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OPENSEQ.org
cI_Ld500_560_cIII_isp_Pdenitr
Genes: A B A+B
Length: 642 190 813
Sequences: 1921 1539 412
Seq/Len: 2.99 8.1 0.51
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.01 0.01 0.03
∞ 0.03 0.04 0.50
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
408_A 15_R 1.19 0.34 0.00
378_R 175_H 1.16 0.32 0.00
282_Y 189_L 1.09 0.27 0.00
13_S 32_G 1.04 0.24 0.00
432_V 19_L 1.04 0.24 0.00
196_S 75_P 1.01 0.22 0.00
358_A 10_D 1.01 0.22 0.00
197_V 150_W 1.01 0.22 0.00
371_M 39_V 1.00 0.22 0.00
104_H 133_T 0.99 0.21 0.00
417_I 188_K 0.99 0.21 0.00
334_V 63_T 0.96 0.20 0.00
629_I 30_A 0.96 0.20 0.00
340_A 41_Q 0.95 0.20 0.00
424_S 187_I 0.94 0.19 0.00
448_L 39_V 0.93 0.18 0.00
385_F 163_G 0.93 0.18 0.00
603_I 50_A 0.92 0.18 0.00
631_G 83_E 0.92 0.18 0.00
154_L 64_G 0.92 0.18 0.00
34_G 180_E 0.92 0.18 0.00
421_Y 159_Y 0.92 0.18 0.00
315_R 19_L 0.92 0.18 0.00
41_L 90_R 0.91 0.18 0.00
440_F 29_V 0.91 0.17 0.00
390_I 128_M 0.90 0.17 0.00
408_A 68_T 0.90 0.17 0.00
140_Q 37_T 0.89 0.17 0.00
138_L 64_G 0.89 0.17 0.00
462_D 35_A 0.89 0.17 0.00
425_G 151_F 0.89 0.16 0.00
519_V 159_Y 0.88 0.16 0.00
237_G 168_G 0.87 0.16 0.00
448_L 26_A 0.87 0.16 0.00
174_I 25_G 0.87 0.16 0.00
162_K 163_G 0.86 0.15 0.00
41_L 101_S 0.86 0.15 0.00
448_L 189_L 0.86 0.15 0.00
346_T 64_G 0.86 0.15 0.00
408_A 78_I 0.86 0.15 0.00
80_T 98_I 0.86 0.15 0.00
162_K 15_R 0.85 0.15 0.00
67_D 183_D 0.85 0.15 0.00
58_P 131_V 0.85 0.15 0.00
334_V 85_E 0.84 0.15 0.00
301_F 75_P 0.84 0.15 0.00
315_R 93_D 0.84 0.14 0.00
26_K 28_T 0.84 0.14 0.00
135_A 151_F 0.84 0.14 0.00
86_V 42_M 0.84 0.14 0.00
81_A 188_K 0.83 0.14 0.00
610_A 50_A 0.82 0.14 0.00
41_L 94_L 0.82 0.14 0.00
340_A 34_A 0.82 0.14 0.00
208_Q 35_A 0.82 0.14 0.00
429_W 131_V 0.82 0.14 0.00
229_F 128_M 0.82 0.14 0.00
21_R 183_D 0.82 0.14 0.00
533_W 52_A 0.82 0.14 0.00
67_D 101_S 0.81 0.14 0.00
230_L 18_F 0.81 0.14 0.00
289_K 189_L 0.81 0.14 0.00
385_F 30_A 0.81 0.13 0.00
373_N 29_V 0.81 0.13 0.00
599_A 148_G 0.81 0.13 0.00
72_W 15_R 0.81 0.13 0.00
208_Q 39_V 0.81 0.13 0.00
367_H 45_S 0.81 0.13 0.00
284_F 23_T 0.80 0.13 0.00
332_A 48_V 0.80 0.13 0.00
295_I 35_A 0.80 0.13 0.00
13_S 159_Y 0.79 0.13 0.00
196_S 32_G 0.79 0.13 0.00
581_V 29_V 0.79 0.13 0.00
292_I 41_Q 0.79 0.13 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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