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OPENSEQ.org
1qop-AB
Genes: A B A+B
Length: 265 390 649
Sequences: 2713 13211 1857
Seq/Len: 10.24 33.87 2.86
MirrorTree (Pazo et al. 2001) 0.63
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.04 2.56
2 0.00 0.04 2.67
5 0.00 0.05 2.71
10 0.00 0.06 2.81
20 0.00 0.07 2.84
100 0.00 0.12 2.93
∞ 0.00 0.17 3.21
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 2.71 1.00 1.00
58_L 173_L 2.44 1.00 1.00
135_E 7_Y 2.20 1.00 0.99
103_A 277_I 1.81 0.99 0.96
134_E 21_M 1.55 0.96 0.91
107_F 282_K 1.54 0.96 0.91
79_A 290_D 1.36 0.91 0.82
77_T 290_D 1.35 0.91 0.82
107_F 277_I 1.29 0.88 0.78
78_P 290_D 1.29 0.88 0.77
58_L 17_P 1.19 0.82 0.69
65_Q 171_E 1.19 0.81 0.69
58_L 196_Y 0.98 0.61 0.46
180_S 181_E 0.98 0.61 0.46
79_A 289_A 0.97 0.60 0.45
157_N 19_I 0.95 0.57 0.41
137_A 5_N 0.91 0.52 0.37
33_S 59_T 0.79 0.37 0.23
225_G 82_G 0.72 0.30 0.17
213_S 339_C 0.72 0.30 0.17
177_L 19_I 0.71 0.29 0.16
77_T 322_D 0.71 0.29 0.16
107_F 281_M 0.70 0.28 0.16
43_A 313_A 0.68 0.26 0.14
117_R 15_Y 0.67 0.25 0.13
129_A 17_P 0.66 0.25 0.13
196_E 329_D 0.66 0.25 0.13
54_F 293_I 0.66 0.24 0.13
178_S 283_A 0.66 0.24 0.13
123_V 52_A 0.65 0.24 0.12
40_L 345_I 0.65 0.23 0.12
62_P 242_D 0.64 0.23 0.12
59_A 84_A 0.64 0.23 0.12
76_V 15_Y 0.64 0.23 0.12
180_S 122_S 0.64 0.23 0.11
42_D 275_V 0.63 0.22 0.11
58_L 169_C 0.63 0.22 0.11
65_Q 174_R 0.63 0.22 0.11
58_L 278_Y 0.63 0.22 0.11
166_V 138_V 0.63 0.21 0.11
158_A 263_T 0.63 0.21 0.11
157_N 180_Y 0.63 0.21 0.11
22_F 257_G 0.62 0.21 0.11
176_L 283_A 0.62 0.21 0.10
116_A 367_K 0.62 0.21 0.10
139_F 84_A 0.62 0.21 0.10
93_P 189_T 0.62 0.21 0.10
145_R 367_K 0.61 0.20 0.10
92_H 189_T 0.61 0.20 0.10
219_S 206_M 0.61 0.20 0.10
225_G 120_L 0.61 0.20 0.10
182_V 128_K 0.61 0.20 0.10
131_V 58_L 0.60 0.20 0.09
35_K 29_E 0.60 0.19 0.09
100_L 174_R 0.60 0.19 0.09
260_M 212_K 0.60 0.19 0.09
159_D 22_P 0.59 0.19 0.09
169_Y 257_G 0.59 0.18 0.09
200_E 131_I 0.59 0.18 0.09
185_A 178_G 0.59 0.18 0.09
178_S 106_I 0.58 0.18 0.09
128_V 251_L 0.58 0.18 0.08
111_I 173_L 0.58 0.18 0.08
134_E 25_N 0.58 0.18 0.08
182_V 191_A 0.58 0.18 0.08
37_I 326_I 0.58 0.18 0.08
177_L 124_L 0.58 0.18 0.08
147_N 126_G 0.57 0.17 0.08
85_L 47_L 0.57 0.17 0.08
31_E 4_L 0.57 0.17 0.08
230_I 17_P 0.57 0.17 0.08
95_I 38_P 0.57 0.17 0.08
89_R 97_A 0.57 0.17 0.08
180_S 178_G 0.56 0.17 0.07
219_S 368_E 0.56 0.17 0.07
180_S 180_Y 0.56 0.17 0.07
65_Q 160_S 0.56 0.17 0.07
162_L 89_Q 0.56 0.16 0.07
107_F 15_Y 0.55 0.16 0.07
37_I 15_Y 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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