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OPENSEQ.org
1qop
Genes: A B A+B
Length: 268 396 650
Sequences: 1769 4674 1355
Seq/Len: 6.6 11.8 2.08
MirrorTree (Pazo et al. 2001) 0.29
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 0.00 0.00 1.61
2 0.00 0.00 1.69
5 0.00 0.01 1.72
10 0.00 0.01 1.77
20 0.00 0.02 1.78
100 0.00 0.06 1.84
∞ 0.01 0.20 2.04
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
108_N 274_R 2.40 1.00 0.99
58_L 173_L 2.10 0.99 0.98
135_E 7_Y 2.03 0.99 0.97
103_A 277_I 1.96 0.99 0.96
107_F 282_K 1.71 0.96 0.92
77_T 290_D 1.40 0.88 0.78
107_F 277_I 1.37 0.86 0.75
134_E 21_M 1.34 0.84 0.72
58_L 17_P 1.24 0.77 0.63
78_P 290_D 1.23 0.76 0.62
65_Q 171_E 1.21 0.75 0.60
58_L 196_Y 1.12 0.67 0.50
79_A 290_D 1.11 0.66 0.49
180_S 181_E 0.93 0.45 0.28
33_S 59_T 0.81 0.33 0.18
201_K 216_L 0.80 0.32 0.17
37_I 15_Y 0.80 0.32 0.17
159_D 22_P 0.80 0.31 0.17
79_A 289_A 0.79 0.31 0.16
54_F 293_I 0.79 0.30 0.16
43_A 313_A 0.79 0.30 0.16
58_L 278_Y 0.78 0.30 0.15
85_L 47_L 0.77 0.29 0.15
236_A 194_H 0.77 0.28 0.15
129_A 17_P 0.76 0.28 0.14
182_V 128_K 0.75 0.27 0.14
62_P 242_D 0.72 0.25 0.12
232_I 327_T 0.71 0.24 0.11
159_D 386_V 0.71 0.23 0.11
169_Y 257_G 0.71 0.23 0.11
63_T 338_L 0.70 0.23 0.10
59_A 84_A 0.70 0.23 0.10
35_K 29_E 0.70 0.23 0.10
111_I 173_L 0.68 0.22 0.10
134_E 25_N 0.67 0.21 0.09
177_L 19_I 0.67 0.21 0.09
157_N 19_I 0.67 0.21 0.09
182_V 122_S 0.67 0.21 0.09
37_I 326_I 0.67 0.20 0.09
198_E 42_A 0.66 0.20 0.09
48_L 368_E 0.65 0.19 0.08
83_E 213_A 0.65 0.19 0.08
23_V 8_F 0.65 0.19 0.08
80_Q 290_D 0.64 0.19 0.08
155_P 351_S 0.64 0.19 0.08
40_L 345_I 0.64 0.18 0.08
192_P 326_I 0.64 0.18 0.07
198_E 329_D 0.63 0.18 0.07
60_D 11_F 0.63 0.18 0.07
28_P 24_L 0.63 0.18 0.07
180_S 180_Y 0.63 0.18 0.07
12_N 39_E 0.63 0.17 0.07
137_A 5_N 0.62 0.17 0.07
243_K 29_E 0.62 0.17 0.07
143_A 293_I 0.61 0.17 0.07
231_A 94_A 0.61 0.17 0.07
200_L 383_I 0.61 0.17 0.07
4_Y 173_L 0.61 0.17 0.07
264_A 318_I 0.61 0.16 0.06
116_A 366_E 0.60 0.16 0.06
241_I 125_L 0.60 0.16 0.06
157_N 180_Y 0.59 0.16 0.06
113_A 62_Q 0.59 0.15 0.06
174_T 156_I 0.59 0.15 0.06
201_K 162_S 0.59 0.15 0.06
22_F 71_T 0.59 0.15 0.06
202_E 131_I 0.59 0.15 0.06
214_I 5_N 0.58 0.15 0.06
82_F 245_N 0.58 0.15 0.06
160_D 154_E 0.58 0.15 0.06
195_H 313_A 0.58 0.15 0.05
107_F 15_Y 0.58 0.15 0.05
109_N 267_G 0.58 0.15 0.05
105_L 20_L 0.58 0.14 0.05
162_L 18_Q 0.57 0.14 0.05
99_L 80_L 0.57 0.14 0.05
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
5927 3.11 1qop A vs B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
1215 2.08 1qop Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.99 Done - Shared
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