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OPENSEQ.org
RsgA-RbfA
Genes: A B A+B
Length: 350 133 416
Sequences: 2498 2471 263
Seq/Len: 7.14 18.58 0.63
MirrorTree (Pazo et al. 2001) 0.67
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
53_D 16_Q 1.50 0.63 0.00
157_I 81_S 1.48 0.62 0.00
121_A 80_R 1.44 0.59 0.00
128_I 112_L 1.41 0.57 0.00
293_Y 53_Y 1.31 0.48 0.00
128_I 51_K 1.29 0.47 0.00
306_T 95_L 1.25 0.44 0.00
64_C 38_V 1.25 0.43 0.00
191_S 32_L 1.24 0.42 0.00
299_Y 81_S 1.23 0.42 0.00
54_V 116_V 1.23 0.41 0.00
65_N 67_A 1.22 0.41 0.00
213_A 80_R 1.22 0.41 0.00
256_Y 92_V 1.18 0.38 0.00
100_V 11_V 1.17 0.37 0.00
44_V 101_N 1.16 0.36 0.00
98_E 48_A 1.14 0.35 0.00
256_Y 83_L 1.12 0.33 0.00
141_I 39_S 1.10 0.32 0.00
222_S 108_R 1.10 0.32 0.00
234_I 55_T 1.09 0.31 0.00
227_L 36_T 1.09 0.31 0.00
327_E 53_Y 1.08 0.30 0.00
157_I 37_T 1.08 0.30 0.00
258_F 83_L 1.07 0.30 0.00
68_R 109_M 1.06 0.29 0.00
264_V 101_N 1.06 0.29 0.00
99_A 55_T 1.05 0.29 0.00
252_A 43_M 1.05 0.28 0.00
194_T 67_A 1.04 0.28 0.00
160_N 37_T 1.03 0.27 0.00
226_A 95_L 1.01 0.26 0.00
198_L 95_L 1.01 0.26 0.00
131_A 91_I 1.01 0.25 0.00
84_G 112_L 1.00 0.25 0.00
263_D 87_M 1.00 0.25 0.00
273_F 16_Q 1.00 0.25 0.00
173_V 32_L 0.97 0.23 0.00
123_I 52_V 0.97 0.23 0.00
61_V 53_Y 0.97 0.23 0.00
178_D 121_E 0.97 0.23 0.00
314_E 113_V 0.97 0.23 0.00
41_E 113_V 0.96 0.23 0.00
128_I 104_V 0.96 0.23 0.00
226_A 56_F 0.96 0.23 0.00
314_E 66_K 0.96 0.23 0.00
82_R 113_V 0.96 0.23 0.00
193_H 32_L 0.95 0.22 0.00
300_R 79_I 0.95 0.22 0.00
216_S 54_V 0.95 0.22 0.00
69_T 4_E 0.95 0.22 0.00
216_S 7_R 0.94 0.22 0.00
199_K 116_V 0.94 0.22 0.00
187_V 56_F 0.94 0.22 0.00
126_I 79_I 0.94 0.22 0.00
252_A 89_L 0.93 0.21 0.00
289_E 11_V 0.93 0.21 0.00
290_F 12_A 0.93 0.21 0.00
216_S 38_V 0.92 0.21 0.00
216_S 35_M 0.92 0.21 0.00
147_A 40_G 0.92 0.20 0.00
258_F 59_D 0.92 0.20 0.00
318_E 32_L 0.92 0.20 0.00
188_L 104_V 0.91 0.20 0.00
158_V 99_Y 0.91 0.20 0.00
136_L 14_E 0.91 0.20 0.00
273_F 87_M 0.90 0.20 0.00
139_N 115_S 0.90 0.19 0.00
216_S 58_N 0.90 0.19 0.00
288_V 48_A 0.90 0.19 0.00
64_C 90_R 0.90 0.19 0.00
190_V 92_V 0.90 0.19 0.00
209_I 8_P 0.90 0.19 0.00
45_I 44_S 0.89 0.19 0.00
329_Y 83_L 0.89 0.19 0.00
131_A 76_S 0.89 0.19 0.00
199_K 43_M 0.89 0.19 0.00
127_V 12_A 0.89 0.19 0.00
99_A 59_D 0.89 0.19 0.00
258_F 20_A 0.88 0.19 0.00
73_L 14_E 0.88 0.18 0.00
198_L 53_Y 0.88 0.18 0.00
