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OPENSEQ.org
1kf6_M_N
Genes: A B A+B
Length: 602 243 721
Sequences: 2766 2044 667
Seq/Len: 4.59 8.41 0.93
MirrorTree (Pazo et al. 2001) 0.89
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 0.71
2 0.01 0.01 0.73
5 0.01 0.01 0.78
10 0.01 0.01 0.79
20 0.01 0.01 0.79
100 0.03 0.01 0.89
∞ 0.14 0.08 1.34
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
327_E 140_A 1.62 0.82 0.06
364_T 143_H 1.42 0.69 0.03
462_E 26_Y 1.36 0.64 0.03
520_A 213_V 1.32 0.60 0.03
198_R 58_R 1.29 0.58 0.02
245_T 61_I 1.28 0.57 0.02
110_G 53_Y 1.27 0.56 0.02
142_Q 179_Y 1.27 0.56 0.02
376_F 49_P 1.25 0.55 0.02
313_V 61_I 1.23 0.53 0.02
470_P 117_K 1.18 0.48 0.02
464_C 111_E 1.14 0.44 0.01
351_V 14_N 1.12 0.43 0.01
522_S 98_I 1.11 0.42 0.01
492_I 49_P 1.09 0.40 0.01
372_I 22_H 1.08 0.40 0.01
331_F 59_M 1.07 0.38 0.01
50_E 73_P 1.06 0.38 0.01
50_E 153_L 1.06 0.37 0.01
321_G 88_M 1.05 0.36 0.01
45_H 191_R 1.05 0.36 0.01
47_V 59_M 1.04 0.36 0.01
247_G 183_S 1.04 0.36 0.01
50_E 150_N 1.04 0.36 0.01
382_S 113_L 1.02 0.34 0.01
332_I 222_A 1.01 0.34 0.01
540_C 167_F 1.01 0.34 0.01
50_E 59_M 1.01 0.33 0.01
294_A 51_L 1.01 0.33 0.01
466_I 217_H 1.00 0.33 0.01
9_A 138_Q 1.00 0.33 0.01
416_A 90_V 1.00 0.32 0.01
184_I 100_R 0.99 0.32 0.01
364_T 15_P 0.99 0.32 0.01
490_V 90_V 0.98 0.31 0.01
254_I 10_V 0.98 0.31 0.01
18_L 83_D 0.98 0.31 0.01
517_E 91_E 0.98 0.31 0.01
102_C 119_Y 0.98 0.31 0.01
540_C 4_K 0.98 0.31 0.01
181_L 100_R 0.98 0.31 0.01
331_F 147_G 0.98 0.30 0.01
492_I 173_I 0.98 0.30 0.01
88_H 138_Q 0.97 0.30 0.01
497_S 49_P 0.97 0.30 0.01
128_A 157_A 0.97 0.30 0.01
516_A 98_I 0.97 0.30 0.01
522_S 24_A 0.96 0.30 0.01
10_I 124_S 0.96 0.30 0.01
412_T 90_V 0.96 0.29 0.01
541_T 67_M 0.96 0.29 0.01
513_L 200_G 0.96 0.29 0.01
376_F 192_M 0.96 0.29 0.01
155_E 54_R 0.95 0.29 0.01
155_E 191_R 0.95 0.28 0.01
254_I 88_M 0.94 0.28 0.01
401_V 107_T 0.93 0.27 0.01
46_T 161_F 0.93 0.27 0.01
455_E 14_N 0.93 0.27 0.01
456_M 95_N 0.93 0.27 0.01
142_Q 175_L 0.93 0.27 0.01
162_L 25_F 0.92 0.26 0.01
174_M 100_R 0.92 0.26 0.01
200_Y 49_P 0.92 0.26 0.01
484_Q 28_V 0.92 0.26 0.01
540_C 52_S 0.91 0.26 0.01
46_T 110_I 0.91 0.26 0.01
