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OPENSEQ.org
cI_C_cIII_isp
Genes: A B A+B
Length: 509 190 678
Sequences: 1997 1442 439
Seq/Len: 3.92 7.59 0.65
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.00 0.00
20 0.01 0.00 0.01
100 0.01 0.01 0.05
∞ 0.03 0.02 0.63
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
284_A 78_I 1.50 0.64 0.00
320_V 78_I 1.17 0.38 0.00
341_A 133_T 1.11 0.33 0.00
283_S 15_R 1.10 0.32 0.00
166_T 78_I 1.09 0.32 0.00
287_A 37_T 1.09 0.32 0.00
296_I 162_S 1.08 0.31 0.00
91_V 128_M 1.03 0.28 0.00
168_I 48_V 1.00 0.26 0.00
156_L 15_R 0.98 0.24 0.00
292_W 78_I 0.97 0.24 0.00
146_M 168_G 0.97 0.24 0.00
92_V 163_G 0.94 0.22 0.00
31_I 28_T 0.94 0.22 0.00
341_A 131_V 0.93 0.21 0.00
334_S 67_L 0.92 0.21 0.00
143_W 141_G 0.92 0.21 0.00
190_L 12_G 0.92 0.21 0.00
400_G 157_S 0.92 0.21 0.00
353_A 185_T 0.91 0.20 0.00
429_L 19_L 0.88 0.19 0.00
315_I 90_R 0.88 0.19 0.00
194_F 35_A 0.86 0.18 0.00
418_V 68_T 0.86 0.18 0.00
137_F 107_K 0.86 0.18 0.00
487_D 129_I 0.86 0.18 0.00
216_S 184_D 0.86 0.18 0.00
101_A 131_V 0.86 0.18 0.00
112_Y 34_A 0.85 0.18 0.00
183_L 33_A 0.85 0.17 0.00
276_L 15_R 0.84 0.17 0.00
415_F 32_G 0.84 0.17 0.00
368_T 188_K 0.84 0.17 0.00
59_G 69_V 0.83 0.17 0.00
44_L 34_A 0.83 0.17 0.00
143_W 151_F 0.83 0.16 0.00
421_I 168_G 0.83 0.16 0.00
154_I 37_T 0.82 0.16 0.00
428_G 107_K 0.82 0.16 0.00
402_G 28_T 0.82 0.16 0.00
377_L 22_A 0.82 0.16 0.00
480_F 150_W 0.82 0.16 0.00
183_L 30_A 0.81 0.16 0.00
429_L 38_L 0.81 0.16 0.00
238_V 42_M 0.81 0.15 0.00
372_R 22_A 0.80 0.15 0.00
166_T 34_A 0.80 0.15 0.00
77_I 35_A 0.80 0.15 0.00
486_L 78_I 0.80 0.15 0.00
170_A 165_I 0.80 0.15 0.00
38_L 9_G 0.80 0.15 0.00
354_G 171_P 0.80 0.15 0.00
353_A 31_A 0.79 0.15 0.00
413_G 32_G 0.79 0.15 0.00
179_Q 55_Q 0.79 0.15 0.00
201_G 88_A 0.79 0.15 0.00
124_L 28_T 0.79 0.15 0.00
344_Q 81_R 0.79 0.15 0.00
270_G 69_V 0.79 0.14 0.00
288_P 15_R 0.78 0.14 0.00
227_F 22_A 0.78 0.14 0.00
473_V 35_A 0.78 0.14 0.00
105_S 34_A 0.77 0.14 0.00
354_G 59_S 0.77 0.14 0.00
423_V 13_A 0.77 0.14 0.00
410_I 20_Y 0.77 0.14 0.00
152_F 179_A 0.77 0.14 0.00
52_Y 93_D 0.76 0.14 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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