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OPENSEQ.org
YidC-Sol YfgM
Genes: A B A+B
Length: 321 259 540
Sequences: 1608 4195 425
Seq/Len: 5.01 16.2 0.79
MirrorTree (Pazo et al. 2001) 0.20
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 0.02 0.00
2 0.07 0.02 0.00
5 0.07 0.03 0.00
10 0.07 0.04 0.01
20 0.07 0.09 0.01
100 0.07 0.12 0.10
∞ 0.07 0.22 0.73
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
239_A 29_A 1.42 0.64 0.00
143_L 46_A 1.15 0.41 0.00
214_I 137_I 1.05 0.33 0.00
278_A 70_S 1.01 0.30 0.00
276_T 120_L 0.99 0.28 0.00
271_V 239_I 0.98 0.28 0.00
279_M 124_D 0.98 0.28 0.00
95_G 128_V 0.94 0.25 0.00
165_E 70_S 0.94 0.25 0.00
109_V 188_M 0.92 0.24 0.00
258_G 101_S 0.90 0.22 0.00
38_S 136_S 0.87 0.21 0.00
86_A 231_G 0.86 0.20 0.00
110_E 136_S 0.85 0.20 0.00
271_V 103_I 0.84 0.19 0.00
51_R 129_F 0.84 0.19 0.00
278_A 150_T 0.83 0.19 0.00
281_S 81_I 0.83 0.18 0.00
60_L 71_R 0.82 0.18 0.00
286_G 105_G 0.82 0.18 0.00
110_E 152_I 0.82 0.18 0.00
52_G 105_G 0.81 0.17 0.00
110_E 70_S 0.81 0.17 0.00
249_N 227_E 0.81 0.17 0.00
33_Q 136_S 0.80 0.17 0.00
65_K 151_E 0.80 0.17 0.00
275_Q 190_I 0.79 0.17 0.00
169_F 89_L 0.79 0.16 0.00
139_K 243_L 0.79 0.16 0.00
264_Y 149_L 0.78 0.16 0.00
318_K 83_A 0.78 0.16 0.00
33_Q 57_V 0.78 0.16 0.00
284_W 245_A 0.77 0.16 0.00
238_T 64_L 0.77 0.16 0.00
252_T 93_Y 0.77 0.16 0.00
245_D 145_C 0.77 0.15 0.00
140_T 146_D 0.77 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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