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OPENSEQ.org
cI_C_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 208 263 443
Sequences: 1081 973 307
Seq/Len: 5.2 3.7 0.69
MirrorTree (Pazo et al. 2001) 0.63
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 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.02 0.01 0.04
∞ 0.05 0.01 0.65
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
92_I 130_R 1.38 0.56 0.00
124_L 202_P 1.32 0.51 0.00
122_F 249_N 1.22 0.43 0.00
110_V 244_L 1.21 0.43 0.00
35_L 181_G 1.16 0.39 0.00
22_E 241_L 1.15 0.38 0.00
125_F 80_L 1.12 0.35 0.00
176_N 201_T 1.11 0.34 0.00
171_V 86_R 1.10 0.34 0.00
158_Y 124_S 1.09 0.33 0.00
92_I 66_Y 1.07 0.32 0.00
21_R 247_L 1.07 0.31 0.00
173_E 72_L 1.06 0.30 0.00
150_R 165_E 1.04 0.30 0.00
29_Q 195_V 1.04 0.29 0.00
133_S 49_R 1.04 0.29 0.00
40_T 240_V 1.03 0.29 0.00
17_I 44_Q 1.03 0.29 0.00
77_F 150_G 1.03 0.28 0.00
124_L 156_A 1.02 0.28 0.00
145_R 249_N 1.01 0.27 0.00
131_G 216_L 1.00 0.27 0.00
156_T 218_W 1.00 0.27 0.00
150_R 222_P 0.98 0.25 0.00
124_L 249_N 0.97 0.25 0.00
171_V 214_A 0.96 0.24 0.00
79_V 177_A 0.96 0.24 0.00
158_Y 155_H 0.95 0.24 0.00
13_L 76_G 0.95 0.23 0.00
181_Y 76_G 0.95 0.23 0.00
94_V 230_V 0.94 0.23 0.00
61_T 140_G 0.94 0.23 0.00
130_S 124_S 0.93 0.23 0.00
35_L 96_D 0.93 0.22 0.00
124_L 151_P 0.93 0.22 0.00
94_V 216_L 0.93 0.22 0.00
52_R 45_H 0.93 0.22 0.00
201_E 204_T 0.93 0.22 0.00
47_L 91_N 0.92 0.22 0.00
23_N 118_G 0.92 0.22 0.00
65_I 219_T 0.92 0.21 0.00
44_V 174_Y 0.92 0.21 0.00
110_V 25_A 0.92 0.21 0.00
73_R 154_I 0.91 0.21 0.00
115_N 239_I 0.91 0.21 0.00
100_E 59_S 0.91 0.21 0.00
168_K 179_F 0.90 0.20 0.00
103_L 207_Q 0.90 0.20 0.00
122_F 51_L 0.89 0.20 0.00
112_P 223_K 0.89 0.20 0.00
85_S 222_P 0.89 0.20 0.00
79_V 199_D 0.89 0.20 0.00
196_V 258_H 0.89 0.20 0.00
182_R 218_W 0.88 0.20 0.00
161_V 163_G 0.88 0.19 0.00
62_L 213_A 0.88 0.19 0.00
121_V 88_Y 0.88 0.19 0.00
79_V 208_M 0.88 0.19 0.00
125_F 113_T 0.87 0.19 0.00
171_V 118_G 0.87 0.19 0.00
45_I 42_F 0.86 0.19 0.00
54_D 228_K 0.86 0.19 0.00
62_L 131_A 0.86 0.18 0.00
39_A 257_K 0.86 0.18 0.00
165_D 171_A 0.86 0.18 0.00
131_G 122_D 0.86 0.18 0.00
138_I 139_T 0.85 0.18 0.00
117_Y 194_Q 0.85 0.18 0.00
159_V 206_D 0.85 0.18 0.00
52_R 240_V 0.85 0.18 0.00
171_V 59_S 0.85 0.18 0.00
54_D 242_A 0.84 0.18 0.00
115_N 142_S 0.84 0.18 0.00
96_V 48_Q 0.84 0.18 0.00
70_N 60_A 0.84 0.17 0.00
131_G 214_A 0.84 0.17 0.00
127_I 180_A 0.84 0.17 0.00
111_F 99_T 0.83 0.17 0.00
117_Y 203_A 0.83 0.17 0.00
168_K 157_V 0.83 0.17 0.00
109_G 13_A 0.83 0.17 0.00
101_D 108_T 0.83 0.17 0.00
142_Y 221_E 0.83 0.17 0.00
112_P 66_Y 0.83 0.17 0.00
204_P 24_A 0.83 0.17 0.00
165_D 213_A 0.83 0.17 0.00
55_P 240_V 0.83 0.17 0.00
33_G 214_A 0.82 0.17 0.00
159_V 156_A 0.82 0.17 0.00
41_L 221_E 0.82 0.17 0.00
33_G 206_D 0.82 0.17 0.00
204_P 18_E 0.82 0.17 0.00
71_P 129_A 0.81 0.16 0.00
112_P 236_I 0.81 0.16 0.00
173_E 70_R 0.81 0.16 0.00
27_S 203_A 0.81 0.16 0.00
25_V 167_E 0.81 0.16 0.00
95_K 33_F 0.81 0.16 0.00
43_G 199_D 0.81 0.16 0.00
36_T 236_I 0.81 0.16 0.00
72_A 81_P 0.81 0.16 0.00
180_E 130_R 0.81 0.16 0.00
167_E 241_L 0.80 0.16 0.00
182_R 176_N 0.80 0.16 0.00
147_H 137_Y 0.80 0.16 0.00
135_L 85_V 0.80 0.16 0.00
168_K 201_T 0.79 0.15 0.00
63_I 193_D 0.79 0.15 0.00
21_R 164_E 0.79 0.15 0.00
94_V 205_V 0.79 0.15 0.00
54_D 85_V 0.79 0.15 0.00
56_N 118_G 0.79 0.15 0.00
63_I 131_A 0.79 0.15 0.00
110_V 255_P 0.79 0.15 0.00
17_I 241_L 0.79 0.15 0.00
170_V 227_R 0.79 0.15 0.00
131_G 46_Q 0.79 0.15 0.00
46_G 247_L 0.78 0.15 0.00
117_Y 183_W 0.78 0.15 0.00
36_T 220_A 0.78 0.15 0.00
42_S 166_K 0.78 0.15 0.00
112_P 124_S 0.78 0.15 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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