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OPENSEQ.org
3RPF_AC
Genes: A B A+B
Length: 143 74 212
Sequences: 1540 2012 999
Seq/Len: 10.77 27.19 4.71
MirrorTree (Pazo et al. 2001) 0.74
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 3.71
2 0.00 0.00 4.04
5 0.00 0.00 4.40
10 0.00 0.00 4.53
20 0.00 0.00 4.60
100 0.00 0.01 4.67
∞ 0.02 0.06 5.53
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 2.47 1.00 1.00
56_T 50_H 1.91 1.00 0.98
120_Y 13_E 1.30 0.95 0.84
50_Y 66_S 1.19 0.91 0.76
53_L 46_A 1.16 0.89 0.73
15_K 56_N 1.14 0.88 0.72
111_F 64_V 1.08 0.85 0.66
56_T 49_D 1.07 0.83 0.65
49_I 72_C 1.06 0.83 0.64
53_L 68_L 1.01 0.78 0.58
28_A 34_E 0.98 0.76 0.55
125_N 67_L 0.96 0.73 0.52
50_Y 64_V 0.96 0.73 0.52
130_A 72_C 0.95 0.72 0.51
58_F 36_L 0.94 0.71 0.50
53_L 66_S 0.93 0.70 0.49
52_A 49_D 0.93 0.70 0.48
121_D 66_S 0.90 0.66 0.44
77_S 9_G 0.89 0.65 0.43
57_W 51_L 0.88 0.64 0.43
42_I 10_P 0.87 0.62 0.41
117_I 72_C 0.87 0.62 0.41
36_V 71_V 0.84 0.59 0.38
53_L 49_D 0.82 0.56 0.35
133_R 71_V 0.82 0.56 0.35
84_G 17_F 0.81 0.54 0.33
113_H 48_N 0.80 0.52 0.32
109_E 36_L 0.79 0.52 0.31
31_V 2_M 0.78 0.51 0.30
50_Y 46_A 0.78 0.51 0.30
98_K 6_R 0.77 0.48 0.28
102_E 59_L 0.76 0.48 0.28
93_M 59_L 0.76 0.47 0.28
85_Q 42_V 0.75 0.46 0.27
61_W 5_V 0.74 0.45 0.26
87_S 68_L 0.73 0.44 0.25
92_S 71_V 0.72 0.42 0.23
50_Y 49_D 0.72 0.42 0.23
26_F 7_F 0.72 0.41 0.23
16_A 24_K 0.71 0.41 0.23
71_V 55_L 0.71 0.41 0.23
92_S 62_G 0.71 0.40 0.22
54_L 71_V 0.71 0.40 0.22
35_I 10_P 0.70 0.39 0.21
14_L 50_H 0.70 0.39 0.21
104_Y 61_D 0.68 0.37 0.20
130_A 12_K 0.67 0.35 0.19
45_L 50_H 0.67 0.35 0.19
130_A 67_L 0.67 0.35 0.18
121_D 11_I 0.67 0.35 0.18
111_F 49_D 0.67 0.34 0.18
87_S 64_V 0.66 0.34 0.18
131_K 42_V 0.66 0.34 0.18
59_E 24_K 0.66 0.33 0.17
115_A 72_C 0.65 0.33 0.17
121_D 46_A 0.65 0.33 0.17
66_K 59_L 0.65 0.33 0.17
94_G 56_N 0.65 0.33 0.17
63_H 22_D 0.65 0.32 0.17
99_N 57_T 0.64 0.32 0.16
122_L 57_T 0.64 0.32 0.16
16_A 28_A 0.64 0.32 0.16
60_K 51_L 0.64 0.31 0.16
54_L 51_L 0.64 0.31 0.16
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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