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OPENSEQ.org
RsgA-RbfA
Genes: A B A+B
Length: 350 133 424
Sequences: 2498 2471 1029
Seq/Len: 7.14 18.58 2.43
MirrorTree (Pazo et al. 2001) 0.63
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 0.03 0.09 0.00
2 0.03 0.09 0.00
5 0.03 0.09 0.02
10 0.03 0.09 0.05
20 0.03 0.09 0.07
100 0.04 0.09 0.54
∞ 0.09 0.09 2.13
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
237_N 43_M 1.33 0.87 0.20
235_L 37_T 1.12 0.71 0.11
67_R 7_R 1.08 0.67 0.10
54_V 38_V 1.03 0.61 0.08
199_K 19_I 0.96 0.54 0.07
213_A 80_R 0.88 0.44 0.05
79_V 41_V 0.87 0.43 0.05
80_V 53_Y 0.87 0.43 0.05
288_V 45_R 0.86 0.42 0.04
190_V 51_K 0.86 0.42 0.04
105_S 53_Y 0.86 0.41 0.04
222_S 25_R 0.85 0.41 0.04
245_L 85_K 0.84 0.40 0.04
127_V 17_K 0.84 0.40 0.04
241_D 73_Q 0.84 0.40 0.04
201_L 103_L 0.84 0.39 0.04
42_G 55_T 0.82 0.38 0.04
128_I 105_E 0.82 0.37 0.04
309_G 85_K 0.82 0.37 0.04
144_Y 89_L 0.81 0.37 0.04
216_S 54_V 0.81 0.36 0.04
301_D 54_V 0.80 0.36 0.04
270_V 109_M 0.80 0.35 0.04
149_E 38_V 0.80 0.35 0.04
79_V 22_I 0.79 0.34 0.03
148_C 38_V 0.79 0.34 0.03
300_R 74_E 0.79 0.34 0.03
81_W 37_T 0.79 0.34 0.03
182_N 70_K 0.78 0.33 0.03
289_E 41_V 0.78 0.33 0.03
212_F 90_R 0.77 0.33 0.03
105_S 57_L 0.77 0.32 0.03
226_A 56_F 0.77 0.32 0.03
157_I 38_V 0.77 0.32 0.03
110_P 49_Y 0.76 0.31 0.03
205_L 70_K 0.76 0.31 0.03
238_D 119_H 0.75 0.30 0.03
270_V 43_M 0.75 0.30 0.03
223_L 11_V 0.75 0.30 0.03
128_I 87_M 0.75 0.30 0.03
126_I 12_A 0.74 0.29 0.03
335_S 11_V 0.74 0.29 0.03
190_V 52_V 0.74 0.29 0.03
254_R 86_A 0.74 0.29 0.03
262_G 113_V 0.74 0.29 0.03
210_S 95_L 0.73 0.28 0.03
262_G 109_M 0.72 0.27 0.03
44_V 23_L 0.72 0.27 0.03
298_K 76_S 0.72 0.27 0.03
262_G 83_L 0.71 0.27 0.03
128_I 104_V 0.71 0.27 0.03
66_I 54_V 0.71 0.26 0.02
292_D 114_T 0.71 0.26 0.02
165_L 73_Q 0.71 0.26 0.02
201_L 96_T 0.71 0.26 0.02
293_Y 53_Y 0.71 0.26 0.02
75_T 95_L 0.71 0.26 0.02
245_L 48_A 0.71 0.26 0.02
280_P 36_T 0.70 0.26 0.02
201_L 71_A 0.70 0.26 0.02
236_T 43_M 0.70 0.25 0.02
314_E 66_K 0.70 0.25 0.02
241_D 53_Y 0.70 0.25 0.02
264_V 40_G 0.70 0.25 0.02
191_S 32_L 0.70 0.25 0.02
160_N 15_M 0.69 0.25 0.02
257_H 113_V 0.69 0.25 0.02
128_I 124_R 0.69 0.24 0.02
281_E 53_Y 0.69 0.24 0.02
285_Q 113_V 0.69 0.24 0.02
184_G 81_S 0.69 0.24 0.02
72_S 10_R 0.68 0.24 0.02
199_K 27_I 0.68 0.24 0.02
123_I 57_L 0.68 0.23 0.02
129_V 37_T 0.68 0.23 0.02
201_L 108_R 0.67 0.23 0.02
311_A 112_L 0.67 0.23 0.02
237_N 107_M 0.67 0.23 0.02
273_F 116_V 0.67 0.23 0.02
212_F 52_V 0.67 0.23 0.02
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
5816 2.43 RsgA-RbfA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.20 Done - Shared
5795 0.63 RsgA-RbfA Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5789 0.08 RsgA-RbfA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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