131_A 109_M 0.88 0.18 0.00
98_E 19_I 0.88 0.18 0.00
287_F 77_G 0.88 0.18 0.00
222_S 88_R 0.88 0.18 0.00
236_T 22_I 0.88 0.18 0.00
207_G 71_A 0.87 0.18 0.00
154_E 32_L 0.87 0.18 0.00
241_D 113_V 0.87 0.18 0.00
105_S 91_I 0.87 0.18 0.00
178_D 119_H 0.87 0.18 0.00
148_C 110_S 0.87 0.18 0.00
158_V 102_S 0.87 0.18 0.00
61_V 55_T 0.87 0.18 0.00
152_Q 32_L 0.86 0.18 0.00
143_R 84_G 0.86 0.18 0.00
273_F 91_I 0.86 0.18 0.00
339_V 40_G 0.86 0.17 0.00
54_V 60_K 0.86 0.17 0.00
197_G 55_T 0.86 0.17 0.00
82_R 3_K 0.86 0.17 0.00
100_V 8_P 0.86 0.17 0.00
120_A 19_I 0.86 0.17 0.00
273_F 110_S 0.86 0.17 0.00
223_L 84_G 0.85 0.17 0.00
274_G 104_V 0.85 0.17 0.00
82_R 85_K 0.85 0.17 0.00
99_A 110_S 0.85 0.17 0.00
178_D 68_G 0.85 0.17 0.00
188_L 32_L 0.85 0.17 0.00
155_P 15_M 0.85 0.17 0.00
327_E 61_D 0.84 0.17 0.00
242_N 52_V 0.84 0.17 0.00
44_V 10_R 0.84 0.17 0.00
160_N 20_A 0.84 0.16 0.00
55_E 115_S 0.84 0.16 0.00
261_G 51_K 0.83 0.16 0.00
148_C 35_M 0.83 0.16 0.00
290_F 95_L 0.83 0.16 0.00
315_A 45_R 0.83 0.16 0.00
281_E 81_S 0.83 0.16 0.00
69_T 40_G 0.83 0.16 0.00
102_E 71_A 0.83 0.16 0.00
298_K 110_S 0.83 0.16 0.00
299_Y 19_I 0.83 0.16 0.00
158_V 90_R 0.83 0.16 0.00
69_T 60_K 0.83 0.16 0.00
194_T 115_S 0.83 0.16 0.00
222_S 89_L 0.82 0.16 0.00
216_S 77_G 0.82 0.16 0.00
275_L 49_Y 0.82 0.16 0.00
83_P 70_K 0.82 0.16 0.00
254_R 87_M 0.82 0.16 0.00
333_L 84_G 0.82 0.16 0.00
117_K 109_M 0.82 0.16 0.00
290_F 60_K 0.82 0.16 0.00
322_A 27_I 0.82 0.15 0.00
60_D 53_Y 0.82 0.15 0.00
255_L 80_R 0.81 0.15 0.00
131_A 4_E 0.81 0.15 0.00
80_V 53_Y 0.81 0.15 0.00
138_L 24_Q 0.81 0.15 0.00
316_V 67_A 0.81 0.15 0.00
235_L 38_V 0.80 0.15 0.00
255_L 30_P 0.80 0.15 0.00
311_A 112_L 0.80 0.15 0.00
313_R 44_S 0.80 0.15 0.00
138_L 108_R 0.80 0.15 0.00
255_L 29_D 0.80 0.15 0.00
224_L 84_G 0.79 0.15 0.00
67_R 7_R 0.79 0.14 0.00
128_I 4_E 0.79 0.14 0.00
64_C 54_V 0.79 0.14 0.00
286_G 36_T 0.79 0.14 0.00
177_M 38_V 0.79 0.14 0.00
331_R 27_I 0.79 0.14 0.00
66_I 14_E 0.79 0.14 0.00
290_F 19_I 0.79 0.14 0.00
170_M 44_S 0.79 0.14 0.00
80_V 79_I 0.79 0.14 0.00
143_R 11_V 0.79 0.14 0.00
123_I 104_V 0.79 0.14 0.00
82_R 87_M 0.79 0.14 0.00
67_R 77_G 0.78 0.14 0.00
263_D 57_L 0.78 0.14 0.00
138_L 116_V 0.78 0.14 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
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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