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OPENSEQ.org
ftszftse Ecoli
Genes: A B A+B
Length: 383 222 534
Sequences: 2098 88685 541
Seq/Len: 5.48 399.48 1.01
MirrorTree (Pazo et al. 2001) 0.06
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 0.09 0.01
2 0.02 0.10 0.04
5 0.02 0.14 0.15
10 0.02 0.19 0.35
20 0.02 0.25 0.89
100 0.03 0.36 3.39
∞ 0.05 0.37 4.52
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
116_V 191_L 1.17 0.49 0.00
42_V 2_I 1.16 0.49 0.00
100_I 28_G 1.10 0.43 0.00
122_D 51_I 1.06 0.39 0.00
262_V 42_S 1.02 0.36 0.00
21_G 48_I 0.98 0.32 0.00
115_V 144_Q 0.95 0.30 0.00
116_V 51_I 0.94 0.30 0.00
116_V 136_I 0.93 0.28 0.00
301_D 48_I 0.90 0.26 0.00
41_A 25_M 0.90 0.26 0.00
289_N 28_G 0.89 0.26 0.00
119_V 59_I 0.89 0.26 0.00
92_L 8_S 0.87 0.24 0.00
116_V 16_Q 0.85 0.23 0.00
116_V 17_A 0.85 0.23 0.00
60_I 64_H 0.85 0.23 0.00
41_A 101_A 0.84 0.22 0.00
80_A 159_L 0.83 0.22 0.00
206_M 95_T 0.82 0.21 0.00
153_L 207_M 0.82 0.21 0.00
38_E 91_L 0.81 0.21 0.00
16_I 120_A 0.81 0.20 0.00
48_A 168_L 0.81 0.20 0.00
241_E 81_I 0.80 0.20 0.00
155_K 6_H 0.78 0.19 0.00
264_I 138_L 0.78 0.19 0.00
118_E 45_L 0.78 0.18 0.00
94_G 39_A 0.77 0.18 0.00
230_A 53_R 0.77 0.18 0.00
216_V 207_M 0.77 0.18 0.00
16_I 146_V 0.76 0.18 0.00
88_L 34_T 0.76 0.18 0.00
306_L 159_L 0.76 0.17 0.00
215_T 22_T 0.75 0.17 0.00
100_I 76_F 0.74 0.17 0.00
84_D 215_L 0.73 0.16 0.00
244_I 210_L 0.73 0.16 0.00
130_V 69_L 0.73 0.16 0.00
78_R 215_L 0.73 0.16 0.00
112_A 42_S 0.73 0.16 0.00
286_A 209_T 0.73 0.16 0.00
274_E 180_F 0.72 0.16 0.00
76_V 146_V 0.72 0.16 0.00
234_D 210_L 0.72 0.15 0.00
144_A 158_V 0.72 0.15 0.00
38_E 138_L 0.71 0.15 0.00
42_V 128_L 0.71 0.15 0.00
151_T 44_L 0.71 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)
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