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OPENSEQ.org
cIp_1_4_cIV_D_4
Genes: A B A+B
Length: 438 50 473
Sequences: 2611 202 73
Seq/Len: 5.96 4.04 0.15
MirrorTree (Pazo et al. 2001) 0.13
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.00
20 0.03 0.00 0.00
100 0.05 0.01 0.01
∞ 0.14 0.01 0.15
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
151_E 39_I 1.68 0.35 0.00
173_V 20_Q 1.37 0.21 0.00
146_E 47_L 1.32 0.19 0.00
52_E 15_M 1.30 0.19 0.00
241_M 20_Q 1.17 0.15 0.00
132_I 29_K 1.17 0.15 0.00
288_Q 20_Q 1.16 0.14 0.00
269_G 24_F 1.14 0.14 0.00
209_S 20_Q 1.14 0.14 0.00
169_F 40_A 1.08 0.12 0.00
26_S 39_I 1.07 0.12 0.00
184_E 27_F 1.04 0.12 0.00
338_V 35_S 1.04 0.11 0.00
276_I 48_A 1.04 0.11 0.00
33_L 35_S 1.02 0.11 0.00
280_A 42_L 1.01 0.11 0.00
119_I 31_A 1.01 0.11 0.00
227_V 35_S 1.00 0.11 0.00
288_Q 38_S 1.00 0.11 0.00
29_L 19_H 1.00 0.11 0.00
269_G 20_Q 0.99 0.10 0.00
327_G 38_S 0.98 0.10 0.00
147_Q 39_I 0.97 0.10 0.00
158_L 16_D 0.96 0.10 0.00
310_P 21_Q 0.95 0.10 0.00
380_E 17_I 0.93 0.09 0.00
231_M 5_H 0.93 0.09 0.00
150_K 47_L 0.93 0.09 0.00
264_Y 31_A 0.92 0.09 0.00
316_L 15_M 0.92 0.09 0.00
429_R 17_I 0.91 0.09 0.00
177_A 27_F 0.90 0.09 0.00
276_I 40_A 0.90 0.09 0.00
342_W 11_K 0.89 0.09 0.00
33_L 47_L 0.89 0.09 0.00
115_I 18_R 0.89 0.09 0.00
124_A 23_T 0.88 0.08 0.00
11_P 45_L 0.88 0.08 0.00
56_E 36_I 0.88 0.08 0.00
376_T 47_L 0.87 0.08 0.00
45_L 46_A 0.87 0.08 0.00
33_L 20_Q 0.87 0.08 0.00
90_I 28_I 0.87 0.08 0.00
239_A 41_V 0.86 0.08 0.00
290_I 34_V 0.85 0.08 0.00
308_D 16_D 0.85 0.08 0.00
337_M 26_G 0.85 0.08 0.00
394_I 31_A 0.84 0.08 0.00
120_L 40_A 0.84 0.08 0.00
145_L 4_H 0.84 0.07 0.00
122_G 42_L 0.84 0.07 0.00
122_G 30_G 0.82 0.07 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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