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OPENSEQ.org
1g4a_F_D
Genes: A B A+B
Length: 443 175 565
Sequences: 1289 934 1045
Seq/Len: 2.91 5.34 1.85
MirrorTree (Pazo et al. 2001) 0.75
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 0.09 0.09 1.57
2 0.09 0.09 1.66
5 0.09 0.09 1.67
10 0.09 0.09 1.69
20 0.09 0.09 1.69
100 0.09 0.09 1.69
∞ 0.09 0.09 1.78
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
155_A 111_D 1.04 0.54 0.00
281_L 111_D 1.04 0.54 0.00
312_I 66_M 1.04 0.54 0.00
155_A 50_T 1.02 0.52 0.00
428_H 13_V 0.99 0.49 0.00
424_Y 42_V 0.99 0.49 0.00
133_D 111_D 0.98 0.48 0.00
352_T 150_K 0.96 0.46 0.00
212_K 156_G 0.94 0.44 0.00
238_E 152_L 0.91 0.40 0.00
100_I 42_V 0.89 0.39 0.00
363_G 3_I 0.89 0.39 0.00
40_L 27_M 0.87 0.37 0.00
315_P 57_F 0.86 0.35 0.00
138_P 21_T 0.86 0.35 0.00
262_C 75_A 0.86 0.35 0.00
84_T 104_L 0.85 0.34 0.00
169_D 111_D 0.85 0.34 0.00
46_H 114_Q 0.84 0.34 0.00
442_I 120_I 0.84 0.33 0.00
281_L 4_V 0.84 0.33 0.00
362_E 65_E 0.84 0.33 0.00
73_L 7_R 0.83 0.33 0.00
99_I 98_A 0.83 0.33 0.00
350_S 106_I 0.83 0.32 0.00
366_I 81_D 0.83 0.32 0.00
163_L 78_L 0.82 0.32 0.00
158_A 161_Y 0.82 0.31 0.00
440_R 150_K 0.82 0.31 0.00
136_I 111_D 0.82 0.31 0.00
281_L 50_T 0.81 0.31 0.00
402_L 58_E 0.81 0.30 0.00
442_I 72_V 0.80 0.30 0.00
98_S 113_V 0.80 0.29 0.00
237_E 170_E 0.80 0.29 0.00
107_A 151_A 0.79 0.28 0.00
211_Q 65_E 0.79 0.28 0.00
359_M 118_D 0.79 0.28 0.00
234_V 68_Q 0.78 0.28 0.00
319_I 60_F 0.78 0.28 0.00
402_L 67_H 0.78 0.28 0.00
94_K 114_Q 0.78 0.27 0.00
347_P 158_I 0.78 0.27 0.00
159_F 50_T 0.77 0.27 0.00
171_K 50_T 0.77 0.27 0.00
108_V 10_G 0.77 0.27 0.00
214_R 170_E 0.77 0.27 0.00
396_H 170_E 0.76 0.26 0.00
169_D 50_T 0.76 0.26 0.00
350_S 103_S 0.76 0.26 0.00
48_V 144_A 0.76 0.26 0.00
424_Y 96_A 0.75 0.25 0.00
56_I 88_L 0.75 0.25 0.00
387_T 38_Y 0.75 0.25 0.00
386_S 49_G 0.74 0.25 0.00
347_P 94_L 0.74 0.24 0.00
231_A 150_K 0.74 0.24 0.00
43_E 94_L 0.74 0.24 0.00
434_A 171_L 0.74 0.24 0.00
127_A 36_R 0.74 0.24 0.00
76_A 104_L 0.73 0.24 0.00
95_E 114_Q 0.73 0.23 0.00
421_D 115_P 0.73 0.23 0.00
232_K 42_V 0.72 0.23 0.00
396_H 152_L 0.72 0.23 0.00
242_D 40_D 0.72 0.22 0.00
313_A 54_F 0.71 0.22 0.00
48_V 14_I 0.71 0.22 0.00
401_R 21_T 0.71 0.22 0.00
288_C 113_V 0.70 0.22 0.00
244_I 134_R 0.70 0.21 0.00
363_G 105_I 0.70 0.21 0.00
441_F 58_E 0.70 0.21 0.00
402_L 120_I 0.70 0.21 0.00
115_A 97_V 0.70 0.21 0.00
173_I 32_K 0.69 0.21 0.00
84_T 34_V 0.69 0.21 0.00
72_K 26_V 0.69 0.20 0.00
48_V 96_A 0.69 0.20 0.00
107_A 147_I 0.69 0.20 0.00
48_V 161_Y 0.69 0.20 0.00
74_A 104_L 0.69 0.20 0.00
423_D 37_L 0.68 0.20 0.00
105_D 118_D 0.68 0.20 0.00
421_D 120_I 0.68 0.20 0.00
202_M 109_N 0.68 0.20 0.00
141_N 100_E 0.68 0.20 0.00
326_L 50_T 0.68 0.20 0.00
353_V 43_I 0.68 0.20 0.00
389_N 63_K 0.68 0.20 0.00
84_T 16_G 0.68 0.20 0.00
441_F 142_L 0.67 0.19 0.00
224_L 21_T 0.67 0.19 0.00
255_I 144_A 0.67 0.19 0.00
315_P 80_K 0.67 0.19 0.00
105_D 121_A 0.67 0.19 0.00
363_G 165_F 0.67 0.19 0.00
404_E 21_T 0.67 0.19 0.00
159_F 107_T 0.66 0.19 0.00
410_A 159_C 0.66 0.19 0.00
338_S 147_I 0.66 0.19 0.00
150_Q 143_S 0.66 0.18 0.00
122_R 8_R 0.66 0.18 0.00
203_F 154_I 0.66 0.18 0.00
311_Q 136_L 0.65 0.18 0.00
40_L 49_G 0.65 0.18 0.00
347_P 120_I 0.65 0.18 0.00
401_R 144_A 0.65 0.18 0.00
156_R 32_K 0.65 0.18 0.00
167_Q 37_L 0.65 0.18 0.00
118_K 156_G 0.65 0.18 0.00
311_Q 4_V 0.65 0.18 0.00
367_E 128_Y 0.65 0.18 0.00
376_I 43_I 0.65 0.18 0.00
307_S 26_V 0.65 0.17 0.00
408_Y 22_L 0.64 0.17 0.00
175_I 154_I 0.64 0.17 0.00
109_K 152_L 0.64 0.17 0.00
421_D 98_A 0.64 0.17 0.00
194_E 159_C 0.64 0.17 0.00
169_D 72_V 0.64 0.17 0.00
261_I 63_K 0.64 0.17 0.00
380_A 36_R 0.64 0.17 0.00
81_V 100_E 0.64 0.17 0.00
363_G 37_L 0.64 0.17 0.00
284_L 113_V 0.63 0.17 0.00
55_M 131_A 0.63 0.17 0.00
92_V 76_V 0.63 0.17 0.00
309_A 66_M 0.63 0.17 0.00
97_D 30_N 0.63 0.17 0.00
170_D 171_L 0.63 0.17 0.00
442_I 94_L 0.63 0.16 0.00
158_A 111_D 0.63 0.16 0.00
442_I 103_S 0.62 0.16 0.00
72_K 96_A 0.62 0.16 0.00
76_A 152_L 0.62 0.16 0.00
375_R 152_L 0.62 0.16 0.00
110_M 131_A 0.62 0.16 0.00
311_Q 152_L 0.62 0.16 0.00
366_I 89_R 0.62 0.16 0.00
236_P 116_E 0.62 0.16 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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