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OPENSEQ.org
Sig-Pcra
Genes: A B A+B
Length: 371 739 966
Sequences: 623 3420 507
Seq/Len: 1.68 4.63 0.52
MirrorTree (Pazo et al. 2001) 0.42
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 0.06 0.00
2 0.02 0.06 0.00
5 0.02 0.06 0.01
10 0.02 0.06 0.01
20 0.02 0.07 0.02
100 0.03 0.08 0.05
∞ 0.04 0.14 0.46
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
137_R 125_I 1.19 0.34 0.00
319_R 259_W 1.12 0.29 0.00
63_L 490_K 1.08 0.27 0.00
260_A 35_S 1.00 0.22 0.00
184_Y 236_V 0.98 0.21 0.00
305_D 116_L 0.96 0.20 0.00
182_K 608_G 0.95 0.20 0.00
334_E 190_L 0.95 0.20 0.00
238_T 275_P 0.93 0.18 0.00
181_R 608_G 0.92 0.18 0.00
119_E 292_I 0.91 0.18 0.00
57_G 124_V 0.90 0.17 0.00
324_L 199_T 0.89 0.17 0.00
126_K 515_F 0.89 0.17 0.00
292_D 55_A 0.88 0.17 0.00
113_N 274_Y 0.87 0.16 0.00
242_I 41_L 0.87 0.16 0.00
292_D 284_Q 0.86 0.16 0.00
47_D 22_T 0.86 0.15 0.00
361_S 356_I 0.86 0.15 0.00
184_Y 197_M 0.86 0.15 0.00
184_Y 172_V 0.86 0.15 0.00
257_L 562_L 0.86 0.15 0.00
102_V 582_E 0.85 0.15 0.00
273_E 306_R 0.84 0.15 0.00
240_E 399_L 0.84 0.15 0.00
251_E 583_E 0.84 0.15 0.00
113_N 422_V 0.83 0.14 0.00
371_E 190_L 0.83 0.14 0.00
119_E 170_D 0.83 0.14 0.00
337_K 35_S 0.83 0.14 0.00
252_K 124_V 0.82 0.14 0.00
169_M 62_I 0.82 0.14 0.00
184_Y 158_P 0.82 0.14 0.00
286_E 414_I 0.82 0.14 0.00
121_I 241_E 0.82 0.14 0.00
322_F 573_F 0.81 0.14 0.00
121_I 537_D 0.81 0.14 0.00
50_D 371_L 0.81 0.14 0.00
301_E 559_A 0.81 0.14 0.00
53_Y 302_N 0.80 0.13 0.00
246_M 123_S 0.80 0.13 0.00
367_K 512_I 0.80 0.13 0.00
165_Q 259_W 0.80 0.13 0.00
251_E 588_H 0.79 0.13 0.00
334_E 93_H 0.79 0.13 0.00
127_I 40_V 0.79 0.13 0.00
250_P 344_H 0.78 0.13 0.00
243_A 587_P 0.78 0.12 0.00
149_I 252_S 0.78 0.12 0.00
371_E 461_L 0.78 0.12 0.00
251_E 278_S 0.78 0.12 0.00
371_E 430_I 0.78 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)
ID Seq/Len Name Options I_Prob Status
9472 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9471 0.49 Sig-Pcra Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9470 0.52 Sig-Pcra Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9469 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9466 0.59 Sig-Pcra Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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