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OPENSEQ.org
TCR_CV_3C5Z
Genes: A B A+B
Length: 202 240 405
Sequences: 3194 3374 83
Seq/Len: 15.81 14.06 0.2
MirrorTree (Pazo et al. 2001) 0.43
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.13 0.14 0.06
2 0.14 0.15 0.09
5 0.16 0.17 0.12
10 0.16 0.18 0.16
20 0.17 0.19 0.19
100 0.19 0.21 0.28
∞ 0.21 0.22 0.36
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
89_C 141_C 2.36 0.79 0.41
173_A 78_L 2.07 0.65 0.23
34_W 155_W 1.94 0.57 0.17
89_C 89_C 1.73 0.45 0.10
89_C 206_C 1.63 0.39 0.07
89_C 21_C 1.57 0.36 0.06
22_C 141_C 1.53 0.34 0.05
74_L 85_A 1.46 0.30 0.04
89_C 19_L 1.39 0.27 0.03
63_A 221_Q 1.38 0.26 0.03
172_S 221_Q 1.36 0.25 0.03
74_L 155_W 1.33 0.24 0.03
22_C 107_L 1.32 0.23 0.03
182_F 32_W 1.30 0.22 0.02
173_A 17_V 1.29 0.22 0.02
34_W 85_A 1.27 0.21 0.02
198_F 202_N 1.25 0.21 0.02
21_H 144_T 1.25 0.20 0.02
34_W 87_Y 1.21 0.19 0.02
22_C 89_C 1.21 0.19 0.02
34_W 141_C 1.21 0.19 0.02
91_L 109_V 1.19 0.18 0.02
74_L 19_L 1.18 0.18 0.02
7_E 83_Q 1.18 0.18 0.02
18_L 164_S 1.18 0.18 0.01
175_A 16_K 1.17 0.18 0.01
85_A 206_C 1.17 0.17 0.01
22_C 17_V 1.15 0.17 0.01
34_W 206_C 1.14 0.17 0.01
28_G 210_F 1.14 0.16 0.01
129_S 127_S 1.14 0.16 0.01
22_C 85_A 1.12 0.16 0.01
76_K 223_R 1.11 0.15 0.01
195_E 194_A 1.10 0.15 0.01
171_N 92_I 1.09 0.15 0.01
193_I 155_W 1.08 0.15 0.01
70_T 159_G 1.07 0.14 0.01
74_L 74_L 1.06 0.14 0.01
29_Y 45_H 1.06 0.14 0.01
150_D 144_T 1.05 0.14 0.01
32_L 89_C 1.05 0.14 0.01
134_C 32_W 1.05 0.14 0.01
176_W 210_F 1.05 0.14 0.01
22_C 21_C 1.04 0.14 0.01
176_W 155_W 1.04 0.14 0.01
132_S 22_H 1.04 0.13 0.01
24_Y 204_F 1.04 0.13 0.01
34_W 139_L 1.03 0.13 0.01
128_S 76_L 1.03 0.13 0.01
89_C 17_V 1.03 0.13 0.01
190_N 89_C 1.03 0.13 0.01
22_C 61_G 1.03 0.13 0.01
24_Y 17_V 1.03 0.13 0.01
166_M 73_S 1.02 0.13 0.01
79_V 139_L 1.02 0.13 0.01
137_T 79_A 1.02 0.13 0.01
34_W 109_V 1.01 0.13 0.01
141_S 152_E 1.01 0.12 0.01
22_C 155_W 1.00 0.12 0.01
198_F 201_R 0.99 0.12 0.01
75_R 131_I 0.99 0.12 0.01
123_L 195_T 0.98 0.12 0.01
114_Q 32_W 0.98 0.12 0.01
35_Y 192_V 0.97 0.12 0.01
7_E 87_Y 0.97 0.12 0.01
60_G 17_V 0.96 0.11 0.01
173_A 59_P 0.96 0.11 0.01
128_S 126_P 0.95 0.11 0.01
9_N 14_G 0.95 0.11 0.01
148_S 125_E 0.95 0.11 0.01
24_Y 139_L 0.94 0.11 0.01
60_G 106_R 0.94 0.11 0.01
176_W 32_W 0.94 0.11 0.01
184_C 32_W 0.94 0.11 0.01
62_E 133_H 0.93 0.11 0.01
22_C 139_L 0.93 0.11 0.01
118_P 108_I 0.93 0.11 0.01
145_V 12_V 0.93 0.10 0.01
111_P 62_Y 0.92 0.10 0.01
74_L 83_Q 0.92 0.10 0.01
59_R 215_E 0.92 0.10 0.01
162_D 117_F 0.92 0.10 0.01
187_A 203_H 0.91 0.10 0.01
117_D 217_D 0.90 0.10 0.01
15_E 89_C 0.90 0.10 0.01
130_D 61_G 0.90 0.10 0.01
