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OPENSEQ.org
RNase R tmRNA E coli
Genes: A B A+B
Length: 813 160 854
Sequences: 2367 2465 614
Seq/Len: 2.91 15.41 0.72
MirrorTree (Pazo et al. 2001) 0.84
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 0.09 0.52
2 0.01 0.09 0.58
5 0.01 0.09 0.60
10 0.01 0.09 0.61
20 0.02 0.09 0.63
100 0.02 0.09 0.73
∞ 0.05 0.09 1.42
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
239_Q 28_E 1.28 0.49 0.00
227_A 148_Q 1.16 0.39 0.00
94_D 96_E 1.15 0.38 0.00
242_E 110_T 1.12 0.36 0.00
406_H 127_I 1.10 0.35 0.00
545_Q 153_R 1.08 0.33 0.00
705_R 65_L 1.07 0.32 0.00
141_I 144_E 1.06 0.32 0.00
373_A 121_A 1.05 0.31 0.00
473_F 121_A 1.04 0.30 0.00
539_L 156_K 1.04 0.30 0.00
352_C 118_W 1.01 0.28 0.00
388_H 94_Q 0.99 0.27 0.00
686_Q 129_V 0.98 0.26 0.00
366_T 70_I 0.98 0.26 0.00
194_V 32_A 0.97 0.25 0.00
635_K 145_R 0.97 0.25 0.00
121_G 88_R 0.96 0.24 0.00
213_V 99_S 0.95 0.24 0.00
261_V 28_E 0.95 0.24 0.00
317_R 145_R 0.95 0.24 0.00
495_T 58_L 0.94 0.24 0.00
76_Y 106_R 0.94 0.23 0.00
707_E 112_V 0.92 0.22 0.00
176_I 52_S 0.92 0.22 0.00
392_G 61_G 0.92 0.22 0.00
632_D 51_I 0.91 0.22 0.00
77_A 111_V 0.91 0.22 0.00
582_I 51_I 0.90 0.21 0.00
366_T 94_Q 0.90 0.21 0.00
535_L 99_S 0.90 0.21 0.00
63_E 115_S 0.90 0.21 0.00
619_A 28_E 0.89 0.21 0.00
601_G 55_Y 0.89 0.20 0.00
720_I 14_I 0.88 0.20 0.00
536_Q 44_L 0.88 0.20 0.00
129_L 64_F 0.88 0.20 0.00
387_W 143_K 0.88 0.20 0.00
602_Y 29_E 0.88 0.20 0.00
143_R 121_A 0.87 0.20 0.00
697_G 87_T 0.87 0.19 0.00
456_H 82_C 0.87 0.19 0.00
259_G 112_V 0.86 0.19 0.00
689_Q 107_E 0.86 0.19 0.00
358_T 94_Q 0.86 0.19 0.00
634_L 81_V 0.86 0.19 0.00
677_L 89_K 0.85 0.19 0.00
626_A 100_L 0.85 0.19 0.00
97_G 92_L 0.85 0.18 0.00
646_V 112_V 0.84 0.18 0.00
326_P 64_F 0.84 0.18 0.00
403_L 94_Q 0.84 0.18 0.00
456_H 41_V 0.84 0.18 0.00
517_R 110_T 0.83 0.17 0.00
145_L 24_Y 0.83 0.17 0.00
35_A 44_L 0.83 0.17 0.00
630_V 92_L 0.82 0.17 0.00
578_L 82_C 0.82 0.17 0.00
647_F 23_E 0.82 0.17 0.00
485_I 131_K 0.82 0.17 0.00
450_T 41_V 0.82 0.17 0.00
585_L 41_V 0.82 0.17 0.00
650_V 115_S 0.81 0.17 0.00
323_V 74_A 0.81 0.17 0.00
708_V 106_R 0.81 0.17 0.00
373_A 120_N 0.81 0.17 0.00
647_F 83_D 0.81 0.17 0.00
632_D 55_Y 0.81 0.16 0.00
682_Y 30_F 0.81 0.16 0.00
208_G 72_P 0.80 0.16 0.00
360_S 30_F 0.80 0.16 0.00
102_E 51_I 0.80 0.16 0.00
606_M 96_E 0.80 0.16 0.00
720_I 61_G 0.80 0.16 0.00
145_L 127_I 0.80 0.16 0.00
613_G 23_E 0.80 0.16 0.00
515_E 27_E 0.80 0.16 0.00
441_E 141_D 0.80 0.16 0.00
74_Q 116_L 0.80 0.16 0.00
347_Q 118_W 0.79 0.16 0.00
348_V 30_F 0.79 0.16 0.00
155_R 27_E 0.79 0.16 0.00
67_Q 118_W 0.79 0.16 0.00
471_A 28_E 0.79 0.16 0.00
314_R 105_N 0.79 0.15 0.00
267_P 58_L 0.79 0.15 0.00
465_L 92_L 0.79 0.15 0.00
451_Q 55_Y 0.79 0.15 0.00
438_F 115_S 0.79 0.15 0.00
668_I 116_L 0.79 0.15 0.00
708_V 155_M 0.78 0.15 0.00
