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OPENSEQ.org
3RPF_C
Genes: A B A+B
Length: 143 74 215
Sequences: 63 66 66
Seq/Len: 0.44 0.89 0.31
MirrorTree (Pazo et al. 2001) 0.52
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
1_L 67_L 1.79 0.62 0.00
12_E 65_I 1.57 0.47 0.00
73_K 45_I 1.42 0.38 0.00
105_E 27_R 1.42 0.37 0.00
132_E 50_H 1.35 0.33 0.00
4_I 3_V 1.35 0.33 0.00
85_Q 58_P 1.33 0.32 0.00
140_S 67_L 1.31 0.30 0.00
19_E 67_L 1.29 0.30 0.00
77_S 61_D 1.26 0.28 0.00
139_G 23_L 1.26 0.28 0.00
6_G 59_L 1.25 0.27 0.00
73_K 36_L 1.25 0.27 0.00
132_E 3_V 1.24 0.27 0.00
72_L 43_C 1.24 0.27 0.00
142_L 32_E 1.23 0.26 0.00
9_D 64_V 1.22 0.26 0.00
41_N 52_I 1.20 0.24 0.00
16_A 3_V 1.18 0.24 0.00
84_G 43_C 1.17 0.23 0.00
126_K 37_K 1.17 0.23 0.00
132_E 16_F 1.16 0.23 0.00
68_L 52_I 1.16 0.23 0.00
126_K 28_A 1.14 0.22 0.00
126_K 15_N 1.13 0.21 0.00
3_I 17_F 1.12 0.21 0.00
40_D 66_S 1.12 0.21 0.00
53_L 66_S 1.11 0.20 0.00
94_G 6_R 1.10 0.20 0.00
98_K 27_R 1.09 0.20 0.00
98_K 36_L 1.09 0.20 0.00
40_D 52_I 1.08 0.19 0.00
108_I 52_I 1.08 0.19 0.00
43_Q 51_L 1.08 0.19 0.00
69_G 19_K 1.07 0.19 0.00
78_L 17_F 1.07 0.19 0.00
56_T 51_L 1.06 0.18 0.00
93_M 36_L 1.06 0.18 0.00
53_L 26_L 1.06 0.18 0.00
131_K 22_D 1.04 0.17 0.00
114_N 67_L 1.02 0.17 0.00
15_K 67_L 1.01 0.16 0.00
125_N 67_L 0.99 0.16 0.00
44_G 26_L 0.98 0.15 0.00
35_I 27_R 0.98 0.15 0.00
92_S 33_K 0.97 0.15 0.00
93_M 27_R 0.97 0.15 0.00
137_L 18_I 0.96 0.15 0.00
68_L 26_L 0.96 0.14 0.00
26_F 56_N 0.96 0.14 0.00
90_C 18_I 0.94 0.14 0.00
12_E 21_N 0.93 0.14 0.00
68_L 20_A 0.92 0.13 0.00
20_E 66_S 0.92 0.13 0.00
72_L 45_I 0.92 0.13 0.00
43_Q 16_F 0.91 0.13 0.00
135_H 27_R 0.91 0.13 0.00
56_T 50_H 0.91 0.13 0.00
18_Q 42_V 0.90 0.13 0.00
72_L 17_F 0.90 0.12 0.00
80_D 55_L 0.90 0.12 0.00
64_K 54_N 0.89 0.12 0.00
138_K 18_I 0.88 0.12 0.00
44_G 19_K 0.87 0.12 0.00
89_L 15_N 0.87 0.12 0.00
22_C 14_E 0.87 0.12 0.00
123_I 56_N 0.87 0.12 0.00
124_H 3_V 0.87 0.12 0.00
136_P 54_N 0.87 0.12 0.00
52_A 8_F 0.87 0.12 0.00
96_N 27_R 0.86 0.12 0.00
20_E 67_L 0.86 0.12 0.00
104_Y 13_E 0.86 0.12 0.00
91_V 50_H 0.86 0.12 0.00
106_N 64_V 0.85 0.11 0.00
17_Y 8_F 0.85 0.11 0.00
42_I 49_D 0.85 0.11 0.00
5_Q 31_Q 0.85 0.11 0.00
98_K 42_V 0.85 0.11 0.00
108_I 13_E 0.84 0.11 0.00
19_E 20_A 0.84 0.11 0.00
74_M 56_N 0.84 0.11 0.00
69_G 66_S 0.84 0.11 0.00
38_K 5_V 0.84 0.11 0.00
104_Y 11_I 0.84 0.11 0.00
10_T 46_A 0.84 0.11 0.00
72_L 67_L 0.83 0.11 0.00
52_A 19_K 0.83 0.11 0.00
88_F 5_V 0.83 0.11 0.00
73_K 61_D 0.83 0.11 0.00
9_D 60_K 0.83 0.11 0.00
83_I 11_I 0.82 0.11 0.00
53_L 29_I 0.82 0.10 0.00
16_A 5_V 0.82 0.10 0.00
139_G 59_L 0.82 0.10 0.00
40_D 36_L 0.82 0.10 0.00
128_I 38_E 0.81 0.10 0.00
142_L 53_D 0.81 0.10 0.00
137_L 47_L 0.81 0.10 0.00
4_I 15_N 0.81 0.10 0.00
26_F 51_L 0.81 0.10 0.00
70_V 35_G 0.81 0.10 0.00
68_L 32_E 0.80 0.10 0.00
123_I 14_E 0.80 0.10 0.00
72_L 31_Q 0.80 0.10 0.00
7_A 61_D 0.80 0.10 0.00
24_K 65_I 0.80 0.10 0.00
53_L 47_L 0.79 0.10 0.00
23_A 38_E 0.79 0.10 0.00
68_L 19_K 0.79 0.10 0.00
131_K 26_L 0.79 0.10 0.00
35_I 60_K 0.79 0.10 0.00
63_H 4_E 0.79 0.10 0.00
135_H 66_S 0.78 0.10 0.00
12_E 18_I 0.78 0.10 0.00
83_I 14_E 0.78 0.09 0.00
24_K 36_L 0.78 0.09 0.00
48_D 49_D 0.78 0.09 0.00
90_C 41_G 0.77 0.09 0.00
30_C 13_E 0.76 0.09 0.00
29_F 29_I 0.76 0.09 0.00
114_N 36_L 0.76 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
13630 0.31 3RPF_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
0140 4.71 3RPF_AC Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0138 0.21 3RPF_AC Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) Killed - Shared
0135 0.2 3RPF_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0134 4.07 3RPF_AC Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.99 Done - Shared
0133 0.2 3RPF_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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