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OPENSEQ.org
3PNL-2
Genes: A B A+B
Length: 347 209 521
Sequences: 1716 2047 851
Seq/Len: 4.95 9.79 1.63
MirrorTree (Pazo et al. 2001) 0.71
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 0.02 1.47
2 0.07 0.05 1.51
5 0.09 0.05 1.53
10 0.10 0.05 1.53
20 0.10 0.05 1.53
100 0.11 0.06 1.54
∞ 0.14 0.09 1.55
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
110_L 88_I 1.35 0.79 0.05
113_D 88_I 1.32 0.77 0.04
109_E 89_R 1.24 0.70 0.04
105_E 119_R 1.08 0.55 0.02
88_E 116_V 1.03 0.50 0.02
98_T 180_Y 0.99 0.45 0.02
26_V 130_C 0.98 0.44 0.02
192_K 27_G 0.96 0.43 0.01
74_P 37_H 0.96 0.42 0.01
117_K 163_S 0.94 0.40 0.01
194_S 30_R 0.90 0.36 0.01
287_V 198_F 0.89 0.35 0.01
1_D 138_E 0.88 0.34 0.01
226_V 205_L 0.87 0.33 0.01
202_M 41_M 0.87 0.33 0.01
113_D 92_Q 0.86 0.33 0.01
109_E 119_R 0.86 0.33 0.01
79_E 123_E 0.84 0.31 0.01
105_E 121_K 0.84 0.31 0.01
321_I 47_K 0.84 0.30 0.01
128_A 191_P 0.84 0.30 0.01
102_L 59_D 0.84 0.30 0.01
142_A 35_A 0.83 0.30 0.01
25_Y 11_L 0.83 0.30 0.01
54_Y 79_S 0.81 0.28 0.01
74_P 129_M 0.81 0.28 0.01
219_F 7_I 0.81 0.28 0.01
70_T 71_L 0.81 0.28 0.01
74_P 195_S 0.80 0.27 0.01
145_V 11_L 0.79 0.26 0.01
67_E 71_L 0.79 0.26 0.01
70_T 78_A 0.79 0.26 0.01
62_G 90_A 0.77 0.24 0.01
75_D 73_S 0.77 0.24 0.01
63_A 79_S 0.76 0.24 0.01
70_T 32_I 0.75 0.23 0.01
70_T 43_R 0.74 0.23 0.01
13_A 91_A 0.73 0.22 0.01
67_E 43_R 0.73 0.22 0.01
110_L 73_S 0.73 0.22 0.01
230_F 27_G 0.72 0.21 0.01
91_L 7_I 0.71 0.20 0.01
199_D 183_E 0.71 0.20 0.01
221_S 185_S 0.71 0.20 0.01
70_T 75_V 0.71 0.20 0.01
51_H 180_Y 0.71 0.20 0.01
105_E 78_A 0.70 0.20 0.01
230_F 101_T 0.70 0.20 0.01
180_I 85_T 0.70 0.20 0.01
93_I 137_V 0.70 0.19 0.01
137_G 180_Y 0.69 0.19 0.01
133_L 67_T 0.69 0.19 0.01
219_F 130_C 0.69 0.19 0.01
282_S 81_P 0.69 0.19 0.01
39_L 41_M 0.69 0.19 0.01
310_Y 26_T 0.68 0.18 0.01
128_A 71_L 0.68 0.18 0.01
102_L 30_R 0.68 0.18 0.01
311_C 69_M 0.67 0.18 0.01
223_D 54_A 0.67 0.18 0.01
271_A 48_V 0.67 0.18 0.01
45_S 39_L 0.67 0.18 0.01
109_E 58_K 0.67 0.17 0.01
194_S 133_W 0.66 0.17 0.01
48_E 77_G 0.66 0.17 0.01
85_D 54_A 0.66 0.17 0.01
12_K 16_D 0.66 0.17 0.01
136_A 26_T 0.66 0.17 0.01
341_P 105_L 0.66 0.17 0.01
95_K 180_Y 0.66 0.17 0.01
95_K 79_S 0.65 0.17 0.01
35_G 179_S 0.65 0.17 0.01
144_T 180_Y 0.65 0.16 0.01
51_H 79_S 0.65 0.16 0.01
41_S 178_A 0.65 0.16 0.01
73_T 51_K 0.65 0.16 0.01
339_H 205_L 0.65 0.16 0.01
162_D 155_E 0.64 0.16 0.01
48_E 37_H 0.64 0.16 0.01
64_C 180_Y 0.64 0.16 0.01
177_S 105_L 0.64 0.16 0.01
102_L 140_L 0.64 0.16 0.01
122_V 49_V 0.64 0.16 0.01
190_A 39_L 0.64 0.16 0.01
297_Q 111_D 0.63 0.15 0.01
212_P 85_T 0.63 0.15 0.00
265_S 99_S 0.63 0.15 0.00
328_D 103_E 0.63 0.15 0.00
187_V 178_A 0.63 0.15 0.00
225_T 197_M 0.63 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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