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OPENSEQ.org
mf_cyB5_p450
Genes: A B A+B
Length: 111 465 543
Sequences: 977 19894 57
Seq/Len: 8.8 42.78 0.1
MirrorTree (Pazo et al. 2001) 0.20
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 0.09 0.01
2 0.03 0.10 0.01
5 0.03 0.12 0.03
10 0.03 0.14 0.06
20 0.03 0.16 0.10
100 0.03 0.22 0.41
∞ 0.07 0.28 0.82
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
45_S 222_K 1.84 0.33 0.00
39_G 388_R 1.73 0.29 0.00
64_D 413_C 1.65 0.26 0.00
60_F 413_C 1.46 0.19 0.00
28_D 404_F 1.43 0.18 0.00
25_D 65_V 1.37 0.17 0.00
36_A 415_G 1.29 0.14 0.00
37_I 127_V 1.28 0.14 0.00
86_L 100_R 1.27 0.14 0.00
25_D 295_T 1.26 0.14 0.00
27_S 370_I 1.25 0.13 0.00
31_K 351_R 1.25 0.13 0.00
24_Y 112_L 1.24 0.13 0.00
25_D 265_V 1.22 0.13 0.00
24_Y 264_D 1.18 0.12 0.00
34_L 300_R 1.18 0.12 0.00
42_Y 261_S 1.17 0.12 0.00
21_L 334_R 1.15 0.11 0.00
44_V 334_R 1.15 0.11 0.00
57_Y 334_R 1.15 0.11 0.00
62_G 334_R 1.15 0.11 0.00
97_W 334_R 1.15 0.11 0.00
105_Y 334_R 1.15 0.11 0.00
109_G 334_R 1.15 0.11 0.00
51_Y 406_F 1.15 0.11 0.00
45_S 372_R 1.11 0.10 0.00
67_R 275_G 1.11 0.10 0.00
86_L 413_C 1.11 0.10 0.00
37_I 192_P 1.10 0.10 0.00
34_L 359_A 1.09 0.10 0.00
42_Y 295_T 1.09 0.10 0.00
17_S 278_E 1.08 0.10 0.00
21_L 413_C 1.07 0.10 0.00
44_V 413_C 1.07 0.10 0.00
57_Y 413_C 1.07 0.10 0.00
62_G 413_C 1.07 0.10 0.00
97_W 413_C 1.07 0.10 0.00
105_Y 413_C 1.07 0.10 0.00
109_G 413_C 1.07 0.10 0.00
41_I 244_S 1.06 0.10 0.00
21_L 331_E 1.06 0.10 0.00
44_V 331_E 1.06 0.10 0.00
57_Y 331_E 1.06 0.10 0.00
62_G 331_E 1.06 0.10 0.00
97_W 331_E 1.06 0.10 0.00
105_Y 331_E 1.06 0.10 0.00
109_G 331_E 1.06 0.10 0.00
58_A 390_S 1.05 0.09 0.00
21_L 386_P 1.05 0.09 0.00
44_V 386_P 1.05 0.09 0.00
57_Y 386_P 1.05 0.09 0.00
62_G 386_P 1.05 0.09 0.00
97_W 386_P 1.05 0.09 0.00
105_Y 386_P 1.05 0.09 0.00
109_G 386_P 1.05 0.09 0.00
45_S 338_P 1.04 0.09 0.00
54_G 333_L 1.04 0.09 0.00
21_L 415_G 1.04 0.09 0.00
44_V 415_G 1.04 0.09 0.00
57_Y 415_G 1.04 0.09 0.00
62_G 415_G 1.04 0.09 0.00
97_W 415_G 1.04 0.09 0.00
105_Y 415_G 1.04 0.09 0.00
109_G 415_G 1.04 0.09 0.00
53_P 419_A 1.04 0.09 0.00
45_S 54_V 1.03 0.09 0.00
36_A 386_P 1.03 0.09 0.00
42_Y 380_D 1.03 0.09 0.00
21_L 388_R 1.03 0.09 0.00
44_V 388_R 1.03 0.09 0.00
57_Y 388_R 1.03 0.09 0.00
62_G 388_R 1.03 0.09 0.00
97_W 388_R 1.03 0.09 0.00
105_Y 388_R 1.03 0.09 0.00
109_G 388_R 1.03 0.09 0.00
68_A 192_P 1.02 0.09 0.00
21_L 409_G 1.02 0.09 0.00
44_V 409_G 1.02 0.09 0.00
57_Y 409_G 1.02 0.09 0.00
62_G 409_G 1.02 0.09 0.00
97_W 409_G 1.02 0.09 0.00
105_Y 409_G 1.02 0.09 0.00
109_G 409_G 1.02 0.09 0.00
110_T 97_A 1.02 0.09 0.00
16_I 117_P 1.00 0.09 0.00
90_E 349_E 1.00 0.09 0.00
45_S 387_E 1.00 0.09 0.00
26_G 334_R 0.99 0.08 0.00
60_F 406_F 0.99 0.08 0.00
45_S 362_I 0.98 0.08 0.00
42_Y 175_L 0.98 0.08 0.00
67_R 41_G 0.97 0.08 0.00
64_D 334_R 0.97 0.08 0.00
17_S 421_I 0.97 0.08 0.00
17_S 130_W 0.96 0.08 0.00
42_Y 434_F 0.96 0.08 0.00
