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OPENSEQ.org
CheY-FliM2
Genes: A B A+B
Length: 129 334 442
Sequences: 1607 1468 332
Seq/Len: 12.46 4.4 0.75
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 0.01 0.26 0.12
2 0.02 0.26 0.14
5 0.05 0.27 0.17
10 0.09 0.27 0.26
20 0.10 0.27 0.52
100 0.12 0.31 0.72
∞ 0.19 0.32 1.17
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
114_A 165_Y 1.30 0.52 0.00
67_E 284_L 1.25 0.48 0.00
73_R 127_V 1.20 0.43 0.00
55_I 105_I 1.19 0.43 0.00
97_A 270_L 1.16 0.41 0.00
81_L 18_D 1.16 0.40 0.00
27_E 316_R 1.15 0.40 0.00
116_L 127_V 1.14 0.39 0.00
96_I 275_I 1.14 0.39 0.00
107_V 78_D 1.12 0.38 0.00
6_L 271_R 1.12 0.38 0.00
42_A 322_N 1.12 0.37 0.00
7_K 69_L 1.11 0.37 0.00
68_L 153_V 1.09 0.35 0.00
54_I 165_Y 1.08 0.34 0.00
15_S 172_I 1.07 0.34 0.00
107_V 279_K 1.07 0.33 0.00
116_L 191_I 1.07 0.33 0.00
7_K 40_P 1.06 0.33 0.00
22_R 312_Q 1.06 0.32 0.00
22_R 294_A 1.05 0.32 0.00
51_F 254_V 1.05 0.32 0.00
97_A 297_D 1.03 0.30 0.00
41_D 11_I 1.00 0.28 0.00
55_I 206_V 1.00 0.28 0.00
50_G 321_I 0.98 0.27 0.00
74_A 57_I 0.98 0.27 0.00
64_D 130_L 0.98 0.27 0.00
54_I 218_C 0.98 0.27 0.00
84_L 310_N 0.98 0.27 0.00
10_V 252_R 0.97 0.26 0.00
54_I 104_L 0.97 0.26 0.00
120_L 123_V 0.97 0.26 0.00
10_V 283_V 0.97 0.26 0.00
97_A 304_S 0.96 0.26 0.00
71_T 79_I 0.96 0.25 0.00
90_A 60_R 0.95 0.25 0.00
67_E 118_F 0.95 0.24 0.00
10_V 69_L 0.94 0.24 0.00
42_A 314_A 0.94 0.24 0.00
41_D 19_S 0.94 0.24 0.00
114_A 275_I 0.94 0.24 0.00
121_N 254_V 0.94 0.24 0.00
56_S 235_P 0.93 0.24 0.00
120_L 296_V 0.93 0.23 0.00
21_V 272_L 0.93 0.23 0.00
66_L 141_V 0.93 0.23 0.00
53_F 314_A 0.92 0.23 0.00
103_A 95_N 0.92 0.23 0.00
95_I 65_F 0.92 0.23 0.00
9_L 202_T 0.92 0.23 0.00
63_M 185_Q 0.91 0.22 0.00
77_A 121_S 0.91 0.22 0.00
51_F 165_Y 0.91 0.22 0.00
96_I 272_L 0.90 0.22 0.00
54_I 157_M 0.89 0.21 0.00
29_G 133_G 0.89 0.21 0.00
114_A 76_S 0.89 0.21 0.00
101_A 188_F 0.88 0.21 0.00
51_F 153_V 0.88 0.20 0.00
42_A 175_L 0.87 0.20 0.00
72_I 275_I 0.87 0.20 0.00
67_E 18_D 0.87 0.20 0.00
22_R 192_T 0.86 0.20 0.00
55_I 273_S 0.86 0.20 0.00
83_V 278_L 0.86 0.20 0.00
103_A 130_L 0.86 0.19 0.00
15_S 304_S 0.86 0.19 0.00
10_V 35_I 0.86 0.19 0.00
84_L 58_N 0.85 0.19 0.00
72_I 222_S 0.85 0.19 0.00
43_L 147_T 0.85 0.19 0.00
107_V 206_V 0.84 0.19 0.00
8_F 210_N 0.84 0.19 0.00
8_F 13_A 0.84 0.18 0.00
41_D 319_H 0.84 0.18 0.00
15_S 311_G 0.84 0.18 0.00
41_D 230_L 0.84 0.18 0.00
108_V 101_N 0.84 0.18 0.00
81_L 315_L 0.84 0.18 0.00
38_D 301_V 0.83 0.18 0.00
80_A 27_P 0.83 0.18 0.00
124_F 275_I 0.83 0.18 0.00
52_G 259_L 0.83 0.18 0.00
120_L 116_V 0.83 0.18 0.00
33_V 215_F 0.83 0.18 0.00
38_D 236_L 0.82 0.18 0.00
6_L 217_I 0.82 0.18 0.00
83_V 21_T 0.82 0.17 0.00
101_A 135_G 0.82 0.17 0.00
37_E 168_A 0.82 0.17 0.00
19_R 316_R 0.82 0.17 0.00
113_A 171_A 0.82 0.17 0.00
101_A 58_N 0.82 0.17 0.00
107_V 260_E 0.82 0.17 0.00
39_G 281_G 0.81 0.17 0.00
71_T 276_L 0.81 0.17 0.00
72_I 155_N 0.81 0.17 0.00
7_K 93_A 0.81 0.17 0.00
45_K 267_D 0.81 0.17 0.00
15_S 234_P 0.81 0.17 0.00
120_L 127_V 0.81 0.17 0.00
114_A 268_I 0.81 0.17 0.00
71_T 273_S 0.81 0.17 0.00
21_V 180_V 0.81 0.17 0.00
102_G 220_P 0.81 0.17 0.00
121_N 36_R 0.81 0.17 0.00
10_V 320_L 0.80 0.17 0.00
24_L 62_A 0.80 0.17 0.00
15_S 9_A 0.80 0.17 0.00
10_V 306_Y 0.80 0.17 0.00
56_S 56_I 0.80 0.16 0.00
15_S 49_E 0.80 0.16 0.00
44_N 267_D 0.80 0.16 0.00
64_D 235_P 0.80 0.16 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
9391 0.34 CheY-FliM3 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9389 0.75 CheY-FliM2 Δgene:(1, 100) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9375 1.54 CheYFliM Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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