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OPENSEQ.org
3RPF_A_C
Genes: A B A+B
Length: 148 74 216
Sequences: 64 66 67
Seq/Len: 0.43 0.89 0.31
MirrorTree (Pazo et al. 2001) 0.53
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 0.30
2 0.01 0.00 0.30
5 0.01 0.00 0.30
10 0.01 0.00 0.30
20 0.01 0.00 0.30
100 0.01 0.00 0.30
∞ 0.01 0.00 0.30
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
5_L 67_L 1.78 0.61 0.00
16_E 65_I 1.51 0.43 0.00
109_E 27_R 1.44 0.38 0.00
77_K 45_I 1.40 0.36 0.00
8_I 3_V 1.37 0.34 0.00
81_S 61_D 1.37 0.34 0.00
44_D 52_I 1.32 0.31 0.00
23_E 67_L 1.30 0.30 0.00
136_E 50_H 1.29 0.29 0.00
143_G 23_L 1.29 0.29 0.00
136_E 3_V 1.27 0.28 0.00
45_N 52_I 1.26 0.28 0.00
73_G 19_K 1.26 0.28 0.00
144_S 67_L 1.25 0.27 0.00
146_L 32_E 1.24 0.27 0.00
10_G 59_L 1.24 0.27 0.00
72_L 52_I 1.22 0.26 0.00
89_Q 58_P 1.22 0.25 0.00
88_G 43_C 1.21 0.25 0.00
77_K 36_L 1.17 0.23 0.00
57_L 66_S 1.16 0.23 0.00
20_A 3_V 1.14 0.22 0.00
102_K 27_R 1.13 0.21 0.00
98_G 6_R 1.11 0.21 0.00
130_K 28_A 1.11 0.20 0.00
82_L 17_F 1.10 0.20 0.00
129_N 67_L 1.09 0.20 0.00
102_K 36_L 1.09 0.20 0.00
130_K 37_K 1.09 0.20 0.00
60_T 51_L 1.09 0.19 0.00
112_I 52_I 1.07 0.19 0.00
135_K 22_D 1.04 0.18 0.00
136_E 16_F 1.04 0.17 0.00
97_M 36_L 1.04 0.17 0.00
13_D 64_V 1.02 0.17 0.00
7_I 17_F 1.02 0.17 0.00
141_L 18_I 1.02 0.17 0.00
92_F 15_N 1.01 0.16 0.00
57_L 26_L 1.01 0.16 0.00
97_M 27_R 1.00 0.16 0.00
47_Q 51_L 1.00 0.16 0.00
76_L 45_I 1.00 0.16 0.00
39_I 27_R 0.99 0.16 0.00
118_N 67_L 0.99 0.16 0.00
30_F 56_N 0.99 0.16 0.00
76_L 43_C 0.98 0.15 0.00
44_D 66_S 0.98 0.15 0.00
46_I 49_D 0.98 0.15 0.00
48_G 26_L 0.97 0.15 0.00
47_Q 16_F 0.96 0.15 0.00
59_K 3_V 0.95 0.14 0.00
141_L 47_L 0.95 0.14 0.00
19_K 67_L 0.94 0.14 0.00
130_K 15_N 0.94 0.14 0.00
94_C 18_I 0.94 0.14 0.00
132_I 38_E 0.93 0.14 0.00
139_H 27_R 0.93 0.14 0.00
72_L 26_L 0.93 0.14 0.00
84_D 55_L 0.93 0.14 0.00
24_E 66_S 0.92 0.13 0.00
96_S 33_K 0.92 0.13 0.00
44_D 36_L 0.92 0.13 0.00
95_V 50_H 0.92 0.13 0.00
26_C 14_E 0.91 0.13 0.00
14_T 46_A 0.90 0.13 0.00
22_Q 42_V 0.90 0.13 0.00
142_K 18_I 0.89 0.12 0.00
11_A 58_P 0.89 0.12 0.00
93_L 15_N 0.89 0.12 0.00
23_E 20_A 0.89 0.12 0.00
30_F 51_L 0.88 0.12 0.00
78_M 56_N 0.88 0.12 0.00
108_Y 11_I 0.87 0.12 0.00
16_E 21_N 0.87 0.12 0.00
139_H 66_S 0.86 0.12 0.00
9_Q 54_N 0.86 0.11 0.00
72_L 20_A 0.86 0.11 0.00
127_I 14_E 0.86 0.11 0.00
100_N 27_R 0.85 0.11 0.00
23_E 24_K 0.85 0.11 0.00
20_A 5_V 0.85 0.11 0.00
102_K 42_V 0.85 0.11 0.00
143_G 59_L 0.84 0.11 0.00
21_Y 8_F 0.84 0.11 0.00
146_L 53_D 0.83 0.11 0.00
76_L 67_L 0.83 0.11 0.00
108_Y 13_E 0.83 0.11 0.00
68_K 46_A 0.83 0.11 0.00
60_T 50_H 0.83 0.11 0.00
68_K 54_N 0.83 0.11 0.00
27_A 38_E 0.83 0.11 0.00
57_L 47_L 0.83 0.11 0.00
128_H 3_V 0.83 0.11 0.00
112_I 13_E 0.82 0.11 0.00
118_N 36_L 0.82 0.10 0.00
56_A 8_F 0.82 0.10 0.00
73_G 66_S 0.82 0.10 0.00
94_C 41_G 0.82 0.10 0.00
76_L 31_Q 0.81 0.10 0.00
52_D 49_D 0.81 0.10 0.00
56_A 19_K 0.81 0.10 0.00
72_L 32_E 0.80 0.10 0.00
24_E 67_L 0.80 0.10 0.00
16_E 18_I 0.80 0.10 0.00
18_L 3_V 0.79 0.10 0.00
129_N 60_K 0.79 0.10 0.00
6_K 5_V 0.79 0.10 0.00
42_K 5_V 0.79 0.10 0.00
148_A 33_K 0.79 0.10 0.00
92_F 5_V 0.79 0.10 0.00
135_K 26_L 0.79 0.10 0.00
7_I 16_F 0.79 0.10 0.00
87_I 11_I 0.79 0.10 0.00
130_K 38_E 0.79 0.10 0.00
39_I 60_K 0.79 0.10 0.00
9_Q 31_Q 0.78 0.10 0.00
13_D 60_K 0.78 0.10 0.00
127_I 56_N 0.78 0.09 0.00
117_H 49_D 0.78 0.09 0.00
130_K 12_K 0.78 0.09 0.00
146_L 35_G 0.78 0.09 0.00
33_F 29_I 0.77 0.09 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
7271 6.11 3RPF_A_C Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7265 0.31 3RPF_A_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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