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OPENSEQ.org
J CTD F
Genes: A B A+B
Length: 306 200 492
Sequences: 1030 113 65
Seq/Len: 3.37 0.56 0.13
MirrorTree (Pazo et al. 2001) 0.50
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 0.00 0.01
2 0.06 0.00 0.01
5 0.08 0.00 0.02
10 0.09 0.00 0.02
20 0.10 0.00 0.03
100 0.14 0.00 0.05
∞ 0.19 0.00 0.13
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
217_F 141_T 1.25 0.16 0.00
165_N 195_R 1.24 0.15 0.00
191_A 24_Q 1.22 0.15 0.00
260_K 20_Y 1.15 0.13 0.00
284_V 93_Q 1.11 0.12 0.00
156_F 141_T 1.11 0.12 0.00
224_Y 141_T 1.09 0.12 0.00
72_K 26_A 1.08 0.12 0.00
141_F 20_Y 1.08 0.11 0.00
180_Y 83_D 1.07 0.11 0.00
255_G 2_V 1.07 0.11 0.00
270_M 83_D 1.07 0.11 0.00
91_L 145_D 1.07 0.11 0.00
88_H 143_I 1.06 0.11 0.00
252_P 14_A 1.05 0.11 0.00
11_Y 16_D 1.04 0.10 0.00
191_A 192_T 1.03 0.10 0.00
44_K 42_A 1.03 0.10 0.00
190_D 173_D 1.02 0.10 0.00
103_L 169_Y 1.02 0.10 0.00
218_N 169_Y 1.01 0.10 0.00
44_K 59_L 1.01 0.10 0.00
83_V 143_I 1.01 0.10 0.00
192_E 53_K 0.99 0.10 0.00
281_T 68_V 0.99 0.10 0.00
250_V 86_N 0.97 0.09 0.00
73_N 156_R 0.96 0.09 0.00
103_L 145_D 0.95 0.09 0.00
106_N 144_D 0.95 0.09 0.00
34_A 195_R 0.94 0.09 0.00
43_I 108_K 0.94 0.09 0.00
72_K 116_S 0.94 0.09 0.00
170_R 93_Q 0.94 0.09 0.00
73_N 64_A 0.93 0.09 0.00
21_P 141_T 0.92 0.08 0.00
165_N 14_A 0.92 0.08 0.00
165_N 145_D 0.92 0.08 0.00
225_N 25_Y 0.91 0.08 0.00
10_Q 88_R 0.91 0.08 0.00
34_A 20_Y 0.90 0.08 0.00
133_N 172_Q 0.89 0.08 0.00
253_M 145_D 0.89 0.08 0.00
65_G 172_Q 0.88 0.08 0.00
258_K 93_Q 0.88 0.08 0.00
39_Q 8_P 0.88 0.08 0.00
150_K 128_K 0.87 0.08 0.00
59_L 89_D 0.87 0.08 0.00
264_G 16_D 0.87 0.07 0.00
138_N 144_D 0.87 0.07 0.00
106_N 174_M 0.86 0.07 0.00
84_S 39_V 0.86 0.07 0.00
126_L 169_Y 0.86 0.07 0.00
240_L 72_E 0.86 0.07 0.00
144_S 189_G 0.86 0.07 0.00
202_I 130_I 0.86 0.07 0.00
19_L 84_N 0.86 0.07 0.00
19_L 38_I 0.85 0.07 0.00
81_A 137_S 0.85 0.07 0.00
134_R 166_Q 0.84 0.07 0.00
24_A 189_G 0.84 0.07 0.00
186_M 3_A 0.84 0.07 0.00
145_A 24_Q 0.84 0.07 0.00
156_F 80_S 0.83 0.07 0.00
9_T 176_T 0.83 0.07 0.00
230_Y 28_N 0.83 0.07 0.00
106_N 146_K 0.83 0.07 0.00
223_R 145_D 0.83 0.07 0.00
92_D 104_E 0.83 0.07 0.00
15_N 183_C 0.83 0.07 0.00
113_D 110_D 0.83 0.07 0.00
252_P 16_D 0.82 0.07 0.00
98_Y 80_S 0.82 0.07 0.00
181_Q 170_F 0.82 0.07 0.00
32_I 37_E 0.81 0.07 0.00
76_T 88_R 0.81 0.07 0.00
265_Y 2_V 0.81 0.07 0.00
128_P 144_D 0.81 0.07 0.00
222_R 26_A 0.81 0.07 0.00
151_N 128_K 0.81 0.07 0.00
189_K 80_S 0.80 0.07 0.00
9_T 178_Y 0.80 0.07 0.00
72_K 124_D 0.80 0.07 0.00
132_D 143_I 0.79 0.07 0.00
284_V 150_Y 0.79 0.07 0.00
152_F 38_I 0.79 0.07 0.00
265_Y 189_G 0.79 0.06 0.00
185_G 8_P 0.79 0.06 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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