May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3Rpf_ac
Genes: A B A+B
Length: 145 74 215
Sequences: 63 66 66
Seq/Len: 0.43 0.89 0.31
MirrorTree (Pazo et al. 2001) 0.51
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
3_L 67_L 1.71 0.57 0.00
14_E 65_I 1.68 0.55 0.00
107_E 27_R 1.40 0.36 0.00
87_Q 58_P 1.40 0.36 0.00
75_K 45_I 1.38 0.35 0.00
42_D 52_I 1.34 0.32 0.00
79_S 61_D 1.31 0.31 0.00
6_I 3_V 1.31 0.30 0.00
134_E 50_H 1.30 0.30 0.00
141_G 23_L 1.29 0.30 0.00
8_G 59_L 1.27 0.28 0.00
134_E 3_V 1.25 0.27 0.00
142_S 67_L 1.25 0.27 0.00
75_K 36_L 1.24 0.27 0.00
21_E 67_L 1.24 0.27 0.00
74_L 43_C 1.22 0.25 0.00
86_G 43_C 1.20 0.24 0.00
18_A 3_V 1.19 0.24 0.00
11_D 64_V 1.17 0.23 0.00
134_E 16_F 1.17 0.23 0.00
144_L 32_E 1.16 0.23 0.00
128_K 37_K 1.15 0.22 0.00
128_K 28_A 1.14 0.22 0.00
127_N 67_L 1.13 0.21 0.00
80_L 17_F 1.12 0.21 0.00
96_G 6_R 1.12 0.21 0.00
45_Q 51_L 1.12 0.21 0.00
43_N 52_I 1.11 0.20 0.00
110_I 52_I 1.10 0.20 0.00
100_K 27_R 1.09 0.20 0.00
55_L 26_L 1.09 0.20 0.00
55_L 66_S 1.09 0.20 0.00
100_K 36_L 1.09 0.19 0.00
116_N 67_L 1.07 0.19 0.00
42_D 66_S 1.07 0.19 0.00
128_K 15_N 1.06 0.18 0.00
28_F 56_N 1.06 0.18 0.00
95_M 36_L 1.06 0.18 0.00
71_G 19_K 1.06 0.18 0.00
5_I 17_F 1.05 0.18 0.00
70_L 52_I 1.02 0.17 0.00
58_T 51_L 1.01 0.16 0.00
139_L 18_I 1.01 0.16 0.00
133_K 22_D 1.00 0.16 0.00
57_K 3_V 0.99 0.15 0.00
94_S 33_K 0.98 0.15 0.00
76_M 56_N 0.97 0.15 0.00
95_M 27_R 0.97 0.15 0.00
70_L 20_A 0.96 0.15 0.00
17_K 67_L 0.96 0.14 0.00
37_I 27_R 0.95 0.14 0.00
46_G 26_L 0.95 0.14 0.00
74_L 45_I 0.94 0.14 0.00
24_C 22_D 0.93 0.14 0.00
14_E 18_I 0.93 0.14 0.00
20_Q 42_V 0.92 0.13 0.00
82_D 55_L 0.91 0.13 0.00
40_K 5_V 0.91 0.13 0.00
137_H 27_R 0.91 0.13 0.00
92_C 18_I 0.89 0.12 0.00
22_E 66_S 0.89 0.12 0.00
44_I 49_D 0.88 0.12 0.00
140_K 18_I 0.88 0.12 0.00
91_L 15_N 0.87 0.12 0.00
54_A 19_K 0.87 0.12 0.00
106_Y 13_E 0.87 0.12 0.00
106_Y 11_I 0.87 0.12 0.00
42_D 36_L 0.87 0.12 0.00
110_I 13_E 0.86 0.12 0.00
74_L 17_F 0.86 0.12 0.00
54_A 8_F 0.86 0.12 0.00
130_I 38_E 0.86 0.12 0.00
133_K 26_L 0.86 0.11 0.00
75_K 61_D 0.85 0.11 0.00
141_G 59_L 0.85 0.11 0.00
19_Y 8_F 0.84 0.11 0.00
21_E 20_A 0.84 0.11 0.00
93_V 50_H 0.84 0.11 0.00
33_V 52_I 0.84 0.11 0.00
137_H 66_S 0.84 0.11 0.00
98_N 27_R 0.83 0.11 0.00
11_D 60_K 0.82 0.11 0.00
70_L 26_L 0.82 0.10 0.00
90_F 5_V 0.82 0.10 0.00
70_L 32_E 0.82 0.10 0.00
74_L 67_L 0.82 0.10 0.00
71_G 66_S 0.82 0.10 0.00
85_I 11_I 0.81 0.10 0.00
58_T 50_H 0.81 0.10 0.00
139_L 47_L 0.81 0.10 0.00
55_L 29_I 0.81 0.10 0.00
6_I 15_N 0.81 0.10 0.00
125_I 56_N 0.81 0.10 0.00
28_F 51_L 0.81 0.10 0.00
100_K 42_V 0.81 0.10 0.00
50_D 49_D 0.81 0.10 0.00
126_H 3_V 0.80 0.10 0.00
125_I 14_E 0.80 0.10 0.00
25_A 38_E 0.80 0.10 0.00
55_L 47_L 0.80 0.10 0.00
43_N 19_K 0.80 0.10 0.00
72_V 35_G 0.80 0.10 0.00
66_K 54_N 0.80 0.10 0.00
24_C 14_E 0.79 0.10 0.00
14_E 21_N 0.79 0.10 0.00
70_L 19_K 0.79 0.10 0.00
18_A 5_V 0.79 0.10 0.00
9_A 58_P 0.79 0.10 0.00
12_T 46_A 0.79 0.10 0.00
7_Q 31_Q 0.78 0.10 0.00
92_C 41_G 0.78 0.10 0.00
21_E 24_K 0.78 0.10 0.00
37_I 60_K 0.78 0.09 0.00
32_C 13_E 0.78 0.09 0.00
128_K 24_K 0.77 0.09 0.00
57_K 65_I 0.77 0.09 0.00
26_K 36_L 0.77 0.09 0.00
7_Q 65_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
10447 0.31 3Rpf_ac Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
0321 4.56 3RPF_AC Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0319 0.21 3RPF_AC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
Page generated in 2.1436 seconds.