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OPENSEQ.org
1QOP
Genes: A B A+B
Length: 265 390 603
Sequences: 2746 6214 1883
Seq/Len: 10.36 15.93 3.12
MirrorTree (Pazo et al. 2001) 0.66
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 0.08 0.03 2.64
2 0.08 0.03 2.72
5 0.08 0.03 2.77
10 0.08 0.04 2.87
20 0.08 0.04 2.87
100 0.08 0.06 2.93
∞ 0.09 0.18 3.20
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 2.78 1.00 1.00
58_L 173_L 2.60 1.00 1.00
103_A 277_I 1.95 1.00 0.98
107_F 282_K 1.58 0.97 0.93
79_A 290_D 1.46 0.95 0.89
78_P 290_D 1.36 0.92 0.83
77_T 290_D 1.34 0.91 0.82
65_Q 171_E 1.26 0.88 0.77
107_F 277_I 1.20 0.84 0.72
79_A 289_A 1.15 0.80 0.67
180_S 181_E 1.07 0.73 0.59
58_L 196_Y 0.84 0.47 0.31
33_S 59_T 0.77 0.38 0.23
54_F 293_I 0.77 0.38 0.23
138_P 282_K 0.76 0.37 0.23
107_F 281_M 0.76 0.37 0.23
77_T 322_D 0.75 0.35 0.21
95_I 182_T 0.74 0.34 0.20
43_A 313_A 0.73 0.34 0.20
157_N 180_Y 0.73 0.33 0.19
116_A 367_K 0.71 0.31 0.18
123_V 52_A 0.71 0.30 0.17
213_S 339_C 0.69 0.29 0.17
108_N 131_I 0.69 0.29 0.16
62_P 242_D 0.68 0.27 0.15
37_I 326_I 0.67 0.27 0.15
59_A 84_A 0.67 0.27 0.15
58_L 169_C 0.67 0.27 0.14
253_L 125_L 0.65 0.25 0.13
180_S 178_G 0.65 0.25 0.13
107_F 275_V 0.65 0.25 0.13
79_A 199_I 0.64 0.24 0.13
65_Q 174_R 0.64 0.24 0.13
221_A 257_G 0.64 0.24 0.12
179_R 279_F 0.64 0.23 0.12
20_V 179_S 0.63 0.23 0.12
71_A 173_L 0.62 0.22 0.11
180_S 180_Y 0.62 0.22 0.11
108_N 212_K 0.62 0.22 0.11
185_A 178_G 0.62 0.22 0.11
58_L 278_Y 0.62 0.22 0.11
155_P 180_Y 0.61 0.21 0.10
19_F 196_Y 0.61 0.21 0.10
260_M 125_L 0.61 0.21 0.10
236_V 173_L 0.60 0.21 0.10
12_N 212_K 0.60 0.21 0.10
196_E 329_D 0.60 0.21 0.10
131_V 58_L 0.60 0.21 0.10
219_S 206_M 0.60 0.20 0.10
158_A 90_V 0.59 0.20 0.10
100_L 174_R 0.59 0.20 0.10
156_P 196_Y 0.59 0.20 0.10
174_T 99_R 0.59 0.20 0.09
73_A 250_G 0.59 0.20 0.09
216_E 388_D 0.59 0.19 0.09
158_A 263_T 0.59 0.19 0.09
89_R 97_A 0.59 0.19 0.09
180_S 122_S 0.58 0.19 0.09
162_L 89_Q 0.58 0.19 0.09
229_A 242_D 0.58 0.19 0.09
4_Y 173_L 0.58 0.19 0.09
128_V 251_L 0.58 0.19 0.09
81_C 87_T 0.58 0.19 0.09
80_Q 290_D 0.57 0.18 0.09
147_N 126_G 0.57 0.18 0.09
126_V 351_S 0.57 0.18 0.09
33_S 149_R 0.57 0.18 0.09
154_C 339_C 0.57 0.18 0.09
174_T 156_I 0.57 0.18 0.09
177_L 124_L 0.57 0.18 0.09
151_I 73_Y 0.57 0.18 0.09
178_S 106_I 0.57 0.18 0.09
43_A 374_N 0.57 0.18 0.09
129_A 281_M 0.57 0.18 0.08
203_A 241_A 0.56 0.17 0.08
169_Y 257_G 0.56 0.17 0.08
48_L 368_E 0.56 0.17 0.08
108_N 287_Q 0.56 0.17 0.08
67_A 316_N 0.56 0.17 0.08
161_D 66_A 0.56 0.17 0.08
198_L 290_D 0.56 0.17 0.08
265_R 351_S 0.55 0.17 0.07
236_V 371_L 0.55 0.17 0.07
74_A 269_P 0.55 0.16 0.07
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
5091 3.12 1QOP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
2063 2.86 1qop-AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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