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OPENSEQ.org
ftszftsq Ecoli
Genes: A B A+B
Length: 383 121 420
Sequences: 2098 181 96
Seq/Len: 5.48 1.5 0.23
MirrorTree (Pazo et al. 2001) 0.58
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 0.02 0.01 0.00
2 0.02 0.01 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.03
20 0.02 0.01 0.19
100 0.03 0.01 0.19
∞ 0.05 0.01 0.19
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
166_D 116_N 1.65 0.44 0.00
176_I 60_T 1.61 0.41 0.00
144_A 54_V 1.54 0.38 0.00
57_T 37_K 1.43 0.31 0.00
64_I 60_T 1.42 0.31 0.00
42_V 60_T 1.41 0.30 0.00
98_V 32_L 1.39 0.29 0.00
60_I 60_T 1.36 0.28 0.00
119_V 97_V 1.35 0.27 0.00
136_N 60_T 1.34 0.27 0.00
297_S 88_E 1.32 0.26 0.00
241_E 81_W 1.28 0.24 0.00
198_E 92_G 1.25 0.23 0.00
16_I 47_I 1.20 0.20 0.00
281_T 93_D 1.20 0.20 0.00
283_R 109_H 1.19 0.20 0.00
198_E 63_L 1.19 0.20 0.00
119_V 26_G 1.17 0.19 0.00
228_G 31_D 1.15 0.18 0.00
116_V 70_L 1.11 0.17 0.00
183_G 95_S 1.09 0.16 0.00
58_I 69_Q 1.09 0.16 0.00
233_E 78_D 1.08 0.16 0.00
76_V 74_R 1.07 0.16 0.00
310_V 75_D 1.06 0.15 0.00
10_D 53_V 1.05 0.15 0.00
76_V 33_L 1.05 0.15 0.00
115_V 89_N 1.05 0.15 0.00
227_S 85_I 1.04 0.15 0.00
214_R 51_V 1.04 0.15 0.00
233_E 54_V 1.04 0.15 0.00
166_D 60_T 1.03 0.14 0.00
297_S 110_V 1.02 0.14 0.00
280_N 81_W 1.02 0.14 0.00
40_F 110_V 1.00 0.13 0.00
279_G 107_M 1.00 0.13 0.00
241_E 53_V 0.99 0.13 0.00
64_I 46_I 0.99 0.13 0.00
245_S 102_T 0.99 0.13 0.00
252_I 85_I 0.98 0.13 0.00
258_R 46_I 0.97 0.13 0.00
76_V 97_V 0.97 0.12 0.00
285_F 91_L 0.96 0.12 0.00
310_V 81_W 0.96 0.12 0.00
252_I 118_V 0.96 0.12 0.00
145_F 73_E 0.95 0.12 0.00
245_S 116_N 0.95 0.12 0.00
140_K 28_I 0.94 0.12 0.00
306_L 88_E 0.94 0.12 0.00
123_L 76_A 0.94 0.12 0.00
315_I 91_L 0.93 0.12 0.00
27_E 23_A 0.93 0.11 0.00
227_S 68_E 0.93 0.11 0.00
101_A 56_T 0.92 0.11 0.00
272_L 109_H 0.92 0.11 0.00
298_L 83_N 0.92 0.11 0.00
176_I 57_A 0.91 0.11 0.00
206_M 75_D 0.91 0.11 0.00
121_K 108_Q 0.91 0.11 0.00
175_G 114_Q 0.91 0.11 0.00
199_L 81_W 0.91 0.11 0.00
228_G 83_N 0.90 0.11 0.00
89_R 112_P 0.90 0.11 0.00
82_D 37_K 0.90 0.11 0.00
166_D 54_V 0.90 0.11 0.00
219_E 86_L 0.89 0.11 0.00
155_K 31_D 0.89 0.10 0.00
282_I 92_G 0.89 0.10 0.00
136_N 57_A 0.88 0.10 0.00
229_V 19_H 0.88 0.10 0.00
237_E 31_D 0.88 0.10 0.00
177_S 33_L 0.88 0.10 0.00
198_E 81_W 0.88 0.10 0.00
237_E 77_L 0.87 0.10 0.00
234_D 78_D 0.87 0.10 0.00
42_V 57_A 0.87 0.10 0.00
140_K 97_V 0.86 0.10 0.00
179_L 91_L 0.86 0.10 0.00
218_S 88_E 0.86 0.10 0.00
255_S 109_H 0.85 0.10 0.00
192_A 87_E 0.85 0.10 0.00
60_I 59_H 0.85 0.10 0.00
60_I 55_T 0.85 0.10 0.00
80_A 45_C 0.84 0.10 0.00
98_V 90_A 0.84 0.10 0.00
175_G 112_P 0.84 0.09 0.00
260_V 88_E 0.83 0.09 0.00
293_V 83_N 0.83 0.09 0.00
58_I 62_L 0.83 0.09 0.00
40_F 109_H 0.83 0.09 0.00
202_R 75_D 0.82 0.09 0.00
50_R 31_D 0.82 0.09 0.00
190_K 33_L 0.82 0.09 0.00
296_T 73_E 0.82 0.09 0.00
86_D 115_E 0.82 0.09 0.00
244_I 68_E 0.82 0.09 0.00
48_A 118_V 0.82 0.09 0.00
35_E 81_W 0.81 0.09 0.00
306_L 79_I 0.81 0.09 0.00
273_D 74_R 0.81 0.09 0.00
191_G 53_V 0.81 0.09 0.00
148_Q 34_R 0.81 0.09 0.00
273_D 37_K 0.81 0.09 0.00
279_G 80_E 0.80 0.09 0.00
286_A 70_L 0.80 0.09 0.00
242_M 21_R 0.80 0.09 0.00
118_E 64_T 0.80 0.09 0.00
119_V 40_L 0.80 0.09 0.00
166_D 104_K 0.80 0.09 0.00
297_S 75_D 0.80 0.09 0.00
315_I 46_I 0.80 0.09 0.00
164_P 107_M 0.80 0.09 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)
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