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OPENSEQ.org
2XDF-2
Genes: A B A+B
Length: 572 85 650
Sequences: 2534 3242 1190
Seq/Len: 4.43 38.14 1.83
MirrorTree (Pazo et al. 2001) 0.71
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 0.01 0.01 1.63
2 0.01 0.01 1.67
5 0.01 0.01 1.78
10 0.01 0.01 1.79
20 0.01 0.01 1.81
100 0.05 0.06 1.90
∞ 0.12 0.14 2.35
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
78_L 47_L 1.32 0.80 0.06
74_G 16_T 1.29 0.78 0.05
6_A 48_F 1.07 0.57 0.03
74_G 20_A 1.06 0.56 0.03
132_I 16_T 1.06 0.56 0.03
122_L 51_Q 1.04 0.54 0.03
329_I 36_T 0.98 0.48 0.02
156_I 42_A 0.93 0.42 0.02
166_E 42_A 0.93 0.42 0.02
82_E 47_L 0.91 0.40 0.02
536_I 3_Q 0.90 0.39 0.02
480_V 22_F 0.88 0.37 0.01
249_K 33_I 0.87 0.35 0.01
219_L 24_K 0.86 0.35 0.01
103_A 42_A 0.85 0.34 0.01
256_K 48_F 0.85 0.34 0.01
73_E 20_A 0.85 0.34 0.01
323_C 81_M 0.85 0.34 0.01
237_K 50_L 0.85 0.34 0.01
177_G 38_N 0.84 0.33 0.01
179_I 5_E 0.84 0.33 0.01
234_V 61_V 0.82 0.32 0.01
231_T 63_I 0.81 0.30 0.01
55_T 71_Q 0.80 0.29 0.01
80_E 27_K 0.79 0.28 0.01
479_S 5_E 0.78 0.28 0.01
54_E 42_A 0.78 0.27 0.01
380_S 29_F 0.78 0.27 0.01
83_E 43_S 0.77 0.26 0.01
82_E 27_K 0.77 0.26 0.01
114_L 51_Q 0.76 0.26 0.01
141_L 50_L 0.76 0.26 0.01
184_G 14_L 0.76 0.26 0.01
318_A 8_I 0.75 0.25 0.01
300_F 57_Q 0.75 0.25 0.01
82_E 46_S 0.74 0.24 0.01
376_I 27_K 0.73 0.23 0.01
310_E 33_I 0.73 0.23 0.01
80_E 47_L 0.73 0.23 0.01
211_V 8_I 0.72 0.23 0.01
214_D 34_T 0.72 0.23 0.01
483_L 26_A 0.72 0.22 0.01
300_F 16_T 0.72 0.22 0.01
268_V 77_L 0.72 0.22 0.01
380_S 65_A 0.71 0.22 0.01
524_M 8_I 0.71 0.22 0.01
123_K 22_F 0.71 0.22 0.01
172_L 6_V 0.71 0.21 0.01
546_V 71_Q 0.70 0.21 0.01
431_T 21_Q 0.70 0.21 0.01
13_G 57_Q 0.70 0.21 0.01
198_L 74_V 0.69 0.21 0.01
98_T 47_L 0.69 0.20 0.01
73_E 24_K 0.69 0.20 0.01
316_Y 1_M 0.69 0.20 0.01
13_G 10_A 0.68 0.20 0.01
484_I 49_K 0.67 0.19 0.01
416_G 5_E 0.66 0.19 0.01
429_V 5_E 0.66 0.18 0.01
268_V 29_F 0.66 0.18 0.01
226_V 59_T 0.65 0.18 0.01
71_I 21_Q 0.65 0.18 0.01
276_T 12_N 0.65 0.18 0.01
389_F 54_G 0.65 0.17 0.01
117_L 51_Q 0.65 0.17 0.01
506_G 57_Q 0.64 0.17 0.01
234_V 33_I 0.64 0.17 0.01
51_A 71_Q 0.64 0.17 0.01
13_G 44_A 0.64 0.17 0.01
82_E 45_K 0.64 0.17 0.01
302_D 80_L 0.64 0.17 0.01
272_A 81_M 0.64 0.17 0.01
217_L 30_T 0.64 0.17 0.01
58_T 71_Q 0.64 0.17 0.01
75_H 61_V 0.64 0.17 0.01
449_S 45_K 0.63 0.17 0.01
291_V 76_H 0.63 0.17 0.01
474_Q 47_L 0.63 0.16 0.01
268_V 70_E 0.63 0.16 0.01
76_I 4_Q 0.63 0.16 0.01
387_I 34_T 0.63 0.16 0.01
156_I 34_T 0.63 0.16 0.01
405_I 81_M 0.63 0.16 0.01
251_E 33_I 0.63 0.16 0.01
218_I 42_A 0.62 0.16 0.01
227_Y 50_L 0.62 0.16 0.01
82_E 24_K 0.62 0.16 0.01
76_I 61_V 0.62 0.16 0.01
114_L 16_T 0.62 0.16 0.01
359_I 51_Q 0.62 0.16 0.01
278_R 44_A 0.62 0.16 0.01
18_L 28_G 0.62 0.16 0.01
489_D 44_A 0.62 0.16 0.01
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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