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OPENSEQ.org
RelA X GntR
Genes: A B A+B
Length: 734 243 915
Sequences: 2717 11754 64
Seq/Len: 3.7 48.37 0.07
MirrorTree (Pazo et al. 2001) 0.29
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 0.02 0.00
2 0.01 0.02 0.00
5 0.01 0.05 0.01
10 0.01 0.06 0.02
20 0.01 0.09 0.07
100 0.01 0.17 0.35
∞ 0.09 0.24 1.28
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
623_V 140_Q 1.37 0.13 0.00
720_I 93_D 1.26 0.11 0.00
599_L 149_I 1.25 0.11 0.00
670_G 61_A 1.25 0.11 0.00
432_V 64_I 1.21 0.10 0.00
623_V 224_V 1.21 0.10 0.00
451_I 34_G 1.21 0.10 0.00
482_K 47_I 1.19 0.10 0.00
331_E 27_L 1.18 0.10 0.00
265_L 93_D 1.16 0.10 0.00
55_I 62_L 1.15 0.09 0.00
413_I 38_S 1.12 0.09 0.00
218_V 54_S 1.12 0.09 0.00
342_A 106_L 1.05 0.08 0.00
498_E 139_F 1.05 0.08 0.00
18_S 24_A 1.05 0.08 0.00
160_Q 105_R 1.05 0.08 0.00
331_E 154_H 1.04 0.08 0.00
129_V 149_I 1.03 0.08 0.00
600_S 207_A 1.03 0.08 0.00
531_D 45_N 1.02 0.07 0.00
600_S 157_I 1.01 0.07 0.00
323_L 157_I 1.01 0.07 0.00
528_N 93_D 1.00 0.07 0.00
465_V 95_R 1.00 0.07 0.00
169_E 195_E 1.00 0.07 0.00
11_Q 47_I 0.99 0.07 0.00
416_S 154_H 0.99 0.07 0.00
720_I 47_I 0.98 0.07 0.00
238_F 59_R 0.97 0.07 0.00
314_T 36_I 0.97 0.07 0.00
490_V 70_I 0.97 0.07 0.00
55_I 104_E 0.97 0.07 0.00
237_D 212_S 0.97 0.07 0.00
341_A 39_G 0.96 0.07 0.00
229_V 67_S 0.96 0.07 0.00
498_E 199_Q 0.96 0.07 0.00
291_P 42_L 0.95 0.07 0.00
620_G 39_G 0.95 0.07 0.00
271_L 94_V 0.95 0.07 0.00
66_M 21_V 0.94 0.07 0.00
70_T 141_D 0.93 0.07 0.00
449_V 68_E 0.93 0.06 0.00
250_R 224_V 0.93 0.06 0.00
657_Y 69_K 0.93 0.06 0.00
142_L 77_G 0.92 0.06 0.00
101_L 102_V 0.92 0.06 0.00
643_V 70_I 0.92 0.06 0.00
88_D 51_F 0.92 0.06 0.00
281_V 34_G 0.91 0.06 0.00
685_N 80_V 0.91 0.06 0.00
661_I 91_I 0.91 0.06 0.00
642_P 144_F 0.91 0.06 0.00
704_A 51_F 0.91 0.06 0.00
234_I 224_V 0.91 0.06 0.00
273_N 154_H 0.91 0.06 0.00
601_K 71_I 0.91 0.06 0.00
663_I 110_D 0.90 0.06 0.00
186_E 95_R 0.90 0.06 0.00
290_K 27_L 0.90 0.06 0.00
55_I 123_E 0.90 0.06 0.00
659_V 94_V 0.89 0.06 0.00
432_V 170_S 0.89 0.06 0.00
325_V 37_E 0.89 0.06 0.00
411_V 216_N 0.89 0.06 0.00
281_V 60_E 0.89 0.06 0.00
394_V 140_Q 0.89 0.06 0.00
141_K 154_H 0.89 0.06 0.00
120_Q 61_A 0.89 0.06 0.00
413_I 164_L 0.88 0.06 0.00
166_E 44_E 0.88 0.06 0.00
98_V 115_V 0.88 0.06 0.00
273_N 73_L 0.88 0.06 0.00
635_E 62_L 0.88 0.06 0.00
531_D 155_S 0.88 0.06 0.00
623_V 28_R 0.88 0.06 0.00
190_T 59_R 0.88 0.06 0.00
494_R 223_K 0.88 0.06 0.00
96_E 51_F 0.88 0.06 0.00
638_E 217_F 0.87 0.06 0.00
712_H 47_I 0.87 0.06 0.00
369_L 198_I 0.87 0.06 0.00
452_L 216_N 0.86 0.06 0.00
532_M 47_I 0.86 0.06 0.00
149_M 21_V 0.86 0.06 0.00
491_E 62_L 0.86 0.06 0.00
724_R 27_L 0.86 0.06 0.00
672_L 27_L 0.86 0.06 0.00
161_R 122_L 0.85 0.06 0.00
247_S 213_L 0.85 0.06 0.00
73_G 42_L 0.85 0.06 0.00
432_V 55_R 0.85 0.06 0.00
221_V 56_S 0.85 0.06 0.00
608_G 164_L 0.85 0.06 0.00
612_V 47_I 0.84 0.06 0.00
683_K 208_L 0.84 0.06 0.00
366_R 91_I 0.84 0.06 0.00
37_D 19_T 0.84 0.06 0.00
444_R 215_Q 0.84 0.06 0.00
546_V 152_I 0.84 0.06 0.00
623_V 21_V 0.84 0.06 0.00
270_I 75_R 0.84 0.06 0.00
623_V 90_E 0.84 0.06 0.00
451_I 48_A 0.84 0.06 0.00
475_H 210_I 0.83 0.05 0.00
665_G 91_I 0.83 0.05 0.00
718_E 103_F 0.83 0.05 0.00
283_G 154_H 0.83 0.05 0.00
66_M 156_Y 0.83 0.05 0.00
173_P 60_E 0.83 0.05 0.00
160_Q 143_L 0.83 0.05 0.00
96_E 45_N 0.83 0.05 0.00
482_K 115_V 0.83 0.05 0.00
191_A 187_F 0.83 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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