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OPENSEQ.org
cI_L_H
Genes: A B A+B
Length: 613 325 921
Sequences: 2612 4760 2054
Seq/Len: 4.26 14.65 2.23
MirrorTree (Pazo et al. 2001) 0.85
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 0.04
2 0.00 0.00 0.07
5 0.00 0.00 1.29
10 0.01 0.01 2.00
20 0.01 0.01 2.04
100 0.01 0.02 2.07
∞ 0.03 0.05 2.19
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
531_L 240_G 1.15 0.71 0.02
424_M 201_I 1.13 0.69 0.02
511_L 85_L 1.00 0.56 0.01
166_A 86_A 0.95 0.49 0.01
392_V 34_F 0.92 0.47 0.01
139_M 125_L 0.92 0.47 0.01
565_L 19_V 0.88 0.42 0.01
496_T 85_L 0.86 0.40 0.01
352_V 118_F 0.86 0.39 0.01
465_T 315_V 0.84 0.38 0.01
424_M 15_V 0.84 0.37 0.01
499_V 269_I 0.82 0.36 0.01
90_S 249_S 0.82 0.36 0.01
183_F 133_A 0.82 0.35 0.01
394_A 277_F 0.82 0.35 0.01
145_G 128_Y 0.82 0.35 0.01
157_Y 166_G 0.81 0.34 0.01
306_R 223_D 0.80 0.33 0.01
87_T 27_T 0.80 0.33 0.01
68_M 89_I 0.80 0.33 0.01
293_L 223_D 0.79 0.32 0.01
417_A 201_I 0.79 0.32 0.01
149_C 199_F 0.78 0.31 0.01
455_L 147_M 0.77 0.31 0.01
316_I 243_I 0.77 0.30 0.01
133_A 309_T 0.77 0.30 0.01
233_L 82_I 0.77 0.30 0.01
499_V 101_V 0.77 0.30 0.01
110_E 297_V 0.76 0.30 0.01
194_T 273_L 0.76 0.29 0.01
427_L 39_L 0.76 0.29 0.01
129_V 78_S 0.75 0.28 0.01
306_R 196_F 0.75 0.28 0.01
142_G 128_Y 0.75 0.28 0.01
168_M 240_G 0.75 0.28 0.01
464_S 309_T 0.74 0.28 0.01
10_L 115_G 0.74 0.28 0.01
531_L 136_S 0.74 0.28 0.01
264_Y 300_F 0.74 0.27 0.01
420_V 92_T 0.73 0.27 0.01
133_A 22_L 0.73 0.27 0.01
32_I 269_I 0.73 0.27 0.01
483_T 116_I 0.73 0.27 0.01
142_G 294_Y 0.73 0.27 0.01
368_L 81_V 0.73 0.26 0.01
260_T 128_Y 0.73 0.26 0.01
145_G 236_L 0.73 0.26 0.01
120_T 214_Q 0.72 0.26 0.01
226_A 117_L 0.72 0.25 0.01
181_L 221_L 0.72 0.25 0.01
86_L 273_L 0.71 0.25 0.01
458_I 20_V 0.71 0.25 0.01
66_T 21_I 0.71 0.24 0.00
77_F 90_A 0.70 0.24 0.00
234_P 163_S 0.70 0.24 0.00
9_I 308_L 0.70 0.24 0.00
73_F 161_G 0.70 0.24 0.00
394_A 111_D 0.70 0.24 0.00
172_V 167_V 0.70 0.24 0.00
244_A 38_R 0.69 0.23 0.00
320_F 199_F 0.69 0.23 0.00
485_L 272_A 0.69 0.23 0.00
105_W 280_M 0.69 0.23 0.00
286_V 249_S 0.69 0.23 0.00
266_I 181_N 0.69 0.23 0.00
445_A 27_T 0.68 0.23 0.00
499_V 133_A 0.68 0.23 0.00
373_P 127_V 0.68 0.22 0.00
260_T 294_Y 0.68 0.22 0.00
432_M 310_L 0.68 0.22 0.00
608_L 164_L 0.68 0.22 0.00
382_G 147_M 0.68 0.22 0.00
202_E 269_I 0.67 0.22 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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