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OPENSEQ.org
cI_B_F
Genes: A B A+B
Length: 613 184 787
Sequences: 2092 2037 1271
Seq/Len: 3.41 11.07 1.61
MirrorTree (Pazo et al. 2001) 0.79
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 0.06
2 0.00 0.00 1.35
5 0.00 0.00 1.43
10 0.00 0.00 1.51
20 0.00 0.00 1.55
100 0.00 0.01 1.58
∞ 0.01 0.02 1.59
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
306_R 21_T 1.12 0.58 0.00
591_L 8_C 0.98 0.45 0.00
385_A 71_V 0.96 0.42 0.00
160_D 159_G 0.90 0.36 0.00
416_V 23_T 0.90 0.36 0.00
391_L 56_I 0.90 0.35 0.00
264_Y 52_G 0.87 0.33 0.00
306_R 71_V 0.87 0.33 0.00
95_V 94_I 0.86 0.32 0.00
272_L 41_G 0.86 0.32 0.00
10_L 71_V 0.85 0.31 0.00
14_G 71_V 0.85 0.31 0.00
430_F 145_S 0.84 0.31 0.00
92_V 152_L 0.84 0.30 0.00
426_S 33_I 0.84 0.30 0.00
231_A 76_L 0.84 0.30 0.00
126_S 158_V 0.84 0.30 0.00
260_T 25_P 0.82 0.29 0.00
297_A 28_A 0.82 0.29 0.00
203_L 143_L 0.81 0.28 0.00
237_T 29_L 0.81 0.27 0.00
353_I 36_L 0.80 0.27 0.00
228_G 5_F 0.80 0.26 0.00
234_P 142_E 0.79 0.26 0.00
279_V 52_G 0.79 0.26 0.00
9_I 22_H 0.79 0.26 0.00
234_P 64_M 0.79 0.26 0.00
431_R 141_V 0.79 0.26 0.00
385_A 17_L 0.78 0.25 0.00
328_W 157_H 0.78 0.25 0.00
204_A 133_L 0.78 0.25 0.00
222_L 152_L 0.77 0.25 0.00
122_L 147_L 0.77 0.25 0.00
306_R 126_A 0.77 0.24 0.00
331_A 129_V 0.77 0.24 0.00
448_V 28_A 0.76 0.24 0.00
394_A 151_G 0.76 0.23 0.00
167_A 145_S 0.76 0.23 0.00
295_G 41_G 0.74 0.22 0.00
171_F 48_A 0.74 0.22 0.00
289_V 93_W 0.74 0.22 0.00
7_T 26_V 0.74 0.22 0.00
88_M 149_L 0.74 0.22 0.00
242_A 154_V 0.74 0.22 0.00
273_F 138_V 0.73 0.22 0.00
237_T 57_I 0.73 0.21 0.00
264_Y 12_A 0.73 0.21 0.00
236_Q 156_F 0.73 0.21 0.00
157_Y 19_V 0.73 0.21 0.00
282_L 13_I 0.73 0.21 0.00
142_G 76_L 0.72 0.21 0.00
185_L 35_S 0.72 0.21 0.00
279_V 76_L 0.72 0.21 0.00
293_L 49_Y 0.72 0.21 0.00
592_R 84_E 0.72 0.21 0.00
148_L 41_G 0.72 0.21 0.00
26_S 144_A 0.71 0.20 0.00
121_N 64_M 0.71 0.20 0.00
382_G 70_V 0.71 0.20 0.00
382_G 134_F 0.71 0.20 0.00
119_Y 145_S 0.70 0.20 0.00
583_L 145_S 0.70 0.20 0.00
414_L 57_I 0.70 0.19 0.00
420_V 103_M 0.69 0.19 0.00
348_A 70_V 0.69 0.19 0.00
121_N 25_P 0.69 0.19 0.00
417_A 130_G 0.69 0.19 0.00
125_A 29_L 0.69 0.19 0.00
87_T 65_V 0.69 0.19 0.00
370_K 131_I 0.69 0.19 0.00
17_L 37_L 0.68 0.18 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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