22_K 310_G 0.96 0.08 0.00
86_L 337_P 0.96 0.08 0.00
45_S 100_R 0.95 0.08 0.00
27_S 54_V 0.95 0.08 0.00
55_G 275_G 0.94 0.08 0.00
100_K 327_M 0.93 0.08 0.00
45_S 403_F 0.93 0.07 0.00
39_G 386_P 0.93 0.07 0.00
63_K 206_K 0.93 0.07 0.00
65_A 413_C 0.93 0.07 0.00
51_Y 334_R 0.92 0.07 0.00
45_S 391_K 0.92 0.07 0.00
43_D 334_R 0.92 0.07 0.00
38_K 337_P 0.92 0.07 0.00
90_E 292_S 0.92 0.07 0.00
30_K 164_S 0.92 0.07 0.00
72_M 112_L 0.91 0.07 0.00
19_E 335_L 0.91 0.07 0.00
21_L 384_F 0.91 0.07 0.00
44_V 384_F 0.91 0.07 0.00
57_Y 384_F 0.91 0.07 0.00
62_G 384_F 0.91 0.07 0.00
97_W 384_F 0.91 0.07 0.00
105_Y 384_F 0.91 0.07 0.00
109_G 384_F 0.91 0.07 0.00
87_G 132_R 0.90 0.07 0.00
42_Y 128_N 0.90 0.07 0.00
64_D 337_P 0.90 0.07 0.00
80_T 55_H 0.90 0.07 0.00
26_G 413_C 0.90 0.07 0.00
17_S 300_R 0.90 0.07 0.00
25_D 206_K 0.89 0.07 0.00
111_V 107_F 0.89 0.07 0.00
26_G 331_E 0.89 0.07 0.00
65_A 265_V 0.89 0.07 0.00
71_K 59_P 0.89 0.07 0.00
26_G 386_P 0.89 0.07 0.00
25_D 37_I 0.89 0.07 0.00
42_Y 333_L 0.88 0.07 0.00
16_I 218_G 0.88 0.07 0.00
64_D 331_E 0.88 0.07 0.00
59_L 297_W 0.88 0.07 0.00
52_G 413_C 0.88 0.07 0.00
42_Y 181_L 0.88 0.07 0.00
42_Y 382_N 0.88 0.07 0.00
26_G 415_G 0.88 0.07 0.00
22_K 356_T 0.87 0.07 0.00
37_I 301_A 0.87 0.07 0.00
108_V 307_K 0.87 0.07 0.00
90_E 142_L 0.87 0.07 0.00
68_A 154_D 0.87 0.07 0.00
64_D 386_P 0.87 0.07 0.00
61_A 409_G 0.87 0.07 0.00
39_G 280_T 0.86 0.07 0.00
85_G 257_E 0.86 0.07 0.00
45_S 138_G 0.86 0.07 0.00
64_D 415_G 0.86 0.07 0.00
17_S 283_L 0.86 0.07 0.00
26_G 409_G 0.86 0.07 0.00
42_Y 185_V 0.86 0.07 0.00
86_L 279_T 0.86 0.07 0.00
17_S 332_V 0.86 0.07 0.00
26_G 388_R 0.85 0.07 0.00
24_Y 88_I 0.85 0.07 0.00
91_L 410_P 0.85 0.07 0.00
92_E 66_F 0.85 0.07 0.00
90_E 346_I 0.85 0.07 0.00
21_L 406_F 0.85 0.06 0.00
44_V 406_F 0.85 0.06 0.00
57_Y 406_F 0.85 0.06 0.00
62_G 406_F 0.85 0.06 0.00
97_W 406_F 0.85 0.06 0.00
105_Y 406_F 0.85 0.06 0.00
109_G 406_F 0.85 0.06 0.00
64_D 409_G 0.85 0.06 0.00
17_S 49_G 0.85 0.06 0.00
27_S 336_Y 0.84 0.06 0.00
95_Q 273_Y 0.84 0.06 0.00
18_E 29_V 0.84 0.06 0.00
79_L 55_H 0.83 0.06 0.00
89_F 72_I 0.83 0.06 0.00
36_A 338_P 0.83 0.06 0.00
64_D 388_R 0.83 0.06 0.00
61_A 275_G 0.83 0.06 0.00
26_G 360_G 0.83 0.06 0.00
25_D 370_I 0.83 0.06 0.00
101_F 363_L 0.83 0.06 0.00
43_D 413_C 0.83 0.06 0.00
24_Y 246_S 0.83 0.06 0.00
51_Y 331_E 0.83 0.06 0.00
51_Y 413_C 0.82 0.06 0.00
17_S 34_Y 0.82 0.06 0.00
48_R 320_S 0.82 0.06 0.00
43_D 331_E 0.82 0.06 0.00
76_E 63_K 0.82 0.06 0.00
91_L 96_W 0.82 0.06 0.00
43_D 386_P 0.82 0.06 0.00
22_K 57_M 0.82 0.06 0.00
41_I 310_G 0.82 0.06 0.00
54_G 428_S 0.82 0.06 0.00
58_A 387_E 0.82 0.06 0.00
101_F 304_E 0.82 0.06 0.00
90_E 300_R 0.81 0.06 0.00
95_Q 147_Y 0.81 0.06 0.00
51_Y 386_P 0.81 0.06 0.00
60_F 334_R 0.81 0.06 0.00
111_V 339_A 0.81 0.06 0.00
41_I 58_D 0.81 0.06 0.00
82_D 206_K 0.81 0.06 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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