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OPENSEQ.org
sar-m88 (A, 1-300) (B, 130-276)
Genes: A B A+B
Length: 300 147 429
Sequences: 7484 2189 120
Seq/Len: 24.95 14.89 0.28
MirrorTree (Pazo et al. 2001) 0.08
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 0.04 0.09 0.01
2 0.04 0.09 0.01
5 0.05 0.11 0.02
10 0.06 0.12 0.03
20 0.07 0.13 0.04
100 0.13 0.14 0.13
∞ 0.22 0.16 0.27
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
74_V 29_M 1.25 0.26 0.00
197_R 29_M 1.22 0.24 0.00
189_L 52_G 1.20 0.23 0.00
31_R 75_S 1.10 0.19 0.00
135_M 106_I 1.10 0.19 0.00
268_V 75_S 1.06 0.17 0.00
252_T 106_I 1.06 0.17 0.00
213_G 86_F 1.05 0.17 0.00
123_C 13_D 1.04 0.16 0.00
264_L 16_I 1.03 0.16 0.00
69_E 5_L 1.03 0.16 0.00
38_L 94_L 1.02 0.16 0.00
240_C 12_F 1.01 0.15 0.00
97_G 48_D 1.00 0.15 0.00
160_A 74_V 0.99 0.15 0.00
254_V 119_L 0.99 0.15 0.00
236_A 22_D 0.99 0.15 0.00
38_L 134_S 0.98 0.14 0.00
19_L 75_S 0.98 0.14 0.00
140_A 64_E 0.98 0.14 0.00
220_L 37_N 0.97 0.14 0.00
237_F 126_D 0.95 0.14 0.00
81_M 71_V 0.95 0.14 0.00
215_D 48_D 0.94 0.13 0.00
240_C 103_L 0.94 0.13 0.00
55_L 18_Y 0.94 0.13 0.00
163_A 40_L 0.94 0.13 0.00
149_F 111_M 0.93 0.13 0.00
81_M 13_D 0.93 0.13 0.00
188_P 26_V 0.93 0.13 0.00
261_I 12_F 0.92 0.13 0.00
211_G 73_V 0.92 0.13 0.00
144_L 129_N 0.92 0.12 0.00
223_L 73_V 0.92 0.12 0.00
284_L 26_V 0.92 0.12 0.00
281_K 72_V 0.92 0.12 0.00
60_N 71_V 0.91 0.12 0.00
211_G 29_M 0.91 0.12 0.00
145_F 48_D 0.91 0.12 0.00
259_G 67_C 0.91 0.12 0.00
59_L 118_I 0.90 0.12 0.00
144_L 52_G 0.90 0.12 0.00
55_L 50_L 0.89 0.12 0.00
161_C 73_V 0.89 0.12 0.00
97_G 16_I 0.89 0.12 0.00
168_A 50_L 0.89 0.12 0.00
105_C 91_A 0.89 0.12 0.00
147_L 13_D 0.89 0.12 0.00
16_L 93_S 0.88 0.12 0.00
61_L 87_Q 0.88 0.12 0.00
81_M 116_P 0.88 0.12 0.00
43_V 72_V 0.88 0.11 0.00
120_L 29_M 0.88 0.11 0.00
272_T 57_S 0.88 0.11 0.00
117_A 29_M 0.87 0.11 0.00
107_R 77_D 0.86 0.11 0.00
127_G 67_C 0.86 0.11 0.00
147_L 50_L 0.86 0.11 0.00
156_L 59_A 0.86 0.11 0.00
62_A 74_V 0.86 0.11 0.00
236_A 68_R 0.86 0.11 0.00
35_A 50_L 0.85 0.10 0.00
16_L 79_L 0.84 0.10 0.00
283_A 114_E 0.84 0.10 0.00
144_L 17_C 0.84 0.10 0.00
105_C 81_S 0.84 0.10 0.00
38_L 61_E 0.84 0.10 0.00
144_L 18_Y 0.84 0.10 0.00
232_Q 51_P 0.83 0.10 0.00
108_T 43_C 0.83 0.10 0.00
265_K 72_V 0.83 0.10 0.00
97_G 103_L 0.83 0.10 0.00
14_G 144_L 0.83 0.10 0.00
164_V 112_K 0.83 0.10 0.00
97_G 43_C 0.83 0.10 0.00
29_E 48_D 0.81 0.10 0.00
163_A 104_I 0.81 0.10 0.00
148_A 120_R 0.81 0.10 0.00
107_R 105_P 0.81 0.10 0.00
189_L 40_L 0.81 0.10 0.00
78_L 107_K 0.80 0.10 0.00
189_L 12_F 0.80 0.10 0.00
140_A 41_K 0.80 0.10 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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