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OPENSEQ.org
PilP-N0PilQ
Genes: A B A+B
Length: 157 75 222
Sequences: 435 496 374
Seq/Len: 2.77 6.61 1.68
MirrorTree (Pazo et al. 2001) 0.69
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 0.00 0.00 1.62
2 0.00 0.00 1.61
5 0.00 0.00 1.61
10 0.00 0.00 1.61
20 0.00 0.00 1.61
100 0.00 0.00 1.61
∞ 0.00 0.00 1.61
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
156_D 17_T 1.39 0.82 0.09
145_W 9_N 1.32 0.78 0.07
87_M 28_L 1.29 0.76 0.07
27_A 5_P 1.28 0.74 0.06
15_L 31_V 1.25 0.72 0.06
116_Y 55_I 1.23 0.70 0.06
140_D 56_V 1.23 0.70 0.06
120_S 70_V 1.21 0.69 0.05
113_P 14_P 1.20 0.68 0.05
128_Y 57_L 1.20 0.68 0.05
144_G 26_S 1.19 0.67 0.05
146_L 5_P 1.19 0.67 0.05
73_R 55_I 1.19 0.67 0.05
70_P 12_D 1.16 0.64 0.04
69_D 50_D 1.15 0.63 0.04
34_P 1_Y 1.15 0.63 0.04
110_R 57_L 1.14 0.62 0.04
73_R 28_L 1.11 0.59 0.04
156_D 9_N 1.11 0.58 0.04
102_M 73_V 1.11 0.58 0.04
92_G 4_R 1.10 0.58 0.04
75_E 73_V 1.09 0.56 0.04
56_A 22_I 1.08 0.56 0.04
138_V 70_V 1.07 0.55 0.03
85_L 56_V 1.07 0.55 0.03
116_Y 35_T 1.07 0.55 0.03
85_L 14_P 1.07 0.54 0.03
72_R 52_A 1.06 0.54 0.03
137_L 59_A 1.06 0.53 0.03
44_Y 51_Q 1.05 0.53 0.03
74_K 52_A 1.05 0.52 0.03
91_I 24_E 1.04 0.51 0.03
80_F 65_R 1.02 0.50 0.03
57_W 35_T 1.02 0.50 0.03
106_K 12_D 1.02 0.50 0.03
102_M 17_T 1.02 0.49 0.03
72_R 50_D 1.01 0.48 0.03
137_L 14_P 1.00 0.47 0.03
72_R 3_G 1.00 0.47 0.03
97_L 71_V 1.00 0.47 0.03
106_K 15_V 1.00 0.47 0.03
119_Q 26_S 1.00 0.47 0.03
152_L 61_G 0.99 0.46 0.03
157_Q 35_T 0.98 0.45 0.03
105_D 73_V 0.97 0.44 0.02
133_E 69_G 0.96 0.43 0.02
127_V 22_I 0.96 0.43 0.02
65_G 28_L 0.95 0.42 0.02
145_W 32_A 0.94 0.41 0.02
118_G 53_L 0.94 0.41 0.02
130_D 24_E 0.94 0.41 0.02
27_A 57_L 0.94 0.41 0.02
145_W 30_I 0.93 0.40 0.02
113_P 66_R 0.93 0.40 0.02
128_Y 24_E 0.92 0.39 0.02
126_G 46_N 0.92 0.39 0.02
18_W 72_W 0.91 0.38 0.02
101_V 60_K 0.91 0.38 0.02
14_N 52_A 0.91 0.38 0.02
86_D 27_N 0.91 0.38 0.02
124_V 27_N 0.91 0.37 0.02
18_W 21_L 0.91 0.37 0.02
150_A 50_D 0.90 0.37 0.02
12_A 31_V 0.90 0.37 0.02
98_I 32_A 0.90 0.37 0.02
60_A 45_M 0.90 0.37 0.02
156_D 32_A 0.90 0.36 0.02
121_D 17_T 0.89 0.36 0.02
78_E 48_P 0.89 0.36 0.02
157_Q 13_V 0.89 0.36 0.02
30_L 35_T 0.89 0.36 0.02
69_D 63_D 0.89 0.36 0.02
129_E 39_N 0.89 0.35 0.02
88_V 25_E 0.89 0.35 0.02
125_T 60_K 0.89 0.35 0.02
99_A 4_R 0.88 0.35 0.02
87_M 23_A 0.88 0.35 0.02
109_Y 31_V 0.88 0.34 0.02
74_K 64_K 0.87 0.34 0.02
22_V 72_W 0.87 0.34 0.02
119_Q 39_N 0.86 0.33 0.02
135_I 40_V 0.86 0.33 0.02
97_L 64_K 0.86 0.33 0.02
80_F 18_V 0.86 0.33 0.02
120_S 54_D 0.85 0.33 0.02
67_R 64_K 0.85 0.32 0.02
134_L 8_F 0.85 0.32 0.02
65_G 26_S 0.85 0.32 0.02
27_A 40_V 0.85 0.32 0.02
93_G 6_V 0.85 0.32 0.01
50_R 31_V 0.85 0.32 0.01
72_R 8_F 0.84 0.32 0.01
98_I 58_R 0.84 0.31 0.01
46_A 32_A 0.84 0.31 0.01
50_R 57_L 0.84 0.31 0.01
127_V 15_V 0.84 0.31 0.01
118_G 68_G 0.84 0.31 0.01
149_P 70_V 0.84 0.31 0.01
116_Y 21_L 0.84 0.31 0.01
81_P 15_V 0.83 0.31 0.01
124_V 58_R 0.83 0.31 0.01
108_T 69_G 0.83 0.30 0.01
148_R 34_D 0.83 0.30 0.01
120_S 25_E 0.83 0.30 0.01
134_L 57_L 0.82 0.30 0.01
97_L 63_D 0.82 0.30 0.01
91_I 42_L 0.82 0.29 0.01
39_F 22_I 0.82 0.29 0.01
12_A 21_L 0.82 0.29 0.01
139_P 30_I 0.81 0.29 0.01
15_L 39_N 0.81 0.29 0.01
19_V 3_G 0.81 0.29 0.01
109_Y 25_E 0.81 0.28 0.01
44_Y 44_L 0.81 0.28 0.01
42_F 30_I 0.81 0.28 0.01
18_W 7_T 0.80 0.28 0.01
112_R 71_V 0.80 0.28 0.01
92_G 8_F 0.80 0.28 0.01
66_T 8_F 0.80 0.28 0.01
56_A 56_V 0.80 0.28 0.01
46_A 5_P 0.80 0.28 0.01
87_M 22_I 0.80 0.27 0.01
141_G 22_I 0.79 0.27 0.01
36_M 7_T 0.79 0.27 0.01
107_V 63_D 0.79 0.27 0.01
44_Y 50_D 0.79 0.27 0.01
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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