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OPENSEQ.org
RsgA-RimP
Genes: A B A+B
Length: 350 150 447
Sequences: 2498 2642 979
Seq/Len: 7.14 17.61 2.19
MirrorTree (Pazo et al. 2001) 0.60
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 0.10 0.00
2 0.03 0.10 0.01
5 0.03 0.10 0.01
10 0.03 0.10 0.03
20 0.03 0.10 0.06
100 0.04 0.10 0.53
∞ 0.09 0.10 1.96
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
128_I 103_L 1.27 0.81 0.08
160_N 52_A 1.18 0.74 0.06
264_V 141_I 1.12 0.68 0.05
155_P 82_D 1.07 0.63 0.04
237_N 50_D 1.04 0.59 0.04
152_Q 136_F 1.00 0.55 0.03
140_I 36_L 0.97 0.52 0.03
312_I 76_V 0.95 0.49 0.03
222_S 99_V 0.93 0.47 0.03
191_S 94_F 0.92 0.45 0.03
81_W 21_F 0.91 0.45 0.03
165_L 141_I 0.91 0.45 0.03
333_L 26_I 0.88 0.41 0.02
44_V 122_G 0.88 0.41 0.02
100_V 113_W 0.88 0.41 0.02
256_Y 16_V 0.87 0.40 0.02
69_T 146_L 0.87 0.40 0.02
201_L 23_L 0.86 0.40 0.02
45_I 44_D 0.85 0.38 0.02
141_I 14_A 0.85 0.38 0.02
319_G 78_S 0.85 0.38 0.02
159_L 47_N 0.85 0.38 0.02
128_I 21_F 0.84 0.38 0.02
282_Q 127_V 0.84 0.38 0.02
295_G 20_G 0.84 0.37 0.02
277_H 38_I 0.83 0.36 0.02
263_D 127_V 0.83 0.36 0.02
152_Q 123_E 0.83 0.36 0.02
288_V 58_V 0.82 0.35 0.02
139_N 89_E 0.82 0.35 0.02
258_F 60_A 0.82 0.35 0.02
97_V 139_S 0.81 0.34 0.02
245_L 56_H 0.81 0.34 0.02
102_E 13_T 0.81 0.34 0.02
239_I 147_V 0.81 0.34 0.02
202_E 93_R 0.81 0.34 0.02
224_L 56_H 0.81 0.34 0.02
300_R 145_N 0.81 0.33 0.02
264_V 70_V 0.81 0.33 0.02
44_V 94_F 0.80 0.33 0.02
136_L 109_N 0.80 0.33 0.02
160_N 59_S 0.80 0.33 0.02
236_T 130_E 0.80 0.33 0.02
239_I 38_I 0.79 0.32 0.02
146_V 57_Q 0.79 0.32 0.02
63_R 21_F 0.79 0.32 0.02
222_S 69_T 0.79 0.32 0.02
328_N 63_D 0.79 0.32 0.02
137_S 46_I 0.79 0.31 0.02
222_S 111_R 0.78 0.31 0.01
201_L 89_E 0.78 0.31 0.01
206_T 101_L 0.78 0.30 0.01
241_D 12_I 0.78 0.30 0.01
157_I 90_H 0.77 0.30 0.01
176_Q 97_E 0.77 0.30 0.01
332_I 73_N 0.77 0.30 0.01
67_R 82_D 0.77 0.29 0.01
123_I 26_I 0.77 0.29 0.01
205_L 11_M 0.76 0.29 0.01
230_L 141_I 0.76 0.29 0.01
201_L 133_D 0.76 0.29 0.01
183_I 144_A 0.76 0.29 0.01
82_R 123_E 0.76 0.28 0.01
64_C 81_L 0.75 0.28 0.01
42_G 72_Y 0.75 0.28 0.01
145_L 144_A 0.75 0.28 0.01
199_K 26_I 0.75 0.28 0.01
176_Q 122_G 0.74 0.28 0.01
133_L 38_I 0.74 0.28 0.01
283_I 87_T 0.74 0.27 0.01
288_V 47_N 0.74 0.27 0.01
121_A 90_H 0.74 0.27 0.01
292_D 26_I 0.74 0.27 0.01
85_K 101_L 0.73 0.27 0.01
305_D 95_V 0.73 0.27 0.01
291_H 101_L 0.73 0.26 0.01
122_N 85_L 0.73 0.26 0.01
69_T 32_R 0.73 0.26 0.01
224_L 126_T 0.73 0.26 0.01
262_G 76_V 0.73 0.26 0.01
244_G 105_M 0.72 0.26 0.01
283_I 50_D 0.72 0.26 0.01
314_E 118_K 0.72 0.26 0.01
264_V 129_V 0.72 0.26 0.01
173_V 132_K 0.72 0.25 0.01
61_V 127_V 0.72 0.25 0.01
199_K 62_L 0.72 0.25 0.01
149_E 62_L 0.72 0.25 0.01
178_D 133_D 0.72 0.25 0.01
218_V 24_V 0.71 0.25 0.01
142_D 84_P 0.71 0.25 0.01
144_Y 25_G 0.71 0.25 0.01
236_T 23_L 0.71 0.25 0.01
265_I 71_A 0.71 0.25 0.01
49_G 84_P 0.71 0.25 0.01
184_G 117_I 0.71 0.24 0.01
160_N 141_I 0.71 0.24 0.01
121_A 50_D 0.71 0.24 0.01
245_L 50_D 0.71 0.24 0.01
213_A 15_P 0.70 0.24 0.01
84_G 125_I 0.70 0.23 0.01
230_L 20_G 0.70 0.23 0.01
273_F 137_A 0.70 0.23 0.01
333_L 131_G 0.70 0.23 0.01
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
5834 2.19 RsgA-RimP Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.08 Done - Shared
5833 0.07 RsgA-RimP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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