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OPENSEQ.org
1MR6_AC
Genes: A B A+B
Length: 761 157 899
Sequences: 4233 4822 2711
Seq/Len: 5.56 30.71 3.02
MirrorTree (Pazo et al. 2001) 0.74
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 0.02 0.01 1.72
2 0.03 0.02 2.87
5 0.04 0.03 2.93
10 0.05 0.04 2.94
20 0.11 0.06 2.95
100 0.14 0.10 2.98
∞ 0.22 0.19 3.06
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
688_V 134_L 2.78 1.00 1.00
691_I 130_L 1.53 0.96 0.91
16_V 108_I 1.47 0.95 0.88
16_V 85_L 1.42 0.94 0.86
16_V 93_H 1.40 0.93 0.85
12_G 93_H 1.40 0.93 0.85
656_Q 142_K 1.25 0.87 0.76
25_D 102_F 1.23 0.85 0.74
652_E 142_K 1.16 0.81 0.67
696_D 123_R 1.15 0.80 0.67
691_I 144_I 1.10 0.75 0.61
8_P 94_E 1.05 0.70 0.55
262_R 30_E 0.98 0.63 0.47
13_V 85_L 0.96 0.61 0.45
17_T 89_Q 0.90 0.53 0.38
653_G 138_T 0.89 0.52 0.36
16_V 98_T 0.87 0.49 0.34
8_P 93_H 0.87 0.49 0.33
17_T 80_A 0.86 0.48 0.32
653_G 139_G 0.85 0.47 0.32
16_V 89_Q 0.84 0.46 0.30
110_K 21_N 0.83 0.44 0.29
656_Q 141_V 0.83 0.44 0.29
21_K 35_T 0.81 0.41 0.27
19_K 80_A 0.78 0.38 0.24
649_L 96_L 0.78 0.38 0.23
13_V 93_H 0.75 0.35 0.21
267_R 40_G 0.73 0.33 0.20
684_L 43_G 0.72 0.31 0.18
20_A 38_K 0.70 0.30 0.17
682_N 97_G 0.69 0.28 0.15
17_T 85_L 0.68 0.27 0.15
691_I 147_V 0.66 0.26 0.14
136_A 5_L 0.65 0.24 0.13
55_E 147_V 0.64 0.23 0.12
690_T 134_L 0.63 0.23 0.12
17_T 93_H 0.62 0.21 0.11
572_E 54_D 0.62 0.21 0.11
624_V 105_P 0.61 0.21 0.11
48_A 15_E 0.61 0.21 0.10
691_I 107_M 0.60 0.20 0.10
590_Y 138_T 0.59 0.19 0.09
8_P 90_A 0.59 0.19 0.09
13_V 90_A 0.59 0.19 0.09
661_M 138_T 0.58 0.19 0.09
268_E 43_G 0.57 0.18 0.08
156_G 44_G 0.57 0.18 0.08
485_A 109_M 0.57 0.17 0.08
232_F 38_K 0.56 0.17 0.08
653_G 96_L 0.56 0.17 0.08
694_S 144_I 0.55 0.17 0.07
64_C 73_V 0.55 0.16 0.07
691_I 127_K 0.55 0.16 0.07
17_T 86_S 0.54 0.16 0.07
161_A 27_Y 0.54 0.16 0.07
675_N 18_V 0.54 0.16 0.07
534_G 152_A 0.54 0.16 0.07
18_G 36_G 0.54 0.16 0.07
103_I 12_R 0.54 0.15 0.07
660_W 138_T 0.54 0.15 0.07
232_F 98_T 0.53 0.15 0.07
48_A 144_I 0.53 0.15 0.07
11_D 96_L 0.53 0.15 0.06
106_V 26_D 0.53 0.15 0.06
14_E 71_K 0.53 0.15 0.06
238_G 99_Q 0.52 0.15 0.06
684_L 45_E 0.52 0.15 0.06
183_M 37_T 0.52 0.15 0.06
215_V 102_F 0.52 0.14 0.06
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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