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OPENSEQ.org
pcp1-cy2
Genes: A B A+B
Length: 90 411 487
Sequences: 5452 9838 281
Seq/Len: 60.58 23.94 0.58
MirrorTree (Pazo et al. 2001) 0.35
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 0.26 0.27 0.37
2 0.31 0.30 0.45
5 0.35 0.33 0.53
10 0.36 0.35 0.55
20 0.36 0.36 0.56
100 0.37 0.37 0.58
∞ 0.39 0.39 0.61
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
42_L 230_A 1.27 0.43 0.00
29_F 238_L 1.18 0.36 0.00
40_T 337_T 1.18 0.35 0.00
31_Q 286_W 1.16 0.34 0.00
55_L 227_A 1.14 0.33 0.00
28_D 233_T 1.10 0.30 0.00
64_L 356_P 1.10 0.30 0.00
63_R 94_K 1.09 0.29 0.00
14_W 44_E 1.09 0.29 0.00
34_G 238_L 1.08 0.29 0.00
5_D 138_I 1.08 0.29 0.00
28_D 2_P 1.06 0.28 0.00
64_L 312_V 1.06 0.27 0.00
36_S 132_D 1.02 0.25 0.00
28_D 116_D 1.01 0.25 0.00
71_L 224_K 1.01 0.25 0.00
14_W 279_T 1.01 0.24 0.00
30_F 215_L 1.01 0.24 0.00
41_R 396_E 1.00 0.24 0.00
14_W 263_D 0.99 0.23 0.00
20_T 377_G 0.99 0.23 0.00
47_H 349_A 0.97 0.22 0.00
53_A 248_A 0.97 0.22 0.00
41_R 223_L 0.97 0.22 0.00
35_D 307_L 0.97 0.22 0.00
35_D 135_S 0.96 0.22 0.00
65_A 254_E 0.96 0.21 0.00
17_L 123_W 0.96 0.21 0.00
2_P 130_L 0.95 0.21 0.00
58_L 224_K 0.94 0.21 0.00
46_L 379_L 0.94 0.20 0.00
28_D 105_W 0.94 0.20 0.00
66_D 393_G 0.94 0.20 0.00
10_V 113_G 0.93 0.20 0.00
45_Q 50_L 0.93 0.20 0.00
36_S 264_R 0.93 0.20 0.00
63_R 115_V 0.93 0.20 0.00
4_G 292_W 0.92 0.20 0.00
10_V 182_Q 0.92 0.20 0.00
67_F 214_A 0.92 0.19 0.00
65_A 156_P 0.92 0.19 0.00
16_Q 288_P 0.92 0.19 0.00
21_G 90_R 0.92 0.19 0.00
49_A 294_H 0.91 0.19 0.00
44_G 50_L 0.90 0.18 0.00
5_D 164_Y 0.90 0.18 0.00
42_L 30_F 0.90 0.18 0.00
68_A 296_A 0.89 0.18 0.00
19_S 183_A 0.89 0.18 0.00
46_L 213_G 0.89 0.18 0.00
50_G 143_L 0.89 0.18 0.00
2_P 194_L 0.88 0.18 0.00
66_D 212_N 0.88 0.18 0.00
34_G 147_Y 0.88 0.18 0.00
1_L 194_L 0.88 0.17 0.00
33_G 132_D 0.88 0.17 0.00
36_S 9_Q 0.88 0.17 0.00
65_A 223_L 0.87 0.17 0.00
10_V 259_L 0.87 0.17 0.00
35_D 194_L 0.87 0.17 0.00
49_A 368_L 0.86 0.17 0.00
46_L 195_P 0.86 0.17 0.00
44_G 31_V 0.86 0.17 0.00
36_S 276_G 0.86 0.17 0.00
42_L 316_R 0.85 0.16 0.00
49_A 100_L 0.85 0.16 0.00
29_F 296_A 0.85 0.16 0.00
46_L 241_V 0.84 0.16 0.00
35_D 239_L 0.84 0.16 0.00
42_L 125_C 0.84 0.16 0.00
73_K 180_W 0.84 0.16 0.00
4_G 146_G 0.83 0.15 0.00
65_A 90_R 0.83 0.15 0.00
67_F 384_D 0.82 0.15 0.00
11_A 38_L 0.82 0.15 0.00
46_L 259_L 0.80 0.14 0.00
12_A 392_A 0.80 0.14 0.00
19_S 159_V 0.80 0.14 0.00
31_Q 344_Q 0.80 0.14 0.00
54_Q 147_Y 0.80 0.14 0.00
4_G 275_L 0.80 0.14 0.00
58_L 146_G 0.80 0.14 0.00
40_T 399_F 0.79 0.14 0.00
51_Y 143_L 0.79 0.14 0.00
66_D 221_H 0.79 0.14 0.00
71_L 317_V 0.79 0.14 0.00
39_A 30_F 0.79 0.14 0.00
34_G 366_V 0.79 0.14 0.00
66_D 179_A 0.79 0.14 0.00
66_D 356_P 0.78 0.14 0.00
28_D 129_L 0.78 0.13 0.00
37_L 309_H 0.78 0.13 0.00
10_V 52_A 0.78 0.13 0.00
71_L 406_L 0.78 0.13 0.00
13_L 40_L 0.78 0.13 0.00
35_D 258_N 0.78 0.13 0.00
23_V 130_L 0.77 0.13 0.00
14_W 7_D 0.77 0.13 0.00
10_V 147_Y 0.77 0.13 0.00
13_L 228_A 0.77 0.13 0.00
45_Q 10_Q 0.77 0.13 0.00
20_T 272_N 0.76 0.13 0.00
53_A 403_C 0.76 0.13 0.00
11_A 275_L 0.76 0.13 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)
ID Seq/Len Name Options I_Prob Status
13028 9.05 pcp1-cy2 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13027 0.58 pcp1-cy2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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