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OPENSEQ.org
NR
Genes: A B A+B
Length: 155 108 257
Sequences: 279 271 192
Seq/Len: 1.8 2.51 0.75
MirrorTree (Pazo et al. 2001) 0.88
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 0.73
2 0.00 0.00 0.73
5 0.00 0.00 0.73
10 0.00 0.00 0.74
20 0.00 0.00 0.74
100 0.00 0.00 0.75
∞ 0.02 0.01 0.76
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
17_L 52_Y 1.76 0.84 0.10
16_V 41_A 1.67 0.80 0.07
131_L 102_V 1.58 0.74 0.06
144_S 35_E 1.48 0.67 0.04
101_L 98_G 1.44 0.64 0.04
144_S 17_I 1.40 0.61 0.04
81_G 26_V 1.40 0.60 0.04
142_H 74_E 1.39 0.60 0.04
78_I 42_S 1.37 0.58 0.03
146_L 24_A 1.36 0.57 0.03
127_F 29_D 1.34 0.56 0.03
149_A 37_L 1.30 0.53 0.03
110_C 12_L 1.30 0.52 0.03
145_V 62_W 1.29 0.52 0.03
137_S 44_E 1.23 0.46 0.02
134_I 18_S 1.19 0.43 0.02
67_D 108_S 1.19 0.43 0.02
115_M 51_V 1.17 0.41 0.02
23_Y 25_V 1.16 0.41 0.02
109_E 13_I 1.16 0.40 0.02
16_V 59_L 1.15 0.40 0.02
90_Q 63_H 1.13 0.38 0.01
115_M 46_V 1.13 0.38 0.01
64_R 78_A 1.13 0.38 0.01
130_N 6_A 1.10 0.36 0.01
104_S 28_G 1.10 0.35 0.01
127_F 98_G 1.08 0.34 0.01
144_S 36_S 1.08 0.34 0.01
126_T 25_V 1.08 0.34 0.01
95_L 53_D 1.07 0.34 0.01
147_K 36_S 1.07 0.34 0.01
118_L 12_L 1.07 0.33 0.01
105_E 12_L 1.07 0.33 0.01
144_S 23_A 1.05 0.32 0.01
94_S 90_I 1.04 0.31 0.01
11_N 108_S 1.04 0.31 0.01
23_Y 51_V 1.03 0.30 0.01
33_L 3_R 1.02 0.30 0.01
143_P 44_E 1.02 0.30 0.01
80_L 74_E 1.01 0.29 0.01
130_N 13_I 1.01 0.29 0.01
58_R 25_V 1.01 0.28 0.01
12_A 108_S 1.00 0.28 0.01
143_P 62_W 1.00 0.28 0.01
141_V 58_T 1.00 0.28 0.01
10_S 59_L 0.99 0.28 0.01
86_R 79_H 0.99 0.28 0.01
149_A 27_F 0.99 0.28 0.01
126_T 60_A 0.99 0.27 0.01
115_M 97_I 0.99 0.27 0.01
117_C 9_N 0.99 0.27 0.01
79_Y 9_N 0.98 0.27 0.01
46_G 68_G 0.98 0.27 0.01
75_C 27_F 0.98 0.27 0.01
147_K 20_T 0.98 0.27 0.01
147_K 23_A 0.98 0.27 0.01
123_P 96_K 0.98 0.27 0.01
133_S 58_T 0.97 0.26 0.01
110_C 9_N 0.97 0.26 0.01
118_L 19_Y 0.97 0.26 0.01
153_A 108_S 0.97 0.26 0.01
113_G 90_I 0.96 0.26 0.01
22_S 35_E 0.96 0.26 0.01
141_V 49_A 0.96 0.26 0.01
7_E 108_S 0.96 0.25 0.01
8_Q 108_S 0.96 0.25 0.01
25_R 22_E 0.95 0.25 0.01
34_Q 20_T 0.95 0.25 0.01
42_E 87_E 0.95 0.25 0.01
9_R 108_S 0.95 0.25 0.01
127_F 25_V 0.95 0.25 0.01
103_I 53_D 0.95 0.25 0.01
81_G 9_N 0.95 0.25 0.01
139_V 26_V 0.94 0.24 0.01
151_R 51_V 0.94 0.24 0.01
130_N 10_Q 0.94 0.24 0.01
144_S 40_I 0.93 0.24 0.01
34_Q 53_D 0.93 0.24 0.01
17_L 36_S 0.93 0.23 0.01
67_D 107_G 0.93 0.23 0.01
72_G 55_Q 0.93 0.23 0.01
77_V 95_Q 0.93 0.23 0.01