190_V 25_F 0.91 0.26 0.01
157_F 220_P 0.91 0.26 0.01
203_N 104_V 0.91 0.26 0.01
125_T 220_P 0.91 0.26 0.01
205_N 104_V 0.90 0.25 0.01
355_A 95_N 0.90 0.25 0.01
184_I 130_G 0.90 0.25 0.01
128_A 159_P 0.90 0.25 0.01
8_L 25_F 0.90 0.25 0.01
25_A 167_F 0.90 0.25 0.01
469_T 107_T 0.89 0.24 0.01
13_A 168_I 0.89 0.24 0.01
103_P 134_Q 0.89 0.24 0.01
257_N 184_R 0.89 0.24 0.01
131_K 147_G 0.89 0.24 0.01
477_I 90_V 0.89 0.24 0.01
485_E 26_Y 0.89 0.24 0.01
200_Y 152_G 0.89 0.24 0.01
244_M 205_T 0.88 0.24 0.01
22_I 36_L 0.88 0.24 0.01
459_A 29_P 0.88 0.24 0.01
426_I 168_I 0.88 0.24 0.01
188_A 100_R 0.88 0.24 0.01
170_G 75_L 0.88 0.23 0.01
327_E 39_A 0.88 0.23 0.01
397_L 228_K 0.88 0.23 0.01
53_S 93_L 0.87 0.23 0.01
520_A 217_H 0.87 0.23 0.01
50_E 55_W 0.87 0.23 0.01
217_A 25_F 0.87 0.23 0.01
38_K 170_P 0.87 0.23 0.01
88_H 195_L 0.87 0.23 0.01
21_A 70_N 0.86 0.23 0.01
478_D 28_V 0.86 0.23 0.01
131_K 60_A 0.86 0.22 0.01
418_A 190_E 0.86 0.22 0.01
159_L 36_L 0.86 0.22 0.01
9_A 60_A 0.86 0.22 0.01
338_A 43_I 0.86 0.22 0.01
184_I 36_L 0.86 0.22 0.01
125_T 167_F 0.85 0.22 0.01
95_T 130_G 0.85 0.22 0.01
382_S 64_S 0.85 0.22 0.01
321_G 213_V 0.85 0.22 0.01
65_Y 65_C 0.85 0.22 0.01
203_N 28_V 0.85 0.22 0.01
36_I 138_Q 0.84 0.21 0.01
464_C 61_I 0.84 0.21 0.01
471_E 47_L 0.84 0.21 0.01
96_Q 207_V 0.84 0.21 0.01
126_W 150_N 0.84 0.21 0.01
339_Y 216_K 0.84 0.21 0.01
204_T 220_P 0.84 0.21 0.01
21_A 194_Q 0.84 0.21 0.01
325_L 232_S 0.84 0.21 0.01
341_G 33_T 0.83 0.21 0.01
309_R 157_A 0.83 0.21 0.01
452_I 36_L 0.83 0.21 0.01
156_H 179_Y 0.83 0.20 0.01
321_G 8_I 0.83 0.20 0.01
508_E 170_P 0.83 0.20 0.01
369_E 61_I 0.83 0.20 0.01
325_L 6_L 0.82 0.20 0.01
501_T 49_P 0.82 0.20 0.01
173_A 177_H 0.82 0.20 0.01
540_C 117_K 0.82 0.20 0.01
47_V 220_P 0.82 0.20 0.01
54_A 96_F 0.82 0.20 0.01
230_V 65_C 0.81 0.20 0.01
112_V 68_M 0.81 0.20 0.01
135_H 207_V 0.81 0.20 0.01
450_A 25_F 0.81 0.20 0.01
284_E 155_Y 0.81 0.20 0.01
78_C 216_K 0.81 0.20 0.01
178_E 91_E 0.81 0.20 0.01
242_I 200_G 0.81 0.20 0.01
132_T 61_I 0.81 0.20 0.01
346_K 190_E 0.81 0.19 0.01
15_G 150_N 0.81 0.19 0.01
469_T 69_V 0.81 0.19 0.01
200_Y 177_H 0.81 0.19 0.01
117_F 191_R 0.81 0.19 0.01
347_E 140_A 0.81 0.19 0.01
