55_E 64_D 0.84 0.20 0.00
88_R 45_P 0.84 0.19 0.00
31_R 64_D 0.84 0.19 0.00
30_T 62_K 0.84 0.19 0.00
58_F 110_D 0.83 0.19 0.00
127_E 15_A 0.83 0.19 0.00
73_F 43_V 0.82 0.18 0.00
135_W 30_V 0.82 0.18 0.00
38_N 64_D 0.81 0.18 0.00
88_R 32_F 0.81 0.18 0.00
21_I 94_R 0.80 0.17 0.00
114_V 50_I 0.80 0.17 0.00
98_Y 87_K 0.80 0.17 0.00
139_P 95_I 0.80 0.17 0.00
148_Y 77_V 0.80 0.17 0.00
29_S 83_L 0.79 0.17 0.00
56_I 75_F 0.79 0.17 0.00
106_I 88_D 0.79 0.17 0.00
108_L 38_G 0.79 0.17 0.00
27_V 27_P 0.79 0.17 0.00
128_V 38_G 0.78 0.16 0.00
124_V 110_D 0.78 0.16 0.00
30_T 30_V 0.78 0.16 0.00
102_Q 88_D 0.78 0.16 0.00
140_E 24_S 0.78 0.16 0.00
31_R 65_V 0.77 0.16 0.00
144_Y 41_K 0.77 0.16 0.00
79_T 39_P 0.77 0.16 0.00
19_D 80_I 0.76 0.15 0.00
128_V 109_S 0.76 0.15 0.00
10_A 53_E 0.76 0.15 0.00
60_P 63_L 0.75 0.15 0.00
139_P 41_K 0.74 0.14 0.00
105_R 75_F 0.74 0.14 0.00
96_I 82_T 0.74 0.14 0.00
109_D 98_A 0.73 0.14 0.00
28_V 104_L 0.73 0.14 0.00
139_P 20_D 0.73 0.14 0.00
68_L 29_L 0.73 0.14 0.00
58_F 73_R 0.73 0.14 0.00
20_L 102_A 0.73 0.14 0.00
40_P 24_S 0.72 0.14 0.00
109_D 63_L 0.72 0.14 0.00
81_K 75_F 0.72 0.14 0.00
47_H 86_F 0.72 0.14 0.00
10_A 70_E 0.72 0.14 0.00
128_V 45_P 0.72 0.14 0.00
100_D 19_T 0.71 0.13 0.00
39_I 25_N 0.71 0.13 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)
ID Seq/Len Name Options I_Prob Status
13585 0.81 msrATrxC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13329 0.81 Complejo msrTrx Δgene:(1, 20) A:(1E-20, 4) B:(1E-20, 4) msa: HHblits (2015_06) 0.00 Done - Shared
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