125_I 85_P 0.93 0.23 0.01
12_A 1_T 0.93 0.23 0.01
57_R 102_V 0.93 0.23 0.01
103_I 106_G 0.92 0.23 0.01
32_V 55_Q 0.92 0.23 0.01
105_E 10_Q 0.92 0.23 0.01
74_L 93_D 0.92 0.23 0.01
95_L 37_L 0.92 0.23 0.01
20_I 104_G 0.92 0.23 0.01
20_I 26_V 0.92 0.23 0.01
20_I 85_P 0.92 0.23 0.01
37_V 37_L 0.91 0.23 0.01
140_R 74_E 0.91 0.22 0.01
134_I 52_Y 0.91 0.22 0.01
143_P 12_L 0.90 0.22 0.01
36_C 12_L 0.90 0.22 0.01
116_F 26_V 0.90 0.22 0.01
35_L 15_R 0.90 0.21 0.01
52_V 20_T 0.89 0.21 0.01
20_I 24_A 0.89 0.21 0.01
99_P 28_G 0.89 0.21 0.01
125_I 23_A 0.89 0.21 0.01
91_V 14_A 0.89 0.21 0.01
51_M 99_S 0.88 0.21 0.01
139_V 44_E 0.88 0.21 0.01
23_Y 88_Q 0.88 0.21 0.01
147_K 1_T 0.88 0.20 0.01
107_G 14_A 0.88 0.20 0.01
26_W 89_P 0.87 0.20 0.01
92_F 56_G 0.87 0.20 0.01
116_F 62_W 0.87 0.20 0.01
93_R 53_D 0.87 0.20 0.01
36_C 27_F 0.87 0.20 0.01
102_S 96_K 0.87 0.20 0.01
135_A 23_A 0.87 0.20 0.01
148_L 98_G 0.87 0.20 0.01
35_L 98_G 0.87 0.20 0.01
60_H 65_E 0.86 0.20 0.01
28_K 89_P 0.86 0.20 0.01
19_G 98_G 0.86 0.19 0.01
130_N 33_A 0.86 0.19 0.01
47_L 89_P 0.86 0.19 0.01
150_R 94_G 0.86 0.19 0.01
23_Y 90_I 0.85 0.19 0.01
142_H 98_G 0.85 0.19 0.01
125_I 50_I 0.85 0.19 0.01
24_V 83_S 0.85 0.19 0.01
10_S 90_I 0.84 0.19 0.01
144_S 20_T 0.84 0.19 0.01
51_M 72_L 0.84 0.19 0.01
41_T 51_V 0.84 0.19 0.01
77_V 57_Q 0.84 0.18 0.01
116_F 9_N 0.84 0.18 0.01
142_H 1_T 0.84 0.18 0.01
66_V 1_T 0.84 0.18 0.01
37_V 88_Q 0.84 0.18 0.01
45_D 50_I 0.84 0.18 0.01
8_Q 59_L 0.84 0.18 0.01
34_Q 3_R 0.83 0.18 0.01
81_G 62_W 0.83 0.18 0.01
59_V 90_I 0.83 0.18 0.01
79_Y 19_Y 0.82 0.18 0.01
39_G 18_S 0.82 0.18 0.01
59_V 84_A 0.82 0.17 0.01
125_I 84_A 0.82 0.17 0.01
7_E 59_L 0.82 0.17 0.01
143_P 20_T 0.82 0.17 0.01
26_W 29_D 0.82 0.17 0.01
153_A 48_S 0.82 0.17 0.01
50_G 51_V 0.81 0.17 0.01
76_N 103_K 0.81 0.17 0.01
114_S 13_I 0.81 0.17 0.01
117_C 85_P 0.81 0.17 0.01
153_A 107_G 0.81 0.17 0.01
82_V 25_V 0.81 0.17 0.01
18_L 82_L 0.81 0.17 0.01
116_F 5_Y 0.80 0.17 0.01
74_L 54_R 0.80 0.16 0.00
35_L 49_A 0.80 0.16 0.00
138_G 102_V 0.80 0.16 0.00
39_G 79_H 0.80 0.16 0.00
105_E 51_V 0.80 0.16 0.00
93_R 38_A 0.80 0.16 0.00
143_P 26_V 0.79 0.16 0.00
117_C 5_Y 0.79 0.16 0.00
95_L 47_S 0.79 0.16 0.00
108_T 92_H 0.79 0.16 0.00
43_Y 40_I 0.79 0.16 0.00
39_G 13_I 0.79 0.16 0.00
38_V 98_G 0.79 0.16 0.00
118_L 101_E 0.79 0.16 0.00
125_I 87_E 0.79 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)
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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