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OPENSEQ.org
1OR7-2
Genes: A B A+B
Length: 189 66 244
Sequences: 25003 320 217
Seq/Len: 132.29 4.85 0.89
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.82
2 0.01 0.00 0.85
5 0.03 0.00 0.85
10 0.06 0.00 0.85
20 0.09 0.00 0.85
100 0.17 0.00 0.85
∞ 0.23 0.00 0.86
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
184_D 35_S 2.20 0.97 0.89
21_Q 66_E 1.68 0.84 0.58
63_L 37_H 1.62 0.81 0.53
142_E 21_N 1.59 0.79 0.50
169_V 62_A 1.48 0.72 0.40
87_Y 6_L 1.44 0.69 0.36
133_V 31_K 1.37 0.64 0.31
84_A 4_E 1.34 0.61 0.28
29_V 56_S 1.30 0.58 0.25
183_I 53_F 1.28 0.56 0.23
76_L 41_D 1.27 0.55 0.23
34_K 63_I 1.25 0.53 0.21
40_S 41_D 1.18 0.47 0.17
126_S 55_I 1.16 0.45 0.16
92_G 43_M 1.14 0.43 0.14
35_V 19_L 1.12 0.41 0.13
138_E 46_D 1.10 0.40 0.13
169_V 16_D 1.10 0.40 0.12
148_I 18_E 1.08 0.38 0.11
145_R 59_V 1.07 0.37 0.11
182_A 54_D 1.06 0.37 0.11
142_E 51_L 1.06 0.36 0.11
143_D 55_I 1.06 0.36 0.11
26_L 33_W 1.06 0.36 0.10
142_E 8_A 1.05 0.35 0.10
37_S 63_I 1.04 0.35 0.10
35_V 46_D 1.03 0.34 0.09
47_D 16_D 1.03 0.34 0.09
159_E 35_S 1.02 0.34 0.09
143_D 16_D 1.02 0.33 0.09
26_L 37_H 1.00 0.32 0.08
35_V 16_D 0.99 0.31 0.08
98_S 40_R 0.99 0.31 0.08
48_V 47_T 0.97 0.29 0.07
143_D 9_L 0.96 0.28 0.07
10_Q 46_D 0.95 0.28 0.07
84_A 8_A 0.95 0.28 0.07
129_L 21_N 0.94 0.27 0.07
63_L 45_G 0.94 0.27 0.07
26_L 26_N 0.94 0.27 0.07
187_V 38_L 0.94 0.27 0.06
39_V 59_V 0.93 0.26 0.06
83_T 33_W 0.93 0.26 0.06
132_I 42_S 0.93 0.26 0.06
103_I 41_D 0.92 0.26 0.06
100_V 20_L 0.92 0.26 0.06
35_V 17_S 0.92 0.25 0.06
60_Y 36_Y 0.91 0.25 0.06
153_L 30_Q 0.91 0.25 0.06
187_V 35_S 0.91 0.25 0.06
81_V 44_R 0.90 0.24 0.05
95_P 6_L 0.89 0.24 0.05
25_N 51_L 0.89 0.23 0.05
91_Q 16_D 0.88 0.23 0.05
34_K 5_Q 0.87 0.23 0.05
88_L 56_S 0.87 0.22 0.05
154_D 39_I 0.86 0.22 0.04
129_L 6_L 0.86 0.22 0.04
102_A 63_I 0.86 0.22 0.04
30_R 1_M 0.86 0.22 0.04
153_L 38_L 0.86 0.21 0.04
146_M 34_E 0.85 0.21 0.04
90_A 4_E 0.84 0.21 0.04
135_R 6_L 0.84 0.20 0.04
47_D 18_E 0.83 0.20 0.04
38_L 37_H 0.83 0.20 0.04
30_R 40_R 0.83 0.20 0.04
25_N 30_Q 0.82 0.19 0.04
30_R 2_Q 0.82 0.19 0.04
47_D 15_L 0.81 0.19 0.04
166_D 12_G 0.81 0.19 0.04
22_K 5_Q 0.81 0.19 0.03
137_I 46_D 0.80 0.18 0.03
142_E 57_S 0.80 0.18 0.03
25_N 15_L 0.80 0.18 0.03
55_A 2_Q 0.80 0.18 0.03
22_K 23_L 0.80 0.18 0.03
129_L 12_G 0.79 0.18 0.03
25_N 59_V 0.79 0.18 0.03
49_P 18_E 0.79 0.18 0.03
33_H 61_A 0.79 0.18 0.03
129_L 24_A 0.79 0.17 0.03
184_D 56_S 0.79 0.17 0.03
119_N 3_K 0.79 0.17 0.03
83_T 45_G 0.78 0.17 0.03
33_H 56_S 0.78 0.17 0.03
184_D 42_S 0.78 0.17 0.03
89_V 59_V 0.78 0.17 0.03
11_V 53_F 0.78 0.17 0.03
138_E 58_R 0.78 0.17 0.03
89_V 38_L 0.77 0.17 0.03
126_S 30_Q 0.77 0.17 0.03
139_S 41_D 0.77 0.17 0.03
22_K 18_E 0.76 0.16 0.03
143_D 53_F 0.76 0.16 0.03
71_A 33_W 0.76 0.16 0.03
185_N 58_R 0.76 0.16 0.03
65_S 34_E 0.76 0.16 0.03
113_A 3_K 0.76 0.16 0.03
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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