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OPENSEQ.org
1R8S
Genes: A B A+B
Length: 164 203 358
Sequences: 12611 1192 161
Seq/Len: 76.9 5.87 0.45
MirrorTree (Pazo et al. 2001) 0.09
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 0.05 0.04 0.03
2 0.06 0.05 0.05
5 0.08 0.05 0.11
10 0.10 0.05 0.23
20 0.13 0.06 0.44
100 0.23 0.07 1.19
∞ 0.29 0.11 1.90
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
14_T 76_V 1.40 0.46 0.00
143_A 88_D 1.35 0.42 0.00
3_I 160_G 1.30 0.39 0.00
6_V 84_H 1.19 0.31 0.00
3_I 85_E 1.08 0.24 0.00
141_T 169_R 1.05 0.23 0.00
86_A 142_S 1.05 0.23 0.00
44_I 165_V 1.00 0.20 0.00
140_A 94_A 0.99 0.20 0.00
78_N 191_N 0.98 0.19 0.00
83_V 65_Y 0.98 0.19 0.00
14_T 16_M 0.97 0.19 0.00
46_F 108_A 0.96 0.18 0.00
67_N 158_K 0.96 0.18 0.00
75_V 183_R 0.95 0.18 0.00
123_T 186_Y 0.92 0.17 0.00
154_D 88_D 0.91 0.16 0.00
6_V 79_A 0.89 0.15 0.00
3_I 47_I 0.89 0.15 0.00
65_F 186_Y 0.89 0.15 0.00
133_H 140_S 0.87 0.15 0.00
4_L 91_L 0.87 0.15 0.00
72_I 144_I 0.87 0.14 0.00
75_V 140_S 0.86 0.14 0.00
107_F 132_S 0.84 0.14 0.00
144_T 174_G 0.84 0.14 0.00
106_V 84_H 0.83 0.13 0.00
67_N 95_L 0.83 0.13 0.00
122_I 191_N 0.82 0.13 0.00
28_T 153_P 0.82 0.13 0.00
82_R 86_F 0.82 0.13 0.00
149_L 87_T 0.82 0.13 0.00
139_Q 119_A 0.81 0.13 0.00
14_T 61_A 0.81 0.13 0.00
102_A 196_I 0.81 0.13 0.00
16_I 164_F 0.81 0.12 0.00
16_I 51_L 0.81 0.12 0.00
11_A 31_I 0.80 0.12 0.00
16_I 163_R 0.80 0.12 0.00
105_L 158_K 0.79 0.12 0.00
122_I 76_V 0.78 0.12 0.00
83_V 136_C 0.78 0.12 0.00
95_A 62_I 0.77 0.11 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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