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OPENSEQ.org
13 (A, 1-530)
Genes: A B A+B
Length: 530 340 818
Sequences: 5110 4321 1752
Seq/Len: 9.64 12.71 2.14
MirrorTree (Pazo et al. 2001) 0.41
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.06 0.06 0.97
2 0.07 0.06 1.12
5 0.07 0.06 1.15
10 0.07 0.06 1.16
20 0.07 0.06 1.18
100 0.08 0.07 1.37
∞ 0.14 0.12 2.01
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
195_P 22_R 1.11 0.66 0.01
171_M 313_D 0.98 0.53 0.01
120_M 254_V 0.85 0.37 0.00
246_E 320_V 0.83 0.35 0.00
321_L 29_L 0.82 0.35 0.00
384_S 276_L 0.80 0.33 0.00
352_E 237_F 0.79 0.32 0.00
267_S 212_W 0.79 0.31 0.00
136_P 71_G 0.78 0.31 0.00
365_T 256_Y 0.78 0.31 0.00
121_L 19_E 0.76 0.29 0.00
466_K 306_K 0.76 0.28 0.00
244_F 39_P 0.76 0.28 0.00
199_V 29_L 0.76 0.28 0.00
461_Q 335_E 0.75 0.28 0.00
224_A 263_R 0.75 0.28 0.00
416_D 303_P 0.74 0.27 0.00
224_A 8_T 0.73 0.26 0.00
314_L 168_L 0.73 0.26 0.00
486_V 28_A 0.72 0.25 0.00
467_V 180_T 0.72 0.25 0.00
212_V 270_T 0.72 0.25 0.00
224_A 311_R 0.71 0.24 0.00
304_G 270_T 0.71 0.24 0.00
152_E 303_P 0.71 0.24 0.00
325_L 57_D 0.70 0.24 0.00
418_E 208_V 0.70 0.24 0.00
336_Y 199_N 0.70 0.23 0.00
67_F 48_I 0.70 0.23 0.00
490_F 252_S 0.70 0.23 0.00
198_V 167_D 0.70 0.23 0.00
261_R 172_L 0.69 0.23 0.00
309_M 8_T 0.69 0.23 0.00
223_L 42_E 0.69 0.23 0.00
351_K 314_L 0.69 0.23 0.00
433_T 192_P 0.69 0.23 0.00
364_T 262_L 0.69 0.22 0.00
121_L 300_E 0.68 0.22 0.00
339_E 266_L 0.68 0.22 0.00
300_T 329_T 0.68 0.21 0.00
331_K 206_I 0.68 0.21 0.00
298_S 202_K 0.66 0.20 0.00
491_S 176_Y 0.66 0.20 0.00
304_G 85_A 0.65 0.20 0.00
123_S 293_M 0.65 0.20 0.00
64_V 52_Y 0.65 0.19 0.00
291_F 174_E 0.65 0.19 0.00
220_L 327_P 0.65 0.19 0.00
469_P 66_R 0.64 0.19 0.00
246_E 43_E 0.64 0.19 0.00
315_A 189_R 0.64 0.19 0.00
419_V 148_R 0.64 0.19 0.00
224_A 318_F 0.64 0.19 0.00
283_D 262_L 0.64 0.18 0.00
116_Q 56_S 0.63 0.18 0.00
136_P 298_P 0.63 0.18 0.00
25_T 17_D 0.62 0.18 0.00
429_S 168_L 0.62 0.18 0.00
286_L 208_V 0.62 0.18 0.00
70_F 29_L 0.62 0.18 0.00
418_E 262_L 0.62 0.17 0.00
240_L 171_S 0.62 0.17 0.00
25_T 56_S 0.62 0.17 0.00
333_E 77_P 0.62 0.17 0.00
356_K 228_S 0.62 0.17 0.00
214_A 24_Y 0.62 0.17 0.00
24_E 29_L 0.62 0.17 0.00
117_V 285_F 0.62 0.17 0.00
355_S 208_V 0.61 0.17 0.00
340_I 250_D 0.61 0.17 0.00
212_V 19_E 0.61 0.17 0.00
194_K 253_D 0.61 0.17 0.00
335_I 276_L 0.61 0.17 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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