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OPENSEQ.org
2vpz_AB
Genes: A B A+B
Length: 734 193 884
Sequences: 5916 2421 1515
Seq/Len: 8.06 12.54 1.71
MirrorTree (Pazo et al. 2001) 0.66
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 0.04 0.00 1.38
2 0.05 0.00 1.55
5 0.07 0.02 1.58
10 0.08 0.03 1.59
20 0.08 0.04 1.63
100 0.14 0.08 1.74
∞ 0.23 0.16 2.10
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
613_E 24_K 2.18 0.99 0.97
51_P 18_A 2.01 0.99 0.95
610_V 25_M 1.31 0.78 0.60
657_A 45_E 1.30 0.76 0.58
198_K 12_L 1.02 0.50 0.30
54_Q 134_T 0.98 0.46 0.26
210_F 49_L 0.89 0.36 0.18
610_V 21_V 0.86 0.33 0.16
206_V 50_V 0.86 0.33 0.16
35_K 26_E 0.84 0.32 0.14
614_M 20_A 0.84 0.31 0.14
657_A 46_Y 0.83 0.30 0.14
200_G 24_K 0.82 0.30 0.13
248_E 62_E 0.81 0.28 0.12
434_V 118_F 0.79 0.27 0.11
622_I 46_Y 0.79 0.27 0.11
279_P 110_A 0.78 0.26 0.11
231_L 113_V 0.77 0.26 0.11
657_A 47_P 0.77 0.26 0.10
51_P 35_N 0.76 0.24 0.10
496_L 53_F 0.76 0.24 0.10
699_I 82_L 0.75 0.24 0.10
429_N 27_N 0.75 0.24 0.09
268_T 85_V 0.72 0.22 0.08
144_C 5_A 0.72 0.21 0.08
625_E 45_E 0.72 0.21 0.08
689_Y 12_L 0.72 0.21 0.08
638_V 54_R 0.72 0.21 0.08
220_W 85_V 0.72 0.21 0.08
527_E 146_E 0.72 0.21 0.08
84_R 88_K 0.71 0.21 0.08
441_Q 78_T 0.71 0.21 0.08
632_L 145_L 0.70 0.20 0.07
649_G 22_A 0.70 0.20 0.07
248_E 107_L 0.70 0.20 0.07
95_I 79_K 0.69 0.20 0.07
99_M 9_D 0.69 0.20 0.07
497_G 104_A 0.69 0.20 0.07
176_L 86_D 0.69 0.19 0.07
623_H 38_I 0.69 0.19 0.07
12_Y 4_Y 0.69 0.19 0.07
411_I 12_L 0.69 0.19 0.07
207_D 24_K 0.69 0.19 0.07
206_V 67_V 0.68 0.19 0.06
620_V 6_M 0.68 0.19 0.06
36_V 103_D 0.68 0.19 0.06
592_L 130_A 0.68 0.19 0.06
284_R 80_D 0.67 0.18 0.06
402_P 62_E 0.67 0.18 0.06
564_Y 24_K 0.67 0.18 0.06
317_A 3_R 0.67 0.18 0.06
57_P 25_M 0.67 0.18 0.06
632_L 147_D 0.67 0.18 0.06
662_D 22_A 0.66 0.17 0.06
610_V 24_K 0.65 0.17 0.06
293_H 1_M 0.65 0.17 0.06
273_E 15_G 0.65 0.17 0.06
483_L 69_V 0.65 0.17 0.06
34_Y 67_V 0.65 0.17 0.06
86_A 4_Y 0.65 0.17 0.06
170_N 9_D 0.65 0.17 0.06
708_N 18_A 0.65 0.17 0.05
288_R 124_E 0.64 0.17 0.05
99_M 18_A 0.64 0.16 0.05
587_E 125_K 0.64 0.16 0.05
713_E 15_G 0.64 0.16 0.05
665_Y 5_A 0.64 0.16 0.05
218_H 69_V 0.64 0.16 0.05
628_K 62_E 0.63 0.16 0.05
294_K 79_K 0.63 0.16 0.05
276_T 147_D 0.63 0.16 0.05
167_D 47_P 0.63 0.16 0.05
401_Y 18_A 0.63 0.16 0.05
55_G 21_V 0.62 0.15 0.05
658_R 64_P 0.62 0.15 0.05
171_A 14_V 0.62 0.15 0.05
260_L 64_P 0.62 0.15 0.05
659_I 157_K 0.62 0.15 0.05
560_K 22_A 0.61 0.15 0.04
631_G 107_L 0.61 0.15 0.04
605_T 136_P 0.61 0.15 0.04
127_L 126_G 0.61 0.14 0.04
70_L 109_P 0.61 0.14 0.04
653_V 145_L 0.60 0.14 0.04
658_R 118_F 0.60 0.14 0.04
37_E 122_R 0.60 0.14 0.04
281_Q 147_D 0.60 0.14 0.04
417_I 60_H 0.60 0.14 0.04
48_R 18_A 0.60 0.14 0.04
51_P 37_W 0.60 0.14 0.04
172_R 68_P 0.60 0.14 0.04
228_D 64_P 0.59 0.14 0.04
586_P 154_K 0.59 0.14 0.04
332_G 9_D 0.59 0.14 0.04
168_W 132_V 0.59 0.14 0.04
535_L 117_T 0.59 0.14 0.04
513_E 68_P 0.59 0.14 0.04
288_R 45_E 0.59 0.14 0.04
712_L 2_P 0.59 0.14 0.04
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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