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OPENSEQ.org
3RPF_AC
Genes: A B A+B
Length: 145 74 214
Sequences: 1559 1967 975
Seq/Len: 10.75 26.58 4.56
MirrorTree (Pazo et al. 2001) 0.73
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 3.77
2 0.00 0.00 4.06
5 0.00 0.00 4.30
10 0.00 0.00 4.39
20 0.00 0.00 4.45
100 0.00 0.01 4.55
∞ 0.02 0.05 5.33
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
50_D 12_K 2.65 1.00 1.00
58_T 50_H 1.92 1.00 0.98
122_Y 13_E 1.32 0.95 0.85
52_Y 66_S 1.25 0.93 0.81
127_N 67_L 1.22 0.92 0.79
55_L 46_A 1.20 0.91 0.77
113_F 64_V 1.11 0.86 0.69
17_K 56_N 1.09 0.85 0.68
58_T 49_D 1.09 0.84 0.67
51_I 72_C 1.06 0.82 0.64
52_Y 64_V 1.02 0.79 0.60
59_W 51_L 1.00 0.77 0.57
52_Y 46_A 0.98 0.75 0.55
55_L 66_S 0.98 0.75 0.55
55_L 68_L 0.96 0.72 0.52
132_A 72_C 0.91 0.67 0.46
3_L 59_L 0.91 0.66 0.46
123_D 66_S 0.90 0.66 0.45
54_A 49_D 0.90 0.65 0.45
79_S 9_G 0.85 0.59 0.38
119_I 72_C 0.84 0.57 0.37
16_L 7_F 0.82 0.55 0.35
87_Q 47_L 0.81 0.54 0.34
118_P 46_A 0.81 0.53 0.33
5_I 72_C 0.80 0.52 0.32
44_I 10_P 0.80 0.52 0.32
87_Q 42_V 0.80 0.52 0.32
55_L 49_D 0.78 0.49 0.30
133_K 42_V 0.78 0.49 0.30
100_K 6_R 0.78 0.49 0.30
89_S 68_L 0.78 0.49 0.30
33_V 2_M 0.77 0.47 0.28
104_E 59_L 0.76 0.47 0.28
101_N 57_T 0.75 0.45 0.26
94_S 71_V 0.73 0.43 0.25
115_H 48_N 0.73 0.42 0.24
135_R 71_V 0.72 0.41 0.24
60_F 36_L 0.72 0.41 0.23
65_H 15_N 0.71 0.40 0.23
113_F 49_D 0.71 0.40 0.23
65_H 33_K 0.68 0.36 0.20
95_M 59_L 0.68 0.36 0.20
110_I 35_G 0.68 0.36 0.20
117_A 72_C 0.68 0.36 0.19
38_V 71_V 0.68 0.35 0.19
123_D 46_A 0.68 0.35 0.19
16_L 50_H 0.67 0.35 0.19
52_Y 49_D 0.67 0.35 0.19
130_I 9_G 0.67 0.34 0.18
87_Q 54_N 0.67 0.34 0.18
68_K 19_K 0.66 0.33 0.17
88_S 36_L 0.66 0.33 0.17
111_E 36_L 0.66 0.33 0.17
123_D 11_I 0.66 0.33 0.17
4_K 18_I 0.65 0.32 0.17
30_A 34_E 0.65 0.32 0.17
69_D 21_N 0.65 0.32 0.17
91_L 67_L 0.65 0.32 0.17
3_L 41_G 0.65 0.32 0.17
130_I 61_D 0.65 0.32 0.16
80_L 71_V 0.64 0.31 0.16
52_Y 71_V 0.64 0.31 0.16
18_A 16_F 0.63 0.30 0.15
18_A 24_K 0.63 0.29 0.15
47_L 50_H 0.62 0.29 0.15
94_S 63_D 0.62 0.29 0.14
72_V 3_V 0.62 0.29 0.14
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
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