564_A 88_R 0.78 0.15 0.00
713_V 126_K 0.78 0.15 0.00
522_L 26_I 0.78 0.15 0.00
458_L 140_S 0.78 0.15 0.00
497_F 41_V 0.78 0.15 0.00
483_F 44_L 0.78 0.15 0.00
474_V 18_K 0.77 0.15 0.00
164_F 109_Y 0.77 0.15 0.00
111_S 152_A 0.77 0.15 0.00
672_V 144_E 0.77 0.15 0.00
285_C 32_A 0.77 0.15 0.00
456_H 37_Q 0.77 0.15 0.00
508_L 125_V 0.77 0.14 0.00
352_C 93_N 0.76 0.14 0.00
538_M 156_K 0.76 0.14 0.00
371_Y 35_A 0.76 0.14 0.00
714_N 63_A 0.76 0.14 0.00
235_Y 35_A 0.76 0.14 0.00
126_A 55_Y 0.75 0.14 0.00
455_A 18_K 0.75 0.14 0.00
52_L 143_K 0.75 0.14 0.00
438_F 41_V 0.75 0.14 0.00
615_H 112_V 0.75 0.14 0.00
626_A 56_V 0.75 0.14 0.00
446_R 34_L 0.75 0.14 0.00
704_D 92_L 0.75 0.14 0.00
498_R 41_V 0.74 0.14 0.00
236_I 14_I 0.74 0.14 0.00
353_M 54_S 0.74 0.14 0.00
245_V 29_E 0.74 0.13 0.00
391_Q 30_F 0.74 0.13 0.00
212_E 30_F 0.74 0.13 0.00
111_S 142_I 0.74 0.13 0.00
31_R 58_L 0.74 0.13 0.00
711_E 140_S 0.74 0.13 0.00
349_D 28_E 0.73 0.13 0.00
167_P 92_L 0.73 0.13 0.00
635_K 153_R 0.73 0.13 0.00
147_P 112_V 0.73 0.13 0.00
293_W 73_M 0.73 0.13 0.00
222_M 144_E 0.73 0.13 0.00
507_E 142_I 0.73 0.13 0.00
268_L 35_A 0.73 0.13 0.00
285_C 58_L 0.73 0.13 0.00
530_P 105_N 0.73 0.13 0.00
585_L 121_A 0.73 0.13 0.00
684_F 151_K 0.73 0.13 0.00
683_R 128_G 0.73 0.13 0.00
347_Q 28_E 0.73 0.13 0.00
522_L 125_V 0.73 0.13 0.00
501_L 55_Y 0.73 0.13 0.00
405_K 58_L 0.73 0.13 0.00
536_Q 153_R 0.73 0.13 0.00
539_L 54_S 0.73 0.13 0.00
674_V 37_Q 0.73 0.13 0.00
309_S 128_G 0.72 0.13 0.00
438_F 16_L 0.72 0.13 0.00
200_P 53_D 0.72 0.13 0.00
36_S 111_V 0.72 0.13 0.00
205_K 123_C 0.72 0.13 0.00
152_I 64_F 0.72 0.13 0.00
75_C 49_A 0.72 0.13 0.00
179_P 112_V 0.72 0.13 0.00
157_F 123_C 0.72 0.13 0.00
359_V 112_V 0.72 0.13 0.00
156_Y 41_V 0.72 0.13 0.00
263_L 65_L 0.72 0.13 0.00
65_D 99_S 0.71 0.12 0.00
47_E 121_A 0.71 0.12 0.00
210_I 22_H 0.71 0.12 0.00
564_A 27_E 0.71 0.12 0.00
144_V 100_L 0.71 0.12 0.00
636_C 63_A 0.71 0.12 0.00
706_V 140_S 0.71 0.12 0.00
91_G 146_E 0.70 0.12 0.00
659_F 14_I 0.70 0.12 0.00
129_L 141_D 0.70 0.12 0.00
162_V 85_T 0.70 0.12 0.00
436_F 57_L 0.70 0.12 0.00
586_L 134_K 0.70 0.12 0.00
512_N 92_L 0.70 0.12 0.00
68_L 106_R 0.70 0.12 0.00
630_V 131_K 0.70 0.12 0.00
62_M 51_I 0.70 0.12 0.00
523_L 34_L 0.70 0.12 0.00
274_E 32_A 0.70 0.12 0.00
485_I 18_K 0.70 0.12 0.00
629_D 57_L 0.70 0.12 0.00
424_R 136_H 0.70 0.12 0.00
205_K 67_G 0.70 0.12 0.00
388_H 150_D 0.69 0.12 0.00
706_V 55_Y 0.69 0.12 0.00
283_V 46_A 0.69 0.12 0.00
178_I 127_I 0.69 0.12 0.00
325_F 26_I 0.69 0.12 0.00
246_A 125_V 0.69 0.12 0.00
58_R 112_V 0.69 0.12 0.00
96_Y 48_K 0.69 0.12 0.00
445_E 148_Q 0.69 0.12 0.00
523_L 110_T 0.69 0.12 0.00
514_P 65_L 0.69 0.12 0.00
55_L 65_L 0.69 0.12 0.00
147_P 12_A 0.69 0.12 0.00
214_L 92_L 0.69 0.11 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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