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OPENSEQ.org
AfQ2 AfM
Genes: A B A+B
Length: 272 459 715
Sequences: 6143 764 79
Seq/Len: 22.58 1.66 0.11
MirrorTree (Pazo et al. 2001) 0.31
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 0.01 0.09 0.04
2 0.01 0.09 0.08
5 0.01 0.09 0.08
10 0.01 0.09 0.09
20 0.03 0.10 0.11
100 0.05 0.10 0.19
∞ 0.16 0.12 0.60
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
36_K 83_I 1.48 0.21 0.00
83_W 202_A 1.22 0.14 0.00
42_V 24_I 1.22 0.13 0.00
51_S 304_T 1.16 0.12 0.00
200_I 220_D 1.15 0.12 0.00
28_A 41_A 1.13 0.11 0.00
205_V 222_T 1.13 0.11 0.00
42_V 26_V 1.12 0.11 0.00
25_D 213_D 1.12 0.11 0.00
58_A 438_E 1.09 0.10 0.00
69_A 29_K 1.08 0.10 0.00
42_V 433_F 1.08 0.10 0.00
44_G 276_R 1.07 0.10 0.00
267_I 26_V 1.06 0.10 0.00
190_L 222_T 1.05 0.10 0.00
67_T 304_T 1.04 0.10 0.00
33_A 222_T 1.03 0.10 0.00
265_H 22_K 1.02 0.09 0.00
257_A 402_S 1.02 0.09 0.00
51_S 142_D 1.01 0.09 0.00
151_V 183_F 1.01 0.09 0.00
94_D 436_A 1.01 0.09 0.00
51_S 402_S 1.01 0.09 0.00
28_A 219_M 1.00 0.09 0.00
119_T 132_A 0.99 0.09 0.00
42_V 41_A 0.99 0.09 0.00
200_I 213_D 0.99 0.09 0.00
10_N 95_T 0.97 0.09 0.00
23_Q 26_V 0.97 0.09 0.00
196_V 311_M 0.97 0.08 0.00
220_D 65_K 0.96 0.08 0.00
51_S 26_V 0.96 0.08 0.00
232_A 203_P 0.96 0.08 0.00
81_G 256_D 0.95 0.08 0.00
246_R 22_K 0.95 0.08 0.00
176_F 232_I 0.94 0.08 0.00
23_Q 211_V 0.93 0.08 0.00
115_A 276_R 0.93 0.08 0.00
220_D 239_E 0.93 0.08 0.00
173_F 292_G 0.93 0.08 0.00
194_T 246_F 0.93 0.08 0.00
34_Y 436_A 0.92 0.08 0.00
196_V 11_S 0.92 0.08 0.00
134_P 140_A 0.91 0.08 0.00
23_Q 83_I 0.91 0.08 0.00
239_V 208_I 0.91 0.08 0.00
253_I 304_T 0.91 0.07 0.00
243_A 200_V 0.91 0.07 0.00
200_I 311_M 0.91 0.07 0.00
62_G 98_R 0.91 0.07 0.00
97_L 356_E 0.90 0.07 0.00
182_N 18_I 0.89 0.07 0.00
264_E 99_M 0.89 0.07 0.00
67_T 314_L 0.89 0.07 0.00
134_P 426_Y 0.88 0.07 0.00
170_K 52_G 0.88 0.07 0.00
74_M 29_K 0.88 0.07 0.00
237_D 98_R 0.88 0.07 0.00
184_E 120_H 0.88 0.07 0.00
93_Q 75_D 0.87 0.07 0.00
27_V 24_I 0.87 0.07 0.00
148_F 86_P 0.87 0.07 0.00
196_V 432_E 0.87 0.07 0.00
253_I 278_Q 0.87 0.07 0.00
112_I 258_L 0.87 0.07 0.00
67_T 362_P 0.86 0.07 0.00
146_P 428_R 0.86 0.07 0.00
81_G 261_L 0.86 0.07 0.00
10_N 155_K 0.86 0.07 0.00
197_A 174_E 0.86 0.07 0.00
257_A 416_C 0.86 0.07 0.00
257_A 386_G 0.86 0.07 0.00
181_P 142_D 0.85 0.07 0.00
209_A 29_K 0.85 0.07 0.00
136_D 219_M 0.85 0.07 0.00
125_P 98_R 0.84 0.07 0.00
253_I 142_D 0.84 0.07 0.00
200_I 265_F 0.84 0.07 0.00
112_I 24_I 0.84 0.07 0.00
93_Q 69_A 0.84 0.07 0.00
257_A 433_F 0.84 0.07 0.00
206_T 24_I 0.84 0.07 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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