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OPENSEQ.org
NR
Genes: A B A+B
Length: 155 108 255
Sequences: 284 345 224
Seq/Len: 1.83 3.19 0.88
MirrorTree (Pazo et al. 2001) 0.87
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 0.84
2 0.00 0.00 0.85
5 0.00 0.00 0.85
10 0.00 0.00 0.86
20 0.00 0.00 0.86
100 0.00 0.00 0.86
∞ 0.02 0.02 0.88
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
115_M 51_V 1.47 0.71 0.01
131_L 102_V 1.46 0.70 0.01
103_I 90_I 1.46 0.70 0.01
101_L 33_A 1.45 0.69 0.01
127_F 29_D 1.44 0.69 0.01
16_V 41_A 1.39 0.65 0.01
101_L 98_G 1.39 0.64 0.01
125_I 23_A 1.37 0.63 0.01
144_S 35_E 1.34 0.60 0.00
47_L 89_P 1.25 0.53 0.00
81_G 26_V 1.25 0.53 0.00
149_A 37_L 1.23 0.51 0.00
145_V 62_W 1.20 0.48 0.00
34_Q 20_T 1.17 0.46 0.00
34_Q 3_R 1.15 0.44 0.00
82_V 25_V 1.15 0.44 0.00
147_K 36_S 1.15 0.44 0.00
90_Q 63_H 1.15 0.44 0.00
57_R 102_V 1.15 0.44 0.00
143_P 62_W 1.14 0.43 0.00
100_V 51_V 1.14 0.43 0.00
141_V 58_T 1.14 0.43 0.00
11_N 108_S 1.14 0.43 0.00
95_L 53_D 1.12 0.41 0.00
9_R 108_S 1.11 0.41 0.00
104_S 25_V 1.10 0.40 0.00
144_S 36_S 1.10 0.39 0.00
126_T 25_V 1.09 0.39 0.00
12_A 108_S 1.09 0.39 0.00
146_L 24_A 1.09 0.38 0.00
139_V 44_E 1.08 0.38 0.00
130_N 10_Q 1.08 0.38 0.00
59_V 90_I 1.07 0.37 0.00
23_Y 25_V 1.07 0.37 0.00
8_Q 108_S 1.06 0.36 0.00
33_L 3_R 1.06 0.36 0.00
104_S 28_G 1.04 0.35 0.00
147_K 23_A 1.04 0.34 0.00
123_P 61_S 1.04 0.34 0.00
153_A 107_G 1.03 0.34 0.00
149_A 27_F 1.03 0.34 0.00
15_Q 13_I 1.03 0.34 0.00
91_V 14_A 1.02 0.33 0.00
121_G 90_I 1.02 0.33 0.00
17_L 36_S 1.02 0.33 0.00
79_Y 48_S 1.02 0.33 0.00
105_E 12_L 1.01 0.32 0.00
115_M 46_V 1.00 0.32 0.00
20_I 26_V 1.00 0.31 0.00
7_E 108_S 1.00 0.31 0.00
137_S 44_E 1.00 0.31 0.00
12_A 1_T 0.99 0.31 0.00
92_F 56_G 0.99 0.31 0.00
113_G 90_I 0.99 0.31 0.00
143_P 12_L 0.98 0.30 0.00
110_C 9_N 0.98 0.30 0.00
153_A 108_S 0.98 0.30 0.00
10_S 59_L 0.98 0.30 0.00
9_R 8_P 0.98 0.29 0.00
127_F 98_G 0.97 0.29 0.00
144_S 17_I 0.97 0.29 0.00
109_E 13_I 0.96 0.28 0.00
63_R 94_G 0.96 0.28 0.00
37_V 37_L 0.95 0.28 0.00
118_L 12_L 0.95 0.28 0.00
80_L 46_V 0.95 0.28 0.00
36_C 27_F 0.95 0.28 0.00
139_V 26_V 0.95 0.27 0.00
101_L 49_A 0.95 0.27 0.00
145_V 101_E 0.95 0.27 0.00
86_R 63_H 0.94 0.27 0.00
78_I 42_S 0.94 0.27 0.00
78_I 16_S 0.94 0.27 0.00