186_A 140_A 0.81 0.19 0.01
286_G 152_G 0.81 0.19 0.01
10_I 100_R 0.80 0.19 0.01
127_F 59_M 0.80 0.19 0.01
97_L 60_A 0.80 0.19 0.01
136_M 58_R 0.80 0.19 0.01
237_L 175_L 0.80 0.19 0.01
136_M 200_G 0.80 0.19 0.01
463_G 53_Y 0.80 0.19 0.01
369_E 100_R 0.80 0.19 0.01
327_E 221_A 0.80 0.19 0.01
522_S 193_A 0.80 0.19 0.01
10_I 53_Y 0.80 0.19 0.01
208_I 56_S 0.80 0.19 0.01
527_K 138_Q 0.80 0.19 0.01
540_C 88_M 0.80 0.19 0.01
328_R 93_L 0.80 0.19 0.01
382_S 120_I 0.80 0.19 0.00
457_G 228_K 0.80 0.19 0.00
216_M 52_S 0.80 0.19 0.00
454_D 140_A 0.80 0.18 0.00
426_I 119_Y 0.80 0.18 0.00
299_W 66_G 0.80 0.18 0.00
347_E 46_N 0.79 0.18 0.00
56_V 52_S 0.79 0.18 0.00
408_G 8_I 0.79 0.18 0.00
135_H 216_K 0.79 0.18 0.00
177_M 107_T 0.79 0.18 0.00
455_E 7_K 0.79 0.18 0.00
204_T 58_R 0.79 0.18 0.00
464_C 52_S 0.79 0.18 0.00
10_I 36_L 0.79 0.18 0.00
355_A 115_A 0.79 0.18 0.00
88_H 125_R 0.79 0.18 0.00
491_R 10_V 0.78 0.18 0.00
162_L 115_A 0.78 0.18 0.00
189_V 50_D 0.78 0.18 0.00
424_A 83_D 0.78 0.18 0.00
6_A 49_P 0.78 0.18 0.00
515_V 100_R 0.78 0.18 0.00
473_M 66_G 0.78 0.18 0.00
33_I 124_S 0.78 0.18 0.00
514_N 50_D 0.78 0.17 0.00
473_M 9_E 0.78 0.17 0.00
71_V 120_I 0.77 0.17 0.00
208_I 59_M 0.77 0.17 0.00
369_E 167_F 0.77 0.17 0.00
503_L 100_R 0.77 0.17 0.00
56_V 145_F 0.77 0.17 0.00
2_Q 4_K 0.77 0.17 0.00
204_T 45_D 0.77 0.17 0.00
213_G 64_S 0.77 0.17 0.00
56_V 229_V 0.77 0.17 0.00
135_H 59_M 0.77 0.17 0.00
127_F 35_S 0.77 0.17 0.00
202_Y 65_C 0.76 0.17 0.00
256_V 51_L 0.76 0.17 0.00
35_L 43_I 0.76 0.17 0.00
287_P 115_A 0.76 0.17 0.00
93_E 219_D 0.76 0.17 0.00
33_I 36_L 0.76 0.17 0.00
508_E 50_D 0.76 0.17 0.00
171_L 135_T 0.76 0.17 0.00
347_E 167_F 0.76 0.17 0.00
45_H 64_S 0.76 0.17 0.00
35_L 114_E 0.76 0.17 0.00
416_A 111_E 0.76 0.17 0.00
88_H 72_V 0.76 0.17 0.00
355_A 81_L 0.76 0.17 0.00
548_F 94_A 0.76 0.17 0.00
240_S 58_R 0.76 0.17 0.00
228_E 77_C 0.76 0.17 0.00
127_F 142_Y 0.76 0.16 0.00
415_A 167_F 0.76 0.16 0.00
36_I 79_T 0.76 0.16 0.00
228_E 57_C 0.75 0.16 0.00
228_E 62_C 0.75 0.16 0.00
323_K 103_V 0.75 0.16 0.00
155_E 184_R 0.75 0.16 0.00
284_E 159_P 0.75 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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