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OPENSEQ.org
Sig-Pcra
Genes: A B A+B
Length: 371 739 965
Sequences: 580 2621 469
Seq/Len: 1.56 3.55 0.49
MirrorTree (Pazo et al. 2001) 0.40
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 0.01 0.00
2 0.02 0.01 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.01
20 0.02 0.01 0.02
100 0.02 0.02 0.05
∞ 0.04 0.08 0.42
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 1.23 0.35 0.00
184_Y 236_V 1.22 0.35 0.00
367_K 512_I 1.16 0.30 0.00
113_N 422_V 1.12 0.28 0.00
260_A 35_S 1.11 0.27 0.00
63_L 490_K 1.06 0.24 0.00
50_D 371_L 1.04 0.23 0.00
319_R 259_W 1.01 0.22 0.00
172_M 29_L 0.99 0.21 0.00
361_S 356_I 0.98 0.20 0.00
182_K 608_G 0.97 0.20 0.00
184_Y 490_K 0.97 0.20 0.00
238_T 275_P 0.97 0.20 0.00
119_E 170_D 0.95 0.19 0.00
236_E 62_I 0.95 0.19 0.00
292_D 55_A 0.95 0.19 0.00
337_K 35_S 0.94 0.18 0.00
301_E 559_A 0.93 0.18 0.00
242_I 263_D 0.92 0.18 0.00
244_E 205_R 0.92 0.17 0.00
184_Y 265_T 0.91 0.17 0.00
257_L 562_L 0.91 0.17 0.00
334_E 191_D 0.90 0.17 0.00
184_Y 197_M 0.90 0.16 0.00
229_L 599_E 0.89 0.16 0.00
47_D 22_T 0.89 0.16 0.00
184_Y 172_V 0.89 0.16 0.00
367_K 131_E 0.88 0.16 0.00
243_A 587_P 0.87 0.15 0.00
103_R 97_V 0.87 0.15 0.00
121_I 537_D 0.87 0.15 0.00
251_E 583_E 0.87 0.15 0.00
125_Q 209_V 0.86 0.15 0.00
102_V 582_E 0.86 0.15 0.00
295_A 115_I 0.86 0.15 0.00
165_Q 259_W 0.86 0.15 0.00
125_Q 482_E 0.86 0.15 0.00
367_K 55_A 0.85 0.15 0.00
181_R 608_G 0.85 0.15 0.00
305_D 116_L 0.85 0.15 0.00
184_Y 624_R 0.85 0.14 0.00
56_L 411_F 0.85 0.14 0.00
282_I 190_L 0.84 0.14 0.00
251_E 581_L 0.84 0.14 0.00
122_A 18_E 0.84 0.14 0.00
273_E 306_R 0.84 0.14 0.00
172_M 534_F 0.84 0.14 0.00
127_I 619_T 0.83 0.14 0.00
122_A 46_A 0.83 0.14 0.00
184_Y 388_D 0.82 0.14 0.00
117_A 17_Q 0.82 0.13 0.00
126_K 521_N 0.82 0.13 0.00
334_E 93_H 0.81 0.13 0.00
126_K 297_N 0.81 0.13 0.00
229_L 295_A 0.81 0.13 0.00
238_T 375_G 0.81 0.13 0.00
371_E 430_I 0.81 0.13 0.00
53_Y 302_N 0.81 0.13 0.00
141_A 354_I 0.80 0.13 0.00
149_I 252_S 0.80 0.13 0.00
54_E 321_I 0.80 0.13 0.00
116_S 208_E 0.80 0.13 0.00
126_K 515_F 0.80 0.13 0.00
334_E 190_L 0.80 0.13 0.00
119_E 136_P 0.79 0.12 0.00
61_V 487_I 0.79 0.12 0.00
324_L 371_L 0.79 0.12 0.00
286_E 414_I 0.79 0.12 0.00
56_L 115_I 0.79 0.12 0.00
45_E 397_A 0.79 0.12 0.00
270_I 391_E 0.78 0.12 0.00
277_H 40_V 0.78 0.12 0.00
57_G 124_V 0.78 0.12 0.00
251_E 278_S 0.78 0.12 0.00
152_R 639_I 0.78 0.12 0.00
181_R 639_I 0.78 0.12 0.00
371_E 177_Y 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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