81_G 9_N 0.94 0.27 0.00
110_C 12_L 0.94 0.27 0.00
103_I 53_D 0.94 0.27 0.00
129_A 24_A 0.94 0.27 0.00
143_P 20_T 0.93 0.26 0.00
115_M 84_A 0.92 0.25 0.00
94_S 90_I 0.92 0.25 0.00
147_K 20_T 0.90 0.24 0.00
80_L 56_G 0.90 0.24 0.00
145_V 44_E 0.90 0.24 0.00
13_V 86_T 0.89 0.23 0.00
105_E 51_V 0.89 0.23 0.00
105_E 10_Q 0.89 0.23 0.00
18_L 82_L 0.89 0.23 0.00
125_I 84_A 0.89 0.23 0.00
72_G 65_E 0.88 0.23 0.00
78_I 74_E 0.88 0.23 0.00
138_G 102_V 0.88 0.23 0.00
115_M 97_I 0.88 0.23 0.00
116_F 5_Y 0.87 0.22 0.00
20_I 44_E 0.87 0.22 0.00
78_I 93_D 0.87 0.22 0.00
118_L 98_G 0.87 0.22 0.00
81_G 23_A 0.87 0.22 0.00
10_S 1_T 0.87 0.22 0.00
134_I 52_Y 0.86 0.22 0.00
77_V 95_Q 0.86 0.22 0.00
115_M 43_S 0.86 0.22 0.00
116_F 12_L 0.86 0.22 0.00
134_I 18_S 0.86 0.21 0.00
105_E 32_A 0.86 0.21 0.00
79_Y 19_Y 0.85 0.21 0.00
75_C 27_F 0.85 0.21 0.00
116_F 22_E 0.85 0.21 0.00
9_R 25_V 0.85 0.21 0.00
19_G 62_W 0.85 0.21 0.00
61_A 102_V 0.85 0.21 0.00
17_L 52_Y 0.84 0.21 0.00
144_S 23_A 0.84 0.21 0.00
147_K 1_T 0.84 0.20 0.00
8_Q 59_L 0.84 0.20 0.00
15_Q 63_H 0.83 0.20 0.00
36_C 12_L 0.83 0.20 0.00
124_R 36_S 0.83 0.20 0.00
32_V 58_T 0.83 0.20 0.00
39_G 13_I 0.83 0.20 0.00
51_M 99_S 0.83 0.20 0.00
65_A 94_G 0.83 0.20 0.00
72_G 11_Q 0.83 0.20 0.00
106_R 24_A 0.82 0.20 0.00
130_N 51_V 0.82 0.19 0.00
36_C 29_D 0.82 0.19 0.00
142_H 22_E 0.82 0.19 0.00
125_I 9_N 0.82 0.19 0.00
142_H 1_T 0.82 0.19 0.00
122_G 77_L 0.82 0.19 0.00
76_N 103_K 0.81 0.19 0.00
141_V 18_S 0.81 0.19 0.00
103_I 96_K 0.81 0.19 0.00
29_E 44_E 0.81 0.19 0.00
38_V 98_G 0.81 0.19 0.00
56_G 86_T 0.81 0.19 0.00
93_R 102_V 0.81 0.19 0.00
95_L 37_L 0.81 0.19 0.00
143_P 32_A 0.81 0.18 0.00
76_N 73_L 0.81 0.18 0.00
34_Q 61_S 0.81 0.18 0.00
75_C 32_A 0.81 0.18 0.00
128_E 100_V 0.81 0.18 0.00
150_R 46_V 0.81 0.18 0.00
130_N 97_I 0.81 0.18 0.00
25_R 16_S 0.80 0.18 0.00
18_L 35_E 0.80 0.18 0.00
123_P 100_V 0.80 0.18 0.00
14_S 7_D 0.80 0.18 0.00
94_S 56_G 0.80 0.18 0.00
139_V 20_T 0.80 0.18 0.00
58_R 51_V 0.80 0.18 0.00
148_L 23_A 0.79 0.18 0.00
100_V 75_Q 0.79 0.18 0.00
69_P 18_S 0.79 0.17 0.00
12_A 107_G 0.79 0.17 0.00
117_C 104_G 0.79 0.17 0.00
76_N 48_S 0.79 0.17 0.00
58_R 25_V 0.78 0.17 0.00
76_N 22_E 0.78 0.17 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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