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OPENSEQ.org
YhcB_RodA
Genes: A B A+B
Length: 132 370 444
Sequences: 262 4924 170
Seq/Len: 1.98 13.31 0.38
MirrorTree (Pazo et al. 2001) 0.36
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 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.02 0.00
20 0.00 0.02 0.02
100 0.00 0.05 0.17
∞ 0.00 0.18 0.34
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
19_V 288_I 1.78 0.68 0.01
63_L 82_C 1.34 0.37 0.00
95_F 320_V 1.27 0.32 0.00
38_L 302_F 1.26 0.32 0.00
87_E 357_M 1.20 0.28 0.00
59_S 338_L 1.19 0.28 0.00
66_M 344_S 1.19 0.27 0.00
76_H 112_P 1.18 0.27 0.00
51_E 319_F 1.18 0.27 0.00
84_L 184_I 1.16 0.26 0.00
62_L 274_L 1.15 0.25 0.00
67_A 170_G 1.14 0.25 0.00
72_Q 99_A 1.13 0.24 0.00
7_L 305_V 1.12 0.24 0.00
20_A 355_I 1.11 0.23 0.00
9_G 347_I 1.08 0.22 0.00
118_S 240_L 1.08 0.22 0.00
13_G 236_G 1.07 0.21 0.00
74_Y 112_P 1.07 0.21 0.00
54_S 272_L 1.06 0.21 0.00
51_E 272_L 1.05 0.20 0.00
63_L 349_L 1.05 0.20 0.00
11_V 25_L 1.04 0.20 0.00
37_E 33_L 1.04 0.20 0.00
66_M 36_W 1.04 0.20 0.00
19_V 62_V 1.03 0.20 0.00
75_Q 310_L 1.03 0.20 0.00
63_L 302_F 1.02 0.19 0.00
30_Q 280_L 1.01 0.19 0.00
118_S 305_V 1.01 0.19 0.00
12_V 280_L 1.01 0.18 0.00
92_A 290_R 0.99 0.18 0.00
13_G 302_F 0.99 0.18 0.00
11_V 87_V 0.98 0.17 0.00
117_Y 255_F 0.98 0.17 0.00
1_M 113_S 0.98 0.17 0.00
11_V 91_A 0.98 0.17 0.00
105_S 275_V 0.97 0.17 0.00
10_L 302_F 0.96 0.17 0.00
84_L 93_G 0.95 0.16 0.00
95_F 277_I 0.94 0.16 0.00
81_S 269_A 0.94 0.16 0.00
48_Y 230_Q 0.94 0.16 0.00
19_V 289_M 0.94 0.16 0.00
7_L 279_I 0.94 0.16 0.00
11_V 302_F 0.93 0.15 0.00
10_L 350_M 0.93 0.15 0.00
8_I 294_I 0.93 0.15 0.00
7_L 53_I 0.93 0.15 0.00
3_W 38_A 0.93 0.15 0.00
60_A 112_P 0.92 0.15 0.00
42_K 355_I 0.92 0.15 0.00
59_S 357_M 0.92 0.15 0.00
81_S 113_S 0.92 0.15 0.00
81_S 160_L 0.92 0.15 0.00
58_R 266_A 0.90 0.14 0.00
128_G 87_V 0.89 0.14 0.00
71_R 356_V 0.89 0.14 0.00
88_L 269_A 0.89 0.14 0.00
1_M 277_I 0.89 0.14 0.00
47_E 32_A 0.88 0.14 0.00
16_I 84_I 0.88 0.14 0.00
47_E 121_P 0.88 0.14 0.00
70_Y 112_P 0.88 0.13 0.00
11_V 61_V 0.87 0.13 0.00
78_A 119_A 0.87 0.13 0.00
91_E 177_S 0.87 0.13 0.00
94_P 320_V 0.87 0.13 0.00
1_M 230_Q 0.87 0.13 0.00
12_V 36_W 0.87 0.13 0.00
125_L 264_I 0.86 0.13 0.00
34_L 205_D 0.86 0.13 0.00
75_Q 237_S 0.85 0.13 0.00
53_V 266_A 0.85 0.13 0.00
51_E 303_G 0.85 0.13 0.00
118_S 52_Q 0.85 0.13 0.00
68_H 28_L 0.85 0.12 0.00
15_I 26_A 0.85 0.12 0.00
18_A 171_L 0.85 0.12 0.00
2_T 148_F 0.84 0.12 0.00
98_R 288_I 0.84 0.12 0.00
81_S 22_L 0.84 0.12 0.00
118_S 302_F 0.84 0.12 0.00
111_V 315_F 0.84 0.12 0.00
49_R 209_Q 0.84 0.12 0.00
121_A 326_S 0.84 0.12 0.00
3_W 322_I 0.84 0.12 0.00
113_M 125_A 0.84 0.12 0.00
58_R 274_L 0.83 0.12 0.00
95_F 41_Q 0.83 0.12 0.00
48_Y 215_L 0.83 0.12 0.00
15_I 87_V 0.83 0.12 0.00
64_D 338_L 0.83 0.12 0.00
12_V 202_L 0.83 0.12 0.00
15_I 141_G 0.82 0.12 0.00
16_I 144_L 0.82 0.12 0.00
78_A 120_V 0.82 0.12 0.00
8_I 215_L 0.82 0.12 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
8974 0.02 YhcB-RodA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
2589 0.38 YhcB_RodA Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done
2581 0.02 YhcB_RodA Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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