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OPENSEQ.org
3RPF_AC
Genes: A B A+B
Length: 143 74 204
Sequences: 1310 1913 831
Seq/Len: 9.16 25.85 4.07
MirrorTree (Pazo et al. 2001) 0.74
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 3.07
2 0.00 0.00 3.36
5 0.00 0.00 3.65
10 0.00 0.01 3.76
20 0.00 0.01 3.83
100 0.00 0.02 3.90
∞ 0.02 0.10 4.75
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. Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on HHsearch results which uses the overall probability and per-site alignment confidence. Inter-chain contacts in the pdb are in shades of red. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
48_D 12_K 2.32 1.00 0.99
56_T 50_H 1.48 0.97 0.91
50_Y 66_S 1.30 0.94 0.83
53_L 46_A 1.27 0.92 0.81
49_I 72_C 1.20 0.89 0.75
53_L 66_S 1.18 0.88 0.74
120_Y 13_E 1.14 0.85 0.70
111_F 64_V 1.13 0.85 0.69
50_Y 46_A 1.08 0.81 0.64
53_L 68_L 0.97 0.71 0.51
61_W 5_V 0.97 0.70 0.51
117_I 72_C 0.92 0.64 0.45
121_D 66_S 0.91 0.63 0.43
124_H 67_L 0.91 0.63 0.43
42_I 10_P 0.90 0.62 0.42
113_H 48_N 0.88 0.59 0.40
77_S 9_G 0.88 0.59 0.39
53_L 49_D 0.86 0.57 0.38
87_S 68_L 0.86 0.56 0.37
57_W 51_L 0.86 0.56 0.37
102_E 36_L 0.84 0.54 0.35
115_A 72_C 0.84 0.54 0.35
50_Y 64_V 0.82 0.52 0.33
51_E 72_C 0.81 0.50 0.32
52_A 49_D 0.81 0.49 0.31
102_E 59_L 0.79 0.47 0.29
93_M 27_R 0.78 0.46 0.28
31_V 34_E 0.78 0.46 0.28
78_L 71_V 0.78 0.45 0.27
54_L 71_V 0.76 0.44 0.26
111_F 49_D 0.76 0.43 0.26
99_N 57_T 0.76 0.43 0.26
72_L 5_V 0.76 0.43 0.26
56_T 41_G 0.75 0.42 0.25
35_I 11_I 0.75 0.42 0.25
12_E 56_N 0.74 0.41 0.24
50_Y 71_V 0.74 0.41 0.24
51_E 67_L 0.74 0.41 0.24
60_K 50_H 0.73 0.40 0.23
67_D 60_K 0.73 0.40 0.23
43_Q 17_F 0.73 0.40 0.23
116_P 46_A 0.72 0.39 0.22
9_D 38_E 0.71 0.37 0.21
94_G 51_L 0.70 0.36 0.20
68_L 64_V 0.70 0.36 0.20
56_T 49_D 0.70 0.36 0.20
108_I 71_V 0.70 0.35 0.20
104_Y 61_D 0.69 0.35 0.19
121_D 11_I 0.69 0.34 0.19
47_F 72_C 0.68 0.34 0.18
45_L 6_R 0.68 0.33 0.18
94_G 18_I 0.68 0.33 0.18
85_Q 15_N 0.68 0.33 0.18
54_L 67_L 0.68 0.33 0.18
92_S 6_R 0.67 0.32 0.17
59_E 24_K 0.66 0.31 0.17
50_Y 49_D 0.66 0.30 0.16
5_Q 65_I 0.65 0.30 0.16
36_V 71_V 0.65 0.29 0.15
94_G 61_D 0.64 0.29 0.15
133_R 17_F 0.64 0.29 0.15
7_A 22_D 0.64 0.29 0.15
109_E 36_L 0.64 0.28 0.15
47_F 68_L 0.64 0.28 0.15
28_A 57_T 0.64 0.28 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)
HHsearch results
3rpfAB:CDContact Map
1fm0E:DContact Map
2q5wE:DContact Map
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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