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OPENSEQ.org
cI_C_E
Genes: A B A+B
Length: 509 147 611
Sequences: 1997 3696 1503
Seq/Len: 3.92 25.14 2.46
MirrorTree (Pazo et al. 2001) 0.74
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 0.01
2 0.00 0.00 0.08
5 0.01 0.00 0.22
10 0.01 0.00 0.68
20 0.01 0.00 1.90
100 0.01 0.01 2.13
∞ 0.03 0.01 2.29
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
392_A 68_F 1.16 0.75 0.03
318_T 120_I 1.09 0.69 0.03
313_R 114_L 0.91 0.48 0.01
486_L 68_F 0.89 0.46 0.01
272_L 69_Y 0.89 0.46 0.01
150_M 86_F 0.88 0.45 0.01
183_L 77_I 0.88 0.44 0.01
42_L 66_A 0.86 0.43 0.01
360_G 69_Y 0.86 0.42 0.01
320_V 26_L 0.86 0.42 0.01
99_V 82_A 0.85 0.41 0.01
141_F 112_A 0.85 0.41 0.01
188_A 22_V 0.84 0.40 0.01
374_M 76_V 0.83 0.39 0.01
352_A 80_V 0.83 0.38 0.01
118_L 115_V 0.82 0.38 0.01
381_M 61_R 0.80 0.36 0.01
279_F 68_F 0.80 0.36 0.01
332_T 18_I 0.80 0.35 0.01
353_A 95_S 0.80 0.35 0.01
362_L 82_A 0.79 0.35 0.01
116_F 33_G 0.79 0.35 0.01
438_A 69_Y 0.78 0.34 0.01
257_V 68_F 0.78 0.33 0.01
355_L 68_F 0.77 0.32 0.01
188_A 19_F 0.76 0.31 0.01
485_I 21_I 0.76 0.31 0.01
294_G 114_L 0.75 0.31 0.01
433_S 39_G 0.75 0.30 0.01
268_A 19_F 0.75 0.30 0.01
70_P 20_L 0.75 0.30 0.01
237_V 52_S 0.74 0.29 0.01
150_M 69_Y 0.74 0.29 0.01
245_P 121_G 0.73 0.29 0.01
278_L 21_I 0.73 0.29 0.01
29_R 60_A 0.73 0.28 0.01
345_M 125_W 0.73 0.28 0.01
411_L 68_F 0.73 0.28 0.01
168_I 29_L 0.72 0.28 0.01
359_C 124_D 0.72 0.28 0.01
261_G 27_C 0.72 0.27 0.01
387_L 23_A 0.72 0.27 0.01
262_I 60_A 0.71 0.27 0.01
347_A 88_W 0.71 0.27 0.01
91_V 124_D 0.71 0.27 0.01
366_I 80_V 0.71 0.27 0.01
347_A 103_A 0.71 0.26 0.01
291_M 36_F 0.71 0.26 0.01
252_P 77_I 0.71 0.26 0.01
188_A 42_R 0.70 0.26 0.01
429_L 112_A 0.70 0.25 0.01
442_R 93_R 0.70 0.25 0.01
143_W 67_K 0.70 0.25 0.01
478_L 32_V 0.70 0.25 0.01
225_L 36_F 0.69 0.25 0.01
428_G 118_V 0.69 0.25 0.01
389_L 66_A 0.69 0.25 0.01
267_A 88_W 0.69 0.25 0.01
413_G 91_S 0.69 0.24 0.01
140_F 76_V 0.69 0.24 0.01
69_M 40_R 0.69 0.24 0.01
386_A 90_T 0.69 0.24 0.01
210_L 31_L 0.69 0.24 0.01
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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