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OPENSEQ.org
4FZA_AB
Genes: A B A+B
Length: 328 283 579
Sequences: 345 74795 165
Seq/Len: 1.05 264.29 0.28
MirrorTree (Pazo et al. 2001) 0.45
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 0.06 0.10 0.02
2 0.06 0.13 0.05
5 0.06 0.17 0.10
10 0.06 0.21 0.17
20 0.06 0.25 0.27
100 0.06 0.32 0.45
∞ 0.07 0.34 0.48
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
72_G 171_W 1.45 0.37 0.00
175_A 68_V 1.30 0.28 0.00
293_Q 10_F 1.28 0.27 0.00
39_K 152_A 1.25 0.25 0.00
293_Q 255_L 1.21 0.24 0.00
15_E 250_T 1.16 0.21 0.00
271_V 102_F 1.15 0.21 0.00
294_A 84_I 1.12 0.20 0.00
10_V 173_A 1.12 0.19 0.00
81_L 73_G 1.09 0.18 0.00
220_K 141_Q 1.06 0.17 0.00
44_M 146_L 1.03 0.16 0.00
282_T 25_F 1.02 0.16 0.00
239_I 136_V 1.01 0.15 0.00
175_A 115_L 1.00 0.15 0.00
321_V 244_D 1.00 0.15 0.00
39_K 127_I 0.99 0.15 0.00
74_L 114_I 0.98 0.14 0.00
292_N 122_H 0.98 0.14 0.00
8_D 219_K 0.98 0.14 0.00
12_N 93_A 0.96 0.14 0.00
81_L 259_F 0.96 0.14 0.00
259_D 38_I 0.95 0.14 0.00
230_L 176_V 0.94 0.13 0.00
319_Y 137_L 0.94 0.13 0.00
200_H 16_I 0.94 0.13 0.00
295_K 86_E 0.94 0.13 0.00
194_A 254_L 0.93 0.13 0.00
45_K 241_L 0.93 0.13 0.00
196_F 234_K 0.93 0.13 0.00
276_V 171_W 0.92 0.12 0.00
324_I 69_T 0.92 0.12 0.00
138_G 128_H 0.91 0.12 0.00
174_I 22_G 0.91 0.12 0.00
321_V 226_V 0.91 0.12 0.00
15_E 179_Q 0.90 0.12 0.00
147_H 235_E 0.90 0.12 0.00
74_L 253_E 0.90 0.12 0.00
294_A 98_R 0.90 0.12 0.00
276_V 201_G 0.90 0.12 0.00
184_D 138_L 0.89 0.12 0.00
294_A 68_V 0.89 0.12 0.00
229_E 195_A 0.89 0.12 0.00
196_F 250_T 0.88 0.11 0.00
196_F 87_Y 0.88 0.11 0.00
61_V 97_L 0.88 0.11 0.00
188_R 249_P 0.87 0.11 0.00
242_K 198_L 0.86 0.11 0.00
293_Q 254_L 0.86 0.11 0.00
239_I 64_D 0.85 0.11 0.00
114_I 238_D 0.85 0.11 0.00
293_Q 251_A 0.84 0.10 0.00
184_D 139_S 0.84 0.10 0.00
317_K 68_V 0.84 0.10 0.00
146_R 249_P 0.83 0.10 0.00
268_A 65_S 0.83 0.10 0.00
223_S 189_W 0.83 0.10 0.00
41_L 217_I 0.83 0.10 0.00
324_I 187_D 0.83 0.10 0.00
170_S 25_F 0.83 0.10 0.00
193_S 126_K 0.82 0.10 0.00
8_D 33_Q 0.82 0.10 0.00
248_E 86_E 0.82 0.10 0.00
132_E 115_L 0.82 0.10 0.00
260_K 57_I 0.81 0.10 0.00
277_A 192_G 0.81 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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