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OPENSEQ.org
cI_C_G
Genes: A B A+B
Length: 509 100 592
Sequences: 1997 1241 1471
Seq/Len: 3.92 12.41 2.48
MirrorTree (Pazo et al. 2001) 0.71
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 0.05
2 0.00 0.00 1.99
5 0.01 0.00 2.13
10 0.01 0.00 2.20
20 0.01 0.00 2.27
100 0.01 0.01 2.32
∞ 0.03 0.02 2.42
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
315_I 16_V 0.98 0.57 0.00
143_W 68_L 0.93 0.50 0.00
233_V 84_H 0.92 0.50 0.00
437_L 70_A 0.91 0.49 0.00
380_K 11_A 0.91 0.49 0.00
346_I 2_I 0.90 0.47 0.00
428_G 41_A 0.86 0.43 0.00
238_V 81_L 0.84 0.40 0.00
123_I 10_L 0.81 0.37 0.00
86_L 10_L 0.81 0.37 0.00
177_Y 84_H 0.81 0.36 0.00
171_A 26_R 0.81 0.36 0.00
393_V 39_I 0.80 0.36 0.00
424_I 14_L 0.80 0.35 0.00
315_I 54_G 0.79 0.34 0.00
363_Y 74_S 0.77 0.32 0.00
368_T 61_M 0.76 0.32 0.00
210_L 34_G 0.76 0.32 0.00
32_A 38_M 0.76 0.31 0.00
389_L 30_F 0.75 0.30 0.00
352_A 40_N 0.75 0.30 0.00
77_I 10_L 0.75 0.30 0.00
255_G 80_L 0.75 0.30 0.00
263_L 62_Y 0.74 0.30 0.00
279_F 63_I 0.74 0.30 0.00
334_S 52_Y 0.74 0.29 0.00
355_L 88_Q 0.73 0.29 0.00
366_I 66_I 0.73 0.28 0.00
341_A 55_Q 0.73 0.28 0.00
191_A 63_I 0.73 0.28 0.00
387_L 83_L 0.73 0.28 0.00
94_T 11_A 0.72 0.28 0.00
151_Y 33_I 0.72 0.28 0.00
187_I 41_A 0.72 0.28 0.00
301_G 40_N 0.72 0.28 0.00
125_G 98_M 0.72 0.27 0.00
122_W 41_A 0.71 0.27 0.00
268_A 80_L 0.71 0.27 0.00
420_V 80_L 0.71 0.27 0.00
415_F 16_V 0.71 0.26 0.00
413_G 18_G 0.70 0.26 0.00
361_Q 7_G 0.70 0.26 0.00
385_P 22_L 0.70 0.26 0.00
277_P 25_R 0.70 0.26 0.00
266_T 46_F 0.70 0.25 0.00
278_L 98_M 0.69 0.25 0.00
469_L 12_A 0.69 0.25 0.00
145_M 40_N 0.69 0.25 0.00
408_F 42_S 0.69 0.25 0.00
320_V 87_R 0.69 0.24 0.00
101_A 79_L 0.69 0.24 0.00
395_T 40_N 0.69 0.24 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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