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OPENSEQ.org
1I7Q_CB_real
Genes: A B A+B
Length: 192 517 647
Sequences: 16224 3866 1937
Seq/Len: 84.5 7.48 2.99
MirrorTree (Pazo et al. 2001) 0.37
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 0.03 0.01 2.23
2 0.03 0.01 2.36
5 0.03 0.01 2.50
10 0.04 0.01 2.61
20 0.05 0.01 2.73
100 0.12 0.03 2.99
∞ 0.20 0.13 3.72
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
99_Q 255_Q 3.98 1.00 1.00
21_R 376_A 2.52 1.00 1.00
103_I 485_Q 2.29 1.00 0.99
99_Q 251_E 2.08 1.00 0.99
31_R 156_E 1.85 0.99 0.97
18_D 371_A 1.81 0.99 0.97
99_Q 254_R 1.62 0.98 0.93
129_A 360_L 1.42 0.94 0.87
58_G 252_A 1.39 0.93 0.85
174_L 360_L 1.37 0.92 0.84
107_K 486_D 1.17 0.81 0.69
62_E 257_E 0.99 0.64 0.48
58_G 257_E 0.97 0.61 0.46
17_V 376_A 0.95 0.59 0.43
68_E 406_A 0.85 0.47 0.32
27_V 447_G 0.78 0.38 0.24
129_A 423_L 0.78 0.38 0.24
21_R 405_R 0.77 0.37 0.23
128_V 242_Y 0.77 0.37 0.23
27_V 376_A 0.76 0.36 0.22
34_I 157_N 0.75 0.34 0.21
31_R 429_V 0.74 0.34 0.20
173_I 384_L 0.73 0.33 0.20
93_Y 242_Y 0.70 0.29 0.17
103_I 254_R 0.70 0.29 0.17
20_L 401_V 0.70 0.29 0.16
124_N 490_E 0.69 0.28 0.16
65_C 309_L 0.69 0.28 0.16
89_I 374_C 0.69 0.28 0.16
183_E 387_V 0.68 0.27 0.15
129_A 447_G 0.68 0.27 0.15
176_T 390_Y 0.67 0.26 0.14
89_I 402_G 0.67 0.26 0.14
39_I 216_L 0.67 0.26 0.14
152_M 413_A 0.66 0.25 0.14
14_Y 264_S 0.66 0.25 0.14
28_V 207_H 0.66 0.25 0.14
129_A 385_T 0.66 0.25 0.14
18_D 357_A 0.65 0.24 0.13
47_E 453_F 0.65 0.24 0.13
182_L 416_A 0.65 0.24 0.12
72_R 453_F 0.64 0.24 0.12
59_T 255_Q 0.64 0.23 0.12
168_F 128_L 0.63 0.23 0.12
175_T 259_F 0.63 0.22 0.11
125_P 434_L 0.63 0.22 0.11
16_L 176_E 0.61 0.21 0.11
111_I 403_T 0.61 0.21 0.10
13_T 18_P 0.61 0.21 0.10
120_A 248_E 0.61 0.20 0.10
50_V 366_A 0.61 0.20 0.10
166_F 216_L 0.60 0.20 0.10
20_L 124_L 0.60 0.20 0.10
53_L 373_I 0.60 0.20 0.10
80_I 310_K 0.60 0.20 0.10
40_I 472_D 0.60 0.20 0.10
43_L 373_I 0.60 0.20 0.10
51_L 178_L 0.60 0.20 0.10
16_L 496_T 0.59 0.20 0.10
153_V 456_V 0.59 0.20 0.10
119_F 148_A 0.59 0.19 0.09
180_R 241_E 0.59 0.19 0.09
102_E 248_E 0.59 0.19 0.09
151_E 202_A 0.59 0.19 0.09
53_L 318_I 0.58 0.19 0.09
82_I 400_V 0.58 0.19 0.09
127_P 356_L 0.58 0.19 0.09
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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