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OPENSEQ.org
70
Genes: A B A+B
Length: 340 310 607
Sequences: 28386 1667 315
Seq/Len: 83.49 5.38 0.52
MirrorTree (Pazo et al. 2001) 0.30
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 0.06 0.08 0.08
2 0.08 0.09 0.12
5 0.10 0.10 0.21
10 0.13 0.10 0.30
20 0.16 0.10 0.48
100 0.28 0.13 1.08
∞ 0.31 0.16 1.45
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
299_A 40_V 1.14 0.30 0.00
82_W 273_Q 1.01 0.23 0.00
103_C 264_E 0.99 0.21 0.00
146_L 295_D 0.96 0.20 0.00
113_A 89_E 0.95 0.19 0.00
214_R 189_I 0.94 0.19 0.00
79_L 16_I 0.93 0.19 0.00
284_L 44_T 0.93 0.18 0.00
203_A 61_D 0.93 0.18 0.00
187_V 183_E 0.93 0.18 0.00
193_A 240_L 0.92 0.18 0.00
216_G 286_I 0.91 0.18 0.00
129_R 44_T 0.91 0.18 0.00
166_C 300_Q 0.90 0.17 0.00
155_N 245_I 0.90 0.17 0.00
312_D 257_Y 0.89 0.17 0.00
329_T 59_K 0.89 0.17 0.00
327_V 257_Y 0.88 0.16 0.00
79_L 269_Y 0.88 0.16 0.00
201_S 27_G 0.86 0.15 0.00
81_I 107_F 0.86 0.15 0.00
61_M 131_Q 0.86 0.15 0.00
229_I 122_Y 0.85 0.15 0.00
260_E 122_Y 0.84 0.15 0.00
244_G 40_V 0.83 0.14 0.00
250_C 266_A 0.83 0.14 0.00
331_S 257_Y 0.83 0.14 0.00
69_L 141_V 0.82 0.14 0.00
64_G 51_I 0.81 0.14 0.00
244_G 194_L 0.80 0.13 0.00
190_L 37_K 0.79 0.13 0.00
139_L 21_K 0.79 0.13 0.00
152_L 199_L 0.79 0.13 0.00
149_C 124_N 0.78 0.13 0.00
315_V 126_L 0.78 0.12 0.00
160_S 189_I 0.77 0.12 0.00
278_F 194_L 0.77 0.12 0.00
264_Y 180_H 0.76 0.12 0.00
157_I 29_S 0.76 0.12 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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