184_C 215_E 0.90 0.10 0.01
114_Q 61_G 0.89 0.10 0.01
6_T 195_T 0.89 0.10 0.01
100_V 215_E 0.89 0.10 0.01
89_C 107_L 0.89 0.10 0.01
15_E 6_P 0.89 0.10 0.01
122_Q 16_K 0.89 0.10 0.01
89_C 155_W 0.89 0.10 0.01
32_L 197_W 0.89 0.10 0.01
88_Y 143_A 0.88 0.10 0.01
21_H 65_S 0.88 0.10 0.01
126_S 154_S 0.88 0.10 0.01
97_N 137_A 0.88 0.10 0.01
173_A 64_A 0.88 0.10 0.01
150_D 107_L 0.87 0.09 0.00
114_Q 137_A 0.87 0.09 0.00
173_A 136_K 0.87 0.09 0.00
34_W 32_W 0.87 0.09 0.00
144_N 9_K 0.87 0.09 0.00
188_F 155_W 0.86 0.09 0.00
63_A 105_S 0.86 0.09 0.00
60_G 221_Q 0.86 0.09 0.00
87_Y 14_G 0.86 0.09 0.00
83_D 148_P 0.86 0.09 0.00
83_D 206_C 0.86 0.09 0.00
76_K 14_G 0.86 0.09 0.00
70_T 76_L 0.86 0.09 0.00
111_P 16_K 0.86 0.09 0.00
22_C 206_C 0.86 0.09 0.00
87_Y 159_G 0.85 0.09 0.00
20_I 6_P 0.85 0.09 0.00
127_K 19_L 0.85 0.09 0.00
150_D 100_Y 0.85 0.09 0.00
181_D 43_L 0.84 0.09 0.00
160_V 213_L 0.84 0.09 0.00
70_T 190_L 0.84 0.09 0.00
105_T 180_N 0.84 0.09 0.00
117_D 116_V 0.84 0.09 0.00
195_E 30_M 0.84 0.09 0.00
108_Q 208_V 0.84 0.09 0.00
157_D 137_A 0.84 0.09 0.00
74_L 109_V 0.83 0.09 0.00
57_S 221_Q 0.83 0.09 0.00
32_L 162_V 0.83 0.09 0.00
57_S 120_E 0.83 0.09 0.00
186_N 32_W 0.83 0.09 0.00
162_D 6_P 0.83 0.09 0.00
88_Y 24_T 0.83 0.09 0.00
30_P 66_R 0.83 0.09 0.00
9_N 89_C 0.83 0.09 0.00
54_E 15_G 0.83 0.09 0.00
76_K 219_W 0.82 0.08 0.00
20_I 141_C 0.82 0.08 0.00
162_D 191_R 0.82 0.08 0.00
77_A 170_P 0.82 0.08 0.00
162_D 148_P 0.82 0.08 0.00
141_S 76_L 0.82 0.08 0.00
125_D 225_K 0.82 0.08 0.00
20_I 206_C 0.82 0.08 0.00
158_K 82_S 0.82 0.08 0.00
62_E 15_G 0.82 0.08 0.00
18_L 145_G 0.82 0.08 0.00
22_C 83_Q 0.82 0.08 0.00
18_L 123_V 0.81 0.08 0.00
106_R 138_T 0.81 0.08 0.00
20_I 155_W 0.81 0.08 0.00
85_A 210_F 0.81 0.08 0.00
91_L 208_V 0.81 0.08 0.00
135_L 50_A 0.81 0.08 0.00
144_N 76_L 0.81 0.08 0.00
123_L 76_L 0.81 0.08 0.00
114_Q 14_G 0.81 0.08 0.00
142_Q 195_T 0.81 0.08 0.00
25_S 154_S 0.81 0.08 0.00
86_V 107_L 0.80 0.08 0.00
127_K 161_E 0.80 0.08 0.00
109_V 136_K 0.80 0.08 0.00
83_D 202_N 0.80 0.08 0.00
83_D 43_L 0.80 0.08 0.00
4_T 74_L 0.80 0.08 0.00
97_N 202_N 0.80 0.08 0.00
127_K 89_C 0.80 0.08 0.00
34_W 74_L 0.79 0.08 0.00
151_S 202_N 0.79 0.08 0.00
18_L 148_P 0.79 0.08 0.00
27_S 199_N 0.79 0.08 0.00
53_K 169_D 0.79 0.08 0.00
18_L 105_S 0.79 0.08 0.00
74_L 87_Y 0.79 0.08 0.00
7_E 204_F 0.79 0.08 0.00
34_W 17_V 0.79 0.08 0.00
83_D 96_G 0.79 0.08 0.00
60_G 193_S 0.78 0.08 0.00
97_N 143_A 0.78 0.08 0.00
24_Y 203_H 0.78 0.08 0.00
139_F 209_Q 0.78 0.08 0.00
133_V 138_T 0.78 0.08 0.00
180_S 96_G 0.78 0.08 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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