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OPENSEQ.org
Atp6_Psp
Genes: A B A+B
Length: 233 74 260
Sequences: 255 2850 207
Seq/Len: 1.09 38.51 0.8
MirrorTree (Pazo et al. 2001) 0.84
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 0.05 0.63
2 0.00 0.05 0.64
5 0.00 0.06 0.65
10 0.00 0.06 0.66
20 0.00 0.06 0.67
100 0.00 0.07 0.67
∞ 0.00 0.10 0.67
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
65_I 26_G 1.72 0.84 0.08
65_I 20_G 1.53 0.73 0.05
207_I 50_A 1.38 0.61 0.03
55_G 23_A 1.38 0.61 0.03
203_G 42_I 1.37 0.60 0.03
137_F 50_A 1.30 0.55 0.03
41_L 22_G 1.30 0.54 0.03
185_C 12_G 1.26 0.51 0.02
21_R 9_V 1.24 0.49 0.02
111_P 9_V 1.22 0.47 0.02
128_V 30_G 1.14 0.41 0.01
32_P 12_G 1.13 0.40 0.01
16_L 13_C 1.10 0.38 0.01
81_T 14_A 1.08 0.36 0.01
73_L 19_A 1.08 0.35 0.01
213_V 52_L 1.07 0.35 0.01
42_P 26_G 1.07 0.35 0.01
63_C 12_G 1.07 0.35 0.01
45_V 47_V 1.06 0.34 0.01
136_T 17_A 1.04 0.33 0.01
65_I 17_A 1.04 0.32 0.01
51_R 44_K 1.04 0.32 0.01
81_T 50_A 1.04 0.32 0.01
118_G 8_M 1.03 0.32 0.01
22_F 61_A 1.03 0.31 0.01
41_L 48_G 1.01 0.30 0.01
197_V 8_M 1.01 0.30 0.01
134_S 14_A 1.00 0.29 0.01
58_A 55_A 1.00 0.29 0.01
34_D 12_G 0.99 0.29 0.01
131_E 60_I 0.99 0.29 0.01
95_W 23_A 0.98 0.28 0.01
54_I 26_G 0.97 0.27 0.01
185_C 13_C 0.96 0.27 0.01
110_F 60_I 0.95 0.26 0.01
134_S 8_M 0.93 0.25 0.01
197_V 43_A 0.93 0.24 0.01
156_L 69_F 0.92 0.24 0.01
50_K 44_K 0.91 0.23 0.01
143_G 61_A 0.90 0.23 0.01
80_P 39_N 0.90 0.23 0.01
114_F 21_V 0.90 0.22 0.01
51_R 32_L 0.89 0.22 0.01
26_Q 16_I 0.89 0.22 0.01
84_L 12_G 0.89 0.22 0.01
204_V 57_T 0.89 0.22 0.01
137_F 41_N 0.89 0.22 0.01
114_F 58_E 0.88 0.22 0.01
207_I 23_A 0.88 0.22 0.01
185_C 35_G 0.88 0.22 0.01
64_T 64_S 0.88 0.21 0.01
82_S 11_A 0.88 0.21 0.01
212_Y 46_L 0.87 0.21 0.01
90_L 61_A 0.87 0.21 0.01
88_T 61_A 0.87 0.21 0.01
135_Y 52_L 0.87 0.21 0.01
135_Y 12_G 0.86 0.20 0.01
92_V 23_A 0.86 0.20 0.01
163_M 52_L 0.86 0.20 0.01
43_A 52_L 0.86 0.20 0.01
160_L 31_S 0.85 0.20 0.01
30_E 37_A 0.84 0.20 0.01
184_C 50_A 0.84 0.19 0.01
119_T 26_G 0.84 0.19 0.01
199_V 35_G 0.84 0.19 0.01
60_T 34_N 0.83 0.19 0.01
194_E 39_N 0.83 0.19 0.01
68_C 55_A 0.83 0.19 0.01
103_L 12_G 0.83 0.18 0.01
196_L 15_T 0.83 0.18 0.01
194_E 63_F 0.83 0.18 0.01
90_L 37_A 0.82 0.18 0.01
182_G 17_A 0.82 0.18 0.01
183_V 53_G 0.82 0.18 0.01
118_G 26_G 0.82 0.18 0.01
114_F 6_S 0.82 0.18 0.01
132_T 17_A 0.82 0.18 0.01
19_V 52_L 0.82 0.18 0.01
188_S 23_A 0.81 0.18 0.01
187_L 14_A 0.81 0.17 0.01
35_P 35_G 0.81 0.17 0.01
34_D 13_C 0.80 0.17 0.00
22_F 8_M 0.80 0.17 0.00
156_L 27_V 0.80 0.17 0.00
92_V 43_A 0.80 0.17 0.00
189_A 10_G 0.80 0.17 0.00
152_A 37_A 0.79 0.17 0.00
117_G 39_N 0.79 0.17 0.00
219_D 48_G 0.79 0.17 0.00
89_G 52_L 0.79 0.17 0.00
201_Q 38_R 0.78 0.16 0.00
201_Q 40_P 0.78 0.16 0.00
92_V 9_V 0.78 0.16 0.00
20_Y 16_I 0.78 0.16 0.00
143_G 30_G 0.78 0.16 0.00
86_F 12_G 0.78 0.16 0.00
155_T 22_G 0.78 0.16 0.00
91_G 36_A 0.78 0.16 0.00
149_N 38_R 0.77 0.16 0.00
149_N 40_P 0.77 0.16 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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