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OPENSEQ.org
T therm UvrA YbaZ
Genes: A B A+B
Length: 952 147 1074
Sequences: 3201 4675 64
Seq/Len: 3.36 31.8 0.06
MirrorTree (Pazo et al. 2001) 0.28
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 0.00
2 0.01 0.02 0.01
5 0.01 0.02 0.01
10 0.01 0.02 0.03
20 0.01 0.02 0.06
100 0.02 0.03 0.19
∞ 0.08 0.12 1.21
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
402_F 70_R 1.34 0.12 0.00
490_T 124_D 1.26 0.10 0.00
83_I 111_F 1.25 0.10 0.00
155_V 19_V 1.25 0.10 0.00
753_I 22_L 1.24 0.10 0.00
808_I 121_I 1.22 0.10 0.00
147_R 96_G 1.22 0.10 0.00
660_A 115_V 1.21 0.10 0.00
26_F 70_R 1.18 0.09 0.00
283_L 87_S 1.18 0.09 0.00
17_I 113_L 1.18 0.09 0.00
162_Y 128_G 1.16 0.09 0.00
272_S 49_F 1.14 0.09 0.00
300_S 81_P 1.12 0.08 0.00
560_W 128_G 1.11 0.08 0.00
576_V 5_T 1.11 0.08 0.00
773_Y 98_S 1.10 0.08 0.00
789_D 143_F 1.07 0.08 0.00
244_E 130_F 1.07 0.08 0.00
787_I 49_F 1.06 0.07 0.00
616_L 91_L 1.06 0.07 0.00
656_V 115_V 1.05 0.07 0.00
575_V 5_T 1.05 0.07 0.00
560_W 45_V 1.05 0.07 0.00
874_L 19_V 1.04 0.07 0.00
761_L 127_L 1.04 0.07 0.00
17_I 23_E 1.04 0.07 0.00
448_L 130_F 1.04 0.07 0.00
6_I 56_F 1.03 0.07 0.00
940_I 67_S 1.02 0.07 0.00
69_D 41_V 1.01 0.07 0.00
653_V 20_R 1.01 0.07 0.00
147_R 72_R 1.00 0.07 0.00
616_L 72_R 1.00 0.07 0.00
420_V 49_F 1.00 0.07 0.00
19_L 78_R 0.99 0.07 0.00
677_A 124_D 0.99 0.07 0.00
657_L 129_G 0.99 0.07 0.00
709_V 131_Q 0.99 0.07 0.00
786_S 89_G 0.98 0.07 0.00
616_L 84_R 0.97 0.06 0.00
131_S 71_L 0.96 0.06 0.00
20_E 121_I 0.96 0.06 0.00
15_K 120_V 0.95 0.06 0.00
20_E 19_V 0.95 0.06 0.00
936_F 43_E 0.95 0.06 0.00
926_V 84_R 0.95 0.06 0.00
83_I 113_L 0.95 0.06 0.00
619_K 108_A 0.95 0.06 0.00
258_S 134_E 0.95 0.06 0.00
515_V 39_L 0.95 0.06 0.00
790_V 49_F 0.95 0.06 0.00
59_S 53_R 0.94 0.06 0.00
711_D 5_T 0.94 0.06 0.00
894_L 103_G 0.94 0.06 0.00
792_D 18_G 0.94 0.06 0.00
349_A 41_V 0.94 0.06 0.00
63_Q 121_I 0.94 0.06 0.00
74_E 67_S 0.94 0.06 0.00
330_H 37_L 0.94 0.06 0.00
6_I 136_L 0.94 0.06 0.00
603_P 130_F 0.93 0.06 0.00
422_S 19_V 0.93 0.06 0.00
629_V 90_A 0.93 0.06 0.00
412_G 124_D 0.92 0.06 0.00
179_V 44_A 0.92 0.06 0.00
133_S 115_V 0.92 0.06 0.00
779_E 71_L 0.92 0.06 0.00
753_I 121_I 0.92 0.06 0.00
877_L 12_L 0.91 0.06 0.00
294_V 91_L 0.91 0.06 0.00
158_R 110_P 0.91 0.06 0.00
142_R 124_D 0.91 0.06 0.00
903_V 114_L 0.91 0.06 0.00
656_V 114_L 0.90 0.06 0.00
278_P 114_L 0.90 0.06 0.00
89_T 134_E 0.90 0.06 0.00
467_I 103_G 0.90 0.06 0.00
292_E 97_L 0.90 0.06 0.00
902_W 143_F 0.90 0.06 0.00
934_G 84_R 0.89 0.06 0.00
179_V 22_L 0.89 0.06 0.00
584_I 143_F 0.89 0.06 0.00
918_V 14_V 0.89 0.06 0.00
329_E 90_A 0.89 0.06 0.00
560_W 122_H 0.89 0.06 0.00
175_A 113_L 0.89 0.06 0.00
618_L 61_L 0.89 0.06 0.00
112_F 90_A 0.89 0.06 0.00
399_L 104_A 0.88 0.06 0.00
262_E 56_F 0.88 0.06 0.00
546_I 98_S 0.88 0.06 0.00
794_T 85_T 0.88 0.06 0.00
174_Y 67_S 0.88 0.06 0.00
330_H 56_F 0.88 0.06 0.00
100_T 48_Y 0.88 0.06 0.00
919_A 19_V 0.88 0.06 0.00
580_T 100_R 0.87 0.06 0.00
824_K 75_E 0.87 0.06 0.00
545_L 20_R 0.87 0.05 0.00
29_I 84_R 0.87 0.05 0.00
197_Y 128_G 0.87 0.05 0.00
130_Q 96_G 0.87 0.05 0.00
400_E 124_D 0.87 0.05 0.00
162_Y 55_D 0.86 0.05 0.00
598_G 115_V 0.86 0.05 0.00
593_G 132_G 0.86 0.05 0.00
577_A 6_P 0.86 0.05 0.00
445_F 114_L 0.86 0.05 0.00
840_I 96_G 0.85 0.05 0.00
456_Q 115_V 0.85 0.05 0.00
653_V 74_Y 0.85 0.05 0.00
84_S 130_F 0.84 0.05 0.00
748_D 17_L 0.84 0.05 0.00
256_H 95_L 0.84 0.05 0.00
825_L 8_G 0.84 0.05 0.00
460_A 90_A 0.84 0.05 0.00
616_L 114_L 0.84 0.05 0.00
177_V 34_E 0.84 0.05 0.00
870_V 126_R 0.83 0.05 0.00
936_F 90_A 0.83 0.05 0.00
40_L 105_A 0.83 0.05 0.00
65_L 56_F 0.83 0.05 0.00
761_L 133_Q 0.83 0.05 0.00
447_G 134_E 0.83 0.05 0.00
510_T 70_R 0.83 0.05 0.00
561_I 6_P 0.83 0.05 0.00
484_L 140_L 0.83 0.05 0.00
616_L 138_L 0.82 0.05 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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