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OPENSEQ.org
RPOB_SALTY_150_445-UVRA_SALTY_401_500
Genes: A B A+B
Length: 296 99 393
Sequences: 1967 18979 266
Seq/Len: 6.65 191.71 0.68
MirrorTree (Pazo et al. 2001) 0.55
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.98 0.01
2 0.00 0.98 0.01
5 0.00 0.98 0.01
10 0.00 0.98 0.03
20 0.00 0.98 0.05
100 0.00 0.98 0.67
∞ 0.00 0.98 2.29
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
132_D 24_N 1.33 0.52 0.00
270_I 78_T 1.33 0.52 0.00
23_Y 44_N 1.30 0.49 0.00
194_H 22_V 1.29 0.48 0.00
164_A 41_F 1.29 0.48 0.00
160_L 84_E 1.20 0.41 0.00
152_Y 6_A 1.20 0.41 0.00
146_K 71_N 1.19 0.41 0.00
131_D 34_S 1.19 0.40 0.00
274_D 16_E 1.18 0.40 0.00
209_D 35_I 1.15 0.37 0.00
78_K 22_V 1.15 0.37 0.00
157_T 7_S 1.15 0.37 0.00
285_D 22_V 1.14 0.36 0.00
230_E 26_P 1.11 0.34 0.00
175_K 35_I 1.11 0.34 0.00
76_F 30_I 1.11 0.34 0.00
280_M 78_T 1.08 0.32 0.00
292_E 16_E 1.08 0.32 0.00
161_I 31_S 1.06 0.30 0.00
284_I 35_I 1.05 0.30 0.00
210_R 80_S 1.05 0.30 0.00
283_L 45_L 1.05 0.30 0.00
55_L 27_L 1.05 0.29 0.00
80_V 78_T 1.04 0.29 0.00
168_L 21_F 1.04 0.29 0.00
184_I 4_P 1.02 0.28 0.00
47_V 71_N 1.01 0.27 0.00
274_D 33_M 1.01 0.27 0.00
231_A 34_S 1.01 0.27 0.00
242_S 64_D 1.00 0.27 0.00
111_K 3_R 1.00 0.26 0.00
210_R 50_Q 1.00 0.26 0.00
172_L 71_N 0.99 0.26 0.00
214_L 59_L 0.99 0.26 0.00
152_Y 25_T 0.99 0.26 0.00
153_V 6_A 0.98 0.25 0.00
260_L 23_E 0.97 0.25 0.00
85_D 7_S 0.97 0.24 0.00
282_K 34_S 0.97 0.24 0.00
91_E 30_I 0.97 0.24 0.00
121_T 6_A 0.96 0.24 0.00
148_V 35_I 0.96 0.24 0.00
237_E 80_S 0.96 0.24 0.00
208_N 41_F 0.95 0.23 0.00
173_L 29_A 0.95 0.23 0.00
237_E 35_I 0.95 0.23 0.00
277_I 66_L 0.94 0.23 0.00
109_N 16_E 0.94 0.23 0.00
71_I 78_T 0.94 0.22 0.00
110_G 14_N 0.94 0.22 0.00
188_F 15_R 0.92 0.21 0.00
163_A 34_S 0.91 0.21 0.00
65_N 25_T 0.91 0.21 0.00
146_K 25_T 0.91 0.21 0.00
198_I 11_T 0.91 0.21 0.00
163_A 14_N 0.90 0.21 0.00
261_L 45_L 0.90 0.20 0.00
123_R 48_S 0.90 0.20 0.00
55_L 28_P 0.90 0.20 0.00
67_T 80_S 0.90 0.20 0.00
174_A 43_T 0.90 0.20 0.00
138_V 46_K 0.90 0.20 0.00
242_S 27_L 0.90 0.20 0.00
24_N 52_A 0.89 0.20 0.00
117_G 35_I 0.89 0.20 0.00
191_D 75_N 0.89 0.20 0.00
209_D 78_T 0.88 0.19 0.00
144_A 31_S 0.88 0.19 0.00
122_A 51_R 0.88 0.19 0.00
165_N 18_R 0.87 0.19 0.00
97_L 86_L 0.87 0.19 0.00
110_G 16_E 0.87 0.19 0.00
293_V 40_D 0.86 0.18 0.00
182_K 26_P 0.86 0.18 0.00
273_K 35_I 0.86 0.18 0.00
137_E 78_T 0.86 0.18 0.00
215_V 28_P 0.85 0.18 0.00
214_L 22_V 0.85 0.18 0.00
209_D 23_E 0.85 0.18 0.00
271_L 66_L 0.85 0.18 0.00
270_I 66_L 0.85 0.18 0.00
156_S 15_R 0.85 0.18 0.00
44_N 27_L 0.84 0.17 0.00
174_A 39_M 0.84 0.17 0.00
244_D 60_K 0.84 0.17 0.00
58_T 32_D 0.84 0.17 0.00
292_E 14_N 0.84 0.17 0.00
270_I 46_K 0.84 0.17 0.00
207_T 91_A 0.83 0.17 0.00
160_L 27_L 0.83 0.17 0.00
69_E 56_E 0.83 0.17 0.00
265_I 29_A 0.83 0.17 0.00
288_N 26_P 0.83 0.17 0.00
177_S 9_E 0.82 0.17 0.00
150_K 75_N 0.82 0.16 0.00
277_I 60_K 0.82 0.16 0.00
245_R 60_K 0.82 0.16 0.00
68_T 35_I 0.82 0.16 0.00
290_K 35_I 0.82 0.16 0.00
208_N 53_K 0.81 0.16 0.00
57_A 36_G 0.81 0.16 0.00
219_R 29_A 0.81 0.16 0.00
78_K 24_N 0.81 0.16 0.00
155_E 56_E 0.80 0.15 0.00
285_D 14_N 0.80 0.15 0.00
200_E 62_I 0.80 0.15 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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.98 > 0.4) of paralogs.
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