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OPENSEQ.org
NR
Genes: A B A+B
Length: 155 108 252
Sequences: 369 140 131
Seq/Len: 2.38 1.3 0.52
MirrorTree (Pazo et al. 2001) 0.92
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 0.00 0.49
2 0.00 0.00 0.50
5 0.00 0.00 0.50
10 0.00 0.00 0.50
20 0.00 0.00 0.50
100 0.00 0.00 0.50
∞ 0.01 0.00 0.50
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
23_Y 37_L 2.04 0.88 0.29
142_H 23_A 1.73 0.73 0.14
129_A 102_V 1.72 0.73 0.14
73_T 90_I 1.56 0.62 0.09
16_V 41_A 1.52 0.59 0.08
56_G 64_R 1.51 0.58 0.08
138_G 23_A 1.48 0.56 0.07
131_L 102_V 1.37 0.47 0.05
81_G 62_W 1.34 0.45 0.05
142_H 40_I 1.34 0.45 0.04
50_G 51_V 1.32 0.44 0.04
94_S 56_G 1.32 0.43 0.04
61_A 43_S 1.29 0.41 0.04
20_I 24_A 1.28 0.41 0.04
103_I 70_L 1.27 0.40 0.04
139_V 85_P 1.27 0.40 0.04
150_R 23_A 1.26 0.39 0.03
37_V 7_D 1.25 0.38 0.03
144_S 23_A 1.24 0.38 0.03
19_G 23_A 1.24 0.37 0.03
134_I 18_S 1.23 0.37 0.03
113_G 98_G 1.23 0.37 0.03
141_V 58_T 1.21 0.35 0.03
133_S 77_L 1.18 0.33 0.03
141_V 52_Y 1.17 0.33 0.03
79_Y 9_N 1.17 0.33 0.03
19_G 98_G 1.16 0.32 0.02
144_S 40_I 1.16 0.32 0.02
54_A 100_V 1.16 0.32 0.02
149_A 10_Q 1.15 0.31 0.02
25_R 22_E 1.14 0.31 0.02
47_L 22_E 1.13 0.30 0.02
13_V 6_A 1.12 0.30 0.02
84_D 76_Q 1.12 0.29 0.02
21_F 80_W 1.10 0.28 0.02
105_E 62_W 1.09 0.28 0.02
141_V 23_A 1.09 0.27 0.02
38_V 4_A 1.09 0.27 0.02
41_T 11_Q 1.08 0.27 0.02
114_S 37_L 1.08 0.27 0.02
18_L 82_L 1.07 0.26 0.02
132_D 12_L 1.07 0.26 0.02
41_T 68_G 1.06 0.26 0.02
64_R 28_G 1.06 0.26 0.02
108_T 90_I 1.05 0.25 0.02
40_P 49_A 1.04 0.24 0.01
20_I 85_P 1.04 0.24 0.01
147_K 4_A 1.04 0.24 0.01
70_D 88_Q 1.03 0.24 0.01
150_R 47_S 1.03 0.24 0.01
38_V 98_G 1.02 0.23 0.01
80_L 14_A 1.02 0.23 0.01
58_R 74_E 1.01 0.23 0.01
112_V 74_E 1.00 0.22 0.01
125_I 23_A 1.00 0.22 0.01
152_Q 97_I 1.00 0.22 0.01
147_K 78_A 1.00 0.22 0.01
139_V 6_A 1.00 0.22 0.01
9_R 8_P 1.00 0.22 0.01
100_V 102_V 1.00 0.22 0.01
79_Y 62_W 1.00 0.22 0.01
85_E 76_Q 0.99 0.22 0.01
26_W 12_L 0.99 0.22 0.01
22_S 105_S 0.99 0.22 0.01
122_G 93_D 0.99 0.22 0.01
149_A 59_L 0.99 0.21 0.01
83_V 80_W 0.99 0.21 0.01
87_E 88_Q 0.99 0.21 0.01
95_L 21_V 0.99 0.21 0.01
61_A 52_Y 0.99 0.21 0.01
99_P 34_E 0.98 0.21 0.01
142_H 45_E 0.98 0.21 0.01
152_Q 42_S 0.98 0.21 0.01
130_N 24_A 0.97 0.21 0.01
139_V 26_V 0.97 0.21 0.01
142_H 74_E 0.97 0.20 0.01
43_Y 2_L 0.97 0.20 0.01
14_S 11_Q 0.96 0.20 0.01
66_V 100_V 0.96 0.20 0.01
19_G 2_L 0.96 0.20 0.01
61_A 47_S 0.96 0.20 0.01
57_R 37_L 0.96 0.20 0.01
16_V 35_E 0.96 0.20 0.01
10_S 87_E 0.95 0.19 0.01
135_A 82_L 0.95 0.19 0.01
87_E 51_V 0.95 0.19 0.01
105_E 12_L 0.94 0.19 0.01
131_L 34_E 0.94 0.19 0.01
99_P 53_D 0.94 0.19 0.01
123_P 95_Q 0.94 0.19 0.01
142_H 49_A 0.94 0.19 0.01
47_L 89_P 0.93 0.19 0.01
133_S 67_T 0.93 0.19 0.01
19_G 33_A 0.93 0.19 0.01
135_A 84_A 0.93 0.19 0.01
38_V 16_S 0.93 0.18 0.01
58_R 77_L 0.93 0.18 0.01
97_G 55_Q 0.93 0.18 0.01
24_V 83_S 0.92 0.18 0.01
129_A 7_D 0.92 0.18 0.01
10_S 59_L 0.92 0.18 0.01
