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OPENSEQ.org
RsgA-S13
Genes: A B A+B
Length: 350 118 414
Sequences: 2498 2218 934
Seq/Len: 7.14 18.8 2.26
MirrorTree (Pazo et al. 2001) 0.40
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 0.00
10 0.03 0.09 0.01
20 0.03 0.09 0.02
100 0.04 0.09 0.22
∞ 0.09 0.09 2.00
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
196_D 30_S 1.13 0.70 0.01
105_S 31_K 1.10 0.67 0.01
247_Q 7_I 1.06 0.62 0.01
238_D 25_V 1.05 0.62 0.01
186_R 49_S 1.02 0.58 0.01
199_K 32_A 0.94 0.49 0.01
322_A 52_Q 0.92 0.46 0.01
138_L 42_D 0.91 0.46 0.01
332_I 7_I 0.90 0.44 0.01
252_A 43_V 0.89 0.44 0.01
224_L 106_A 0.88 0.42 0.01
69_T 52_Q 0.86 0.40 0.01
226_A 53_I 0.86 0.40 0.01
140_I 71_R 0.85 0.39 0.01
176_Q 39_I 0.85 0.39 0.01
324_T 15_A 0.85 0.39 0.01
323_E 35_A 0.85 0.39 0.01
215_Q 16_V 0.85 0.39 0.01
135_E 15_A 0.85 0.39 0.01
330_H 63_F 0.85 0.39 0.01
247_Q 53_I 0.85 0.39 0.01
330_H 22_I 0.85 0.38 0.01
295_G 37_A 0.83 0.37 0.01
273_F 18_A 0.82 0.36 0.01
136_L 7_I 0.82 0.36 0.01
154_E 85_C 0.82 0.36 0.01
150_T 32_A 0.82 0.36 0.01
221_S 103_K 0.82 0.35 0.01
213_A 17_I 0.81 0.35 0.01
218_V 13_K 0.81 0.35 0.01
194_T 30_S 0.81 0.35 0.01
156_I 25_V 0.81 0.34 0.01
324_T 104_T 0.81 0.34 0.01
296_L 56_L 0.80 0.34 0.01
194_T 102_T 0.80 0.33 0.01
130_S 18_A 0.79 0.32 0.01
195_Q 30_S 0.78 0.32 0.01
131_A 16_V 0.78 0.31 0.01
62_H 7_I 0.78 0.31 0.01
122_N 68_D 0.77 0.31 0.01
100_V 73_I 0.77 0.31 0.01
258_F 101_R 0.77 0.31 0.01
330_H 37_A 0.76 0.30 0.01
236_T 23_Y 0.76 0.30 0.01
67_R 50_E 0.76 0.30 0.01
137_S 33_I 0.76 0.29 0.01
273_F 49_S 0.75 0.29 0.01
42_G 35_A 0.75 0.29 0.01
121_A 68_D 0.75 0.28 0.01
210_S 113_R 0.75 0.28 0.01
127_V 23_Y 0.74 0.28 0.01
257_H 30_S 0.73 0.27 0.00
62_H 23_Y 0.72 0.26 0.00
314_E 12_H 0.72 0.26 0.00
309_G 85_C 0.72 0.26 0.00
128_I 50_E 0.72 0.26 0.00
73_L 101_R 0.71 0.25 0.00
122_N 71_R 0.71 0.25 0.00
201_L 103_K 0.71 0.25 0.00
167_D 35_A 0.71 0.25 0.00
50_M 74_S 0.71 0.25 0.00
333_L 39_I 0.71 0.25 0.00
233_E 30_S 0.71 0.25 0.00
206_T 39_I 0.71 0.25 0.00
122_N 106_A 0.70 0.25 0.00
242_N 53_I 0.70 0.24 0.00
330_H 28_T 0.70 0.24 0.00
235_L 49_S 0.70 0.24 0.00
223_L 101_R 0.70 0.24 0.00
54_V 47_E 0.70 0.24 0.00
97_V 53_I 0.70 0.24 0.00
222_S 113_R 0.70 0.24 0.00
327_E 49_S 0.70 0.24 0.00
60_D 30_S 0.69 0.24 0.00
118_P 75_M 0.69 0.24 0.00
95_G 20_T 0.69 0.23 0.00
151_L 45_I 0.69 0.23 0.00
275_L 53_I 0.69 0.23 0.00
282_Q 22_I 0.68 0.23 0.00
241_D 49_S 0.68 0.23 0.00
273_F 101_R 0.68 0.23 0.00
258_F 94_G 0.68 0.22 0.00
143_R 92_R 0.68 0.22 0.00
221_S 6_G 0.68 0.22 0.00
155_P 61_A 0.68 0.22 0.00
289_E 82_D 0.67 0.22 0.00
104_T 35_A 0.67 0.22 0.00
68_R 94_G 0.67 0.22 0.00
237_N 28_T 0.67 0.22 0.00
159_L 55_T 0.67 0.22 0.00
124_D 72_E 0.67 0.22 0.00
84_G 49_S 0.67 0.22 0.00
173_V 58_D 0.67 0.22 0.00
218_V 89_L 0.67 0.22 0.00
177_M 34_L 0.67 0.22 0.00
190_V 27_K 0.67 0.22 0.00
100_V 55_T 0.67 0.22 0.00
235_L 7_I 0.67 0.21 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
5796 2.26 RsgA-S13 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
5793 0.25 RsgA-S13 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5791 0.02 RsgA-S13 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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