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OPENSEQ.org
RsgA-KsgA
Genes: A B A+B
Length: 350 273 563
Sequences: 2498 3757 1011
Seq/Len: 7.14 13.76 1.8
MirrorTree (Pazo et al. 2001) 0.57
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 0.07 0.01
2 0.03 0.07 0.04
5 0.03 0.07 0.06
10 0.03 0.07 0.07
20 0.03 0.07 0.10
100 0.04 0.07 0.23
∞ 0.09 0.08 1.62
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
44_V 108_L 1.23 0.72 0.02
200_P 41_M 1.09 0.59 0.01
336_M 50_A 0.93 0.42 0.01
300_R 194_L 0.93 0.41 0.01
71_R 65_I 0.91 0.39 0.01
178_D 263_Y 0.90 0.39 0.01
253_A 260_M 0.89 0.38 0.01
299_Y 61_Q 0.88 0.37 0.01
158_V 126_L 0.87 0.36 0.01
120_A 190_A 0.86 0.34 0.01
213_A 220_Q 0.85 0.34 0.01
213_A 119_S 0.85 0.34 0.01
311_A 190_A 0.85 0.34 0.01
290_F 97_F 0.85 0.34 0.01
75_T 44_I 0.85 0.34 0.01
336_M 186_K 0.85 0.33 0.01
288_V 257_Y 0.82 0.31 0.01
212_F 146_N 0.82 0.31 0.01
226_A 148_L 0.82 0.31 0.01
42_G 50_A 0.82 0.30 0.01
155_P 154_S 0.81 0.30 0.01
235_L 174_L 0.81 0.30 0.01
305_D 151_G 0.80 0.29 0.01
127_V 38_G 0.80 0.29 0.01
298_K 153_N 0.79 0.28 0.01
222_S 233_F 0.77 0.26 0.00
242_N 65_I 0.77 0.26 0.00
262_G 150_A 0.76 0.25 0.00
236_T 65_I 0.76 0.25 0.00
47_R 225_I 0.75 0.25 0.00
264_V 99_E 0.75 0.25 0.00
202_E 208_R 0.75 0.25 0.00
44_V 40_A 0.74 0.24 0.00
238_D 58_R 0.74 0.24 0.00
275_L 51_L 0.73 0.23 0.00
275_L 259_Q 0.73 0.23 0.00
314_E 23_Q 0.73 0.23 0.00
74_V 148_L 0.73 0.23 0.00
332_I 26_I 0.73 0.23 0.00
129_V 24_F 0.73 0.23 0.00
200_P 57_E 0.73 0.23 0.00
146_V 30_V 0.73 0.23 0.00
328_N 179_S 0.73 0.23 0.00
224_L 137_H 0.73 0.23 0.00
126_I 23_Q 0.73 0.23 0.00
332_I 252_I 0.72 0.23 0.00
195_Q 260_M 0.72 0.23 0.00
154_E 87_I 0.72 0.23 0.00
244_G 23_Q 0.72 0.23 0.00
244_G 27_D 0.72 0.22 0.00
215_Q 13_K 0.71 0.21 0.00
237_N 18_N 0.71 0.21 0.00
293_Y 87_I 0.70 0.21 0.00
52_A 118_I 0.70 0.21 0.00
183_I 159_R 0.70 0.21 0.00
292_D 208_R 0.70 0.21 0.00
186_R 127_F 0.70 0.21 0.00
102_E 42_V 0.70 0.21 0.00
264_V 129_Y 0.70 0.21 0.00
156_I 105_G 0.70 0.21 0.00
226_A 62_L 0.70 0.21 0.00
110_P 166_Y 0.70 0.21 0.00
81_W 255_A 0.70 0.20 0.00
102_E 107_P 0.70 0.20 0.00
156_I 213_I 0.69 0.20 0.00
45_I 33_I 0.69 0.20 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
5797 1.8 RsgA-KsgA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.02 Done - Shared
5792 0.11 RsgA-KsgA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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