27_P 22_E 0.92 0.18 0.01
81_G 12_L 0.92 0.18 0.01
100_V 54_R 0.92 0.18 0.01
14_S 105_S 0.92 0.18 0.01
88_R 44_E 0.92 0.18 0.01
113_G 90_I 0.91 0.18 0.01
123_P 96_K 0.90 0.17 0.01
12_A 99_S 0.90 0.17 0.01
148_L 98_G 0.90 0.17 0.01
90_Q 63_H 0.90 0.17 0.01
125_I 36_S 0.90 0.17 0.01
80_L 100_V 0.90 0.17 0.01
77_V 75_Q 0.89 0.17 0.01
132_D 9_N 0.89 0.17 0.01
135_A 58_T 0.89 0.17 0.01
112_V 51_V 0.89 0.17 0.01
101_L 98_G 0.89 0.17 0.01
138_G 12_L 0.89 0.17 0.01
78_I 82_L 0.89 0.17 0.01
93_R 102_V 0.89 0.17 0.01
150_R 49_A 0.89 0.17 0.01
81_G 33_A 0.89 0.17 0.01
98_H 78_A 0.89 0.17 0.01
52_V 60_A 0.88 0.17 0.01
16_V 59_L 0.88 0.16 0.01
92_F 17_I 0.88 0.16 0.01
81_G 22_E 0.87 0.16 0.01
133_S 58_T 0.87 0.16 0.01
37_V 97_I 0.87 0.16 0.01
115_M 18_S 0.87 0.16 0.01
150_R 21_V 0.87 0.16 0.01
115_M 84_A 0.86 0.16 0.01
71_L 47_S 0.86 0.16 0.01
109_E 100_V 0.86 0.15 0.01
40_P 17_I 0.86 0.15 0.01
36_C 27_F 0.86 0.15 0.01
36_C 29_D 0.86 0.15 0.01
75_C 27_F 0.86 0.15 0.01
75_C 29_D 0.86 0.15 0.01
110_C 27_F 0.86 0.15 0.01
110_C 29_D 0.86 0.15 0.01
116_F 27_F 0.86 0.15 0.01
116_F 29_D 0.86 0.15 0.01
117_C 27_F 0.86 0.15 0.01
117_C 29_D 0.86 0.15 0.01
127_F 27_F 0.86 0.15 0.01
127_F 29_D 0.86 0.15 0.01
146_L 27_F 0.86 0.15 0.01
146_L 29_D 0.86 0.15 0.01
25_R 2_L 0.86 0.15 0.01
142_H 104_G 0.85 0.15 0.01
125_I 2_L 0.85 0.15 0.01
59_V 84_A 0.85 0.15 0.01
64_R 68_G 0.85 0.15 0.01
134_I 49_A 0.85 0.15 0.01
40_P 40_I 0.85 0.15 0.01
134_I 80_W 0.85 0.15 0.01
41_T 82_L 0.85 0.15 0.01
22_S 82_L 0.84 0.15 0.01
152_Q 28_G 0.84 0.15 0.01
42_E 104_G 0.84 0.15 0.01
103_I 8_P 0.84 0.15 0.01
58_R 68_G 0.84 0.15 0.01
145_V 98_G 0.84 0.15 0.01
105_E 23_A 0.84 0.15 0.01
23_Y 25_V 0.84 0.15 0.01
77_V 106_G 0.83 0.14 0.01
87_E 18_S 0.83 0.14 0.01
44_A 66_S 0.83 0.14 0.01
23_Y 75_Q 0.82 0.14 0.01
77_V 14_A 0.82 0.14 0.01
113_G 97_I 0.82 0.14 0.01
105_E 9_N 0.82 0.14 0.01
91_V 57_Q 0.82 0.14 0.01
64_R 66_S 0.82 0.14 0.01
102_S 24_A 0.82 0.14 0.01
81_G 9_N 0.82 0.14 0.01
144_S 36_S 0.82 0.14 0.01
136_R 12_L 0.82 0.14 0.01
40_P 21_V 0.82 0.14 0.01
98_H 101_E 0.82 0.14 0.01
47_L 19_Y 0.82 0.14 0.01
148_L 23_A 0.81 0.14 0.01
10_S 90_I 0.81 0.14 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)
ID Seq/Len Name Options I_Prob Status
1131 0 N and R Δgene:(0, 5) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2013_03) Killed
1120 0 N and R Δgene:(0, 2) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2013_03) Killed
1119 0.88 NR Δgene:(0, 5) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1118 0.52 NR Δgene:(0, 5) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) 0.29 Done
1117 0.88 NR Δgene:(0, 2) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1116 0.75 NR Δgene:(0, 2) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.10 Done - Shared
1115 0.75 NR Δgene:(0, 5) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.27 Done - Shared
1114 0.37 NR Δgene:(0, 2) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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