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OPENSEQ.org
1qop A vs B
Genes: A B A+B
Length: 268 396 609
Sequences: 2733 5701 1894
Seq/Len: 10.2 14.4 3.11
MirrorTree (Pazo et al. 2001) 0.69
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 2.60
2 0.08 0.03 2.69
5 0.08 0.04 2.75
10 0.08 0.04 2.83
20 0.08 0.04 2.85
100 0.08 0.06 2.89
∞ 0.09 0.18 3.13
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 2.77 1.00 1.00
58_L 173_L 2.61 1.00 1.00
103_A 277_I 1.91 0.99 0.98
107_F 282_K 1.58 0.97 0.92
79_A 290_D 1.49 0.96 0.90
78_P 290_D 1.41 0.94 0.86
77_T 290_D 1.36 0.92 0.84
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 1.06 0.72 0.58
58_L 196_Y 0.85 0.47 0.32
95_I 182_T 0.82 0.44 0.28
54_F 293_I 0.81 0.42 0.28
33_S 59_T 0.79 0.40 0.26
157_N 180_Y 0.76 0.36 0.22
37_I 326_I 0.75 0.35 0.21
198_E 329_D 0.74 0.35 0.21
138_P 282_K 0.74 0.34 0.20
107_F 281_M 0.73 0.34 0.20
43_A 313_A 0.72 0.32 0.19
215_S 339_C 0.70 0.29 0.17
58_L 169_C 0.67 0.27 0.15
65_Q 174_R 0.67 0.27 0.15
59_A 84_A 0.67 0.27 0.15
116_A 367_K 0.67 0.27 0.15
77_T 322_D 0.67 0.26 0.14
223_A 257_G 0.65 0.25 0.14
107_F 275_V 0.65 0.25 0.13
221_S 206_M 0.64 0.24 0.13
62_P 242_D 0.64 0.24 0.13
71_A 173_L 0.64 0.24 0.12
180_S 180_Y 0.63 0.23 0.12
79_A 199_I 0.63 0.23 0.12
179_R 279_F 0.63 0.23 0.12
180_S 178_G 0.63 0.23 0.12
174_T 156_I 0.63 0.23 0.12
255_L 125_L 0.63 0.23 0.12
185_A 178_G 0.63 0.23 0.12
19_F 196_Y 0.62 0.23 0.12
108_N 212_K 0.62 0.22 0.11
262_M 125_L 0.61 0.22 0.11
131_V 58_L 0.61 0.21 0.11
205_A 241_A 0.61 0.21 0.10
100_L 174_R 0.61 0.21 0.10
108_N 131_I 0.61 0.21 0.10
155_P 180_Y 0.60 0.21 0.10
238_V 173_L 0.60 0.21 0.10
123_V 52_A 0.60 0.21 0.10
180_S 122_S 0.60 0.20 0.10
162_L 89_Q 0.60 0.20 0.10
147_N 126_G 0.60 0.20 0.10
156_P 196_Y 0.60 0.20 0.10
158_A 90_V 0.60 0.20 0.10
4_Y 173_L 0.59 0.20 0.10
20_V 179_S 0.59 0.20 0.10
158_A 263_T 0.59 0.20 0.10
89_R 97_A 0.59 0.20 0.10
154_C 339_C 0.59 0.19 0.09
12_N 212_K 0.58 0.19 0.09
58_L 278_Y 0.58 0.19 0.09
81_C 87_T 0.58 0.19 0.09
120_Q 217_D 0.58 0.19 0.09
126_V 351_S 0.58 0.19 0.09
129_A 281_M 0.58 0.19 0.09
258_F 257_G 0.58 0.19 0.09
80_Q 290_D 0.58 0.19 0.09
231_A 242_D 0.58 0.19 0.09
33_S 149_R 0.58 0.18 0.09
108_N 287_Q 0.57 0.18 0.09
43_A 374_N 0.57 0.18 0.09
169_Y 257_G 0.57 0.18 0.09
218_E 388_D 0.57 0.18 0.09
238_V 371_L 0.57 0.18 0.08
177_L 124_L 0.57 0.18 0.08
178_S 106_I 0.56 0.17 0.08
147_N 326_I 0.56 0.17 0.08
166_V 138_V 0.56 0.17 0.08
54_F 191_A 0.55 0.17 0.08
40_L 283_A 0.55 0.17 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
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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