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OPENSEQ.org
TsaD-vs-RsfS
Genes: A B A+B
Length: 337 105 435
Sequences: 3839 2682 1330
Seq/Len: 11.39 25.54 3.06
MirrorTree (Pazo et al. 2001) 0.23
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 0.07 0.01 0.00
2 0.07 0.01 0.01
5 0.08 0.01 0.02
10 0.08 0.01 0.03
20 0.08 0.01 0.11
100 0.08 0.01 0.47
∞ 0.11 0.01 3.01
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
58_L 47_H 0.89 0.52 0.00
81_G 46_R 0.84 0.46 0.00
273_R 38_I 0.80 0.41 0.00
246_T 47_H 0.79 0.40 0.00
259_G 21_D 0.79 0.39 0.00
235_I 28_Q 0.79 0.39 0.00
112_M 59_S 0.78 0.38 0.00
236_A 101_E 0.77 0.37 0.00
58_L 14_I 0.76 0.36 0.00
103_D 61_A 0.76 0.36 0.00
265_M 61_A 0.74 0.34 0.00
76_V 62_A 0.74 0.34 0.00
58_L 82_L 0.74 0.34 0.00
176_D 21_D 0.73 0.32 0.00
291_F 66_P 0.72 0.32 0.00
62_A 51_I 0.71 0.31 0.00
299_T 79_V 0.71 0.31 0.00
246_T 89_V 0.70 0.30 0.00
97_S 22_I 0.69 0.28 0.00
28_Q 36_C 0.69 0.28 0.00
48_S 93_E 0.68 0.27 0.00
88_L 22_I 0.68 0.27 0.00
8_T 27_V 0.67 0.27 0.00
236_A 83_G 0.67 0.27 0.00
184_S 90_M 0.67 0.26 0.00
183_L 87_V 0.67 0.26 0.00
247_L 75_A 0.66 0.26 0.00
275_L 13_K 0.65 0.25 0.00
151_Y 92_E 0.65 0.24 0.00
147_G 32_S 0.65 0.24 0.00
169_T 5_A 0.64 0.24 0.00
140_T 51_I 0.64 0.24 0.00
174_G 89_V 0.63 0.23 0.00
31_S 85_V 0.63 0.23 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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