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OPENSEQ.org
1i7q
Genes: A B A+B
Length: 519 193 653
Sequences: 2316 22398 1299
Seq/Len: 4.46 116.05 1.99
MirrorTree (Pazo et al. 2001) 0.45
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 0.04 1.49
2 0.00 0.05 1.59
5 0.01 0.07 1.72
10 0.01 0.08 1.78
20 0.01 0.10 1.82
100 0.02 0.16 1.97
∞ 0.05 0.21 2.33
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
257_Q 100_Q 3.79 1.00 1.00
378_A 22_R 2.23 1.00 0.99
487_Q 104_I 2.16 0.99 0.98
253_E 100_Q 1.87 0.98 0.95
373_A 19_D 1.47 0.90 0.82
158_E 32_R 1.35 0.84 0.73
256_R 100_Q 1.34 0.83 0.72
254_A 59_G 1.21 0.74 0.61
362_L 175_L 1.18 0.71 0.57
362_L 130_A 1.17 0.70 0.56
392_Y 177_T 1.04 0.56 0.41
449_G 130_A 1.02 0.54 0.39
436_L 126_P 1.01 0.53 0.38
159_N 38_E 0.97 0.49 0.34
378_A 28_V 0.95 0.47 0.31
182_V 25_G 0.95 0.46 0.30
425_L 130_A 0.94 0.46 0.30
244_Y 94_Y 0.90 0.41 0.26
259_E 63_E 0.86 0.37 0.22
244_Y 52_L 0.84 0.35 0.21
378_A 18_V 0.84 0.35 0.20
259_E 59_G 0.83 0.34 0.20
498_T 49_Q 0.82 0.33 0.19
323_Y 130_A 0.81 0.31 0.17
152_D 67_M 0.80 0.31 0.17
488_D 108_K 0.80 0.31 0.17
359_A 103_E 0.80 0.30 0.17
311_L 14_T 0.79 0.30 0.17
436_L 67_M 0.78 0.29 0.16
256_R 104_I 0.78 0.29 0.15
209_H 29_V 0.77 0.28 0.14
454_Y 81_I 0.76 0.27 0.14
312_K 151_G 0.76 0.27 0.14
377_Q 160_D 0.75 0.27 0.14
392_Y 18_V 0.75 0.26 0.13
378_A 6_L 0.74 0.26 0.13
266_S 173_S 0.73 0.25 0.12
483_A 110_S 0.73 0.25 0.12
398_L 76_G 0.73 0.25 0.12
177_A 175_L 0.72 0.24 0.12
214_L 96_G 0.72 0.24 0.12
391_R 116_G 0.72 0.24 0.12
416_Y 26_H 0.72 0.24 0.11
309_S 59_G 0.71 0.23 0.11
242_E 30_I 0.70 0.23 0.11
246_A 48_E 0.70 0.23 0.11
415_A 153_M 0.70 0.22 0.11
243_E 128_P 0.70 0.22 0.10
213_Q 46_H 0.70 0.22 0.10
240_S 46_H 0.70 0.22 0.10
389_V 184_E 0.69 0.22 0.10
387_T 71_L 0.69 0.22 0.10
301_T 130_A 0.69 0.22 0.10
500_N 136_V 0.69 0.21 0.10
194_A 116_G 0.69 0.21 0.10
492_R 156_A 0.68 0.21 0.10
214_L 148_A 0.68 0.21 0.09
206_R 48_E 0.68 0.21 0.09
390_D 25_G 0.68 0.20 0.09
485_V 110_S 0.67 0.20 0.09
250_E 48_E 0.67 0.20 0.09
309_S 130_A 0.66 0.20 0.09
380_S 7_L 0.66 0.19 0.09
373_A 174_I 0.66 0.19 0.08
392_Y 23_A 0.66 0.19 0.08
294_F 72_Q 0.66 0.19 0.08
416_Y 18_V 0.65 0.19 0.08
202_S 48_E 0.65 0.19 0.08
403_V 112_I 0.65 0.19 0.08
244_Y 125_N 0.65 0.18 0.08
145_L 175_L 0.65 0.18 0.08
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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