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OPENSEQ.org
L1-vs-TsaB
Genes: A B A+B
Length: 234 231 453
Sequences: 3196 3108 1337
Seq/Len: 13.66 13.45 2.95
MirrorTree (Pazo et al. 2001) 0.71
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 0.09 0.00 0.00
2 0.09 0.00 0.00
5 0.09 0.00 0.00
10 0.09 0.00 0.01
20 0.09 0.00 0.05
100 0.09 0.00 0.50
∞ 0.10 0.00 2.88
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
73_V 80_G 1.26 0.86 0.18
129_Q 119_M 0.99 0.63 0.08
163_Y 38_I 0.93 0.56 0.07
98_E 59_L 0.92 0.55 0.06
94_L 92_V 0.91 0.54 0.06
115_I 18_W 0.91 0.54 0.06
221_G 123_Y 0.90 0.52 0.06
197_K 123_Y 0.90 0.52 0.06
59_V 80_G 0.86 0.47 0.05
51_D 118_R 0.85 0.47 0.05
54_K 118_R 0.85 0.46 0.05
122_R 79_Q 0.85 0.46 0.05
63_T 194_M 0.83 0.43 0.04
119_D 68_F 0.81 0.41 0.04
128_G 81_L 0.81 0.41 0.04
99_D 59_L 0.80 0.40 0.04
129_Q 34_H 0.79 0.39 0.04
40_E 68_F 0.79 0.39 0.04
49_G 88_P 0.79 0.39 0.04
177_K 226_K 0.78 0.38 0.04
64_V 125_A 0.78 0.38 0.04
214_I 51_T 0.78 0.37 0.04
200_K 123_Y 0.77 0.36 0.04
54_K 62_G 0.76 0.36 0.04
40_E 80_G 0.76 0.35 0.03
53_R 13_C 0.76 0.35 0.03
154_K 148_I 0.76 0.35 0.03
151_E 190_A 0.76 0.35 0.03
170_I 14_S 0.74 0.33 0.03
77_V 16_A 0.74 0.33 0.03
158_A 73_I 0.74 0.33 0.03
170_I 165_T 0.73 0.32 0.03
175_I 10_T 0.73 0.32 0.03
58_N 83_L 0.72 0.31 0.03
192_L 35_T 0.71 0.30 0.03
27_I 120_G 0.71 0.30 0.03
139_N 36_Q 0.71 0.30 0.03
45_A 36_Q 0.71 0.29 0.03
170_I 216_V 0.70 0.29 0.03
46_V 80_G 0.70 0.29 0.03
142_V 118_R 0.70 0.29 0.03
195_A 73_I 0.70 0.29 0.03
104_I 42_V 0.70 0.29 0.03
109_M 94_T 0.70 0.29 0.03
192_L 97_T 0.70 0.29 0.03
54_K 116_D 0.70 0.29 0.03
50_I 222_V 0.70 0.29 0.03
22_D 151_E 0.69 0.28 0.03
212_V 50_G 0.69 0.28 0.03
44_V 60_A 0.69 0.28 0.03
183_D 129_R 0.69 0.28 0.03
212_V 43_Q 0.69 0.28 0.03
198_K 11_E 0.69 0.27 0.03
162_R 33_E 0.69 0.27 0.03
28_A 147_E 0.69 0.27 0.03
190_E 71_V 0.69 0.27 0.03
139_N 116_D 0.69 0.27 0.03
110_N 191_A 0.68 0.27 0.03
25_E 167_W 0.67 0.26 0.02
183_D 48_T 0.67 0.26 0.02
155_N 77_I 0.67 0.26 0.02
108_E 79_Q 0.67 0.26 0.02
53_R 15_V 0.67 0.26 0.02
44_V 121_E 0.67 0.25 0.02
47_N 119_M 0.67 0.25 0.02
122_R 221_N 0.66 0.25 0.02
58_N 36_Q 0.66 0.25 0.02
59_V 89_M 0.66 0.25 0.02
214_I 128_Q 0.66 0.25 0.02
204_A 101_G 0.66 0.25 0.02
217_T 70_G 0.66 0.24 0.02
160_Q 116_D 0.65 0.24 0.02
88_K 52_S 0.65 0.24 0.02
120_A 79_Q 0.65 0.24 0.02
108_E 113_A 0.65 0.24 0.02
199_A 118_R 0.65 0.24 0.02
183_D 99_A 0.65 0.24 0.02
161_V 12_A 0.65 0.23 0.02
167_K 135_W 0.64 0.23 0.02
89_A 59_L 0.64 0.23 0.02
45_A 13_C 0.64 0.23 0.02
15_V 174_G 0.64 0.23 0.02
162_R 221_N 0.64 0.23 0.02
196_L 189_P 0.63 0.22 0.02
224_V 17_L 0.63 0.22 0.02
56_D 32_R 0.63 0.22 0.02
7_R 114_A 0.63 0.22 0.02
14_K 191_A 0.63 0.22 0.02
169_G 189_P 0.63 0.22 0.02
17_A 174_G 0.63 0.22 0.02
110_N 98_M 0.62 0.22 0.02
136_L 112_L 0.62 0.22 0.02
214_I 144_L 0.62 0.22 0.02
106_K 59_L 0.62 0.22 0.02
45_A 189_P 0.62 0.21 0.02
100_L 82_A 0.62 0.21 0.02
75_V 99_A 0.62 0.21 0.02
126_Q 221_N 0.62 0.21 0.02
142_V 165_T 0.62 0.21 0.02
163_Y 227_L 0.62 0.21 0.02
52_A 201_M 0.61 0.21 0.02
218_M 88_P 0.61 0.21 0.02
225_D 127_Y 0.61 0.21 0.02
216_T 194_M 0.61 0.21 0.02
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)
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