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OPENSEQ.org
C D jackhammer
Genes: A B A+B
Length: 250 246 462
Sequences: 282 302 196
Seq/Len: 1.13 1.23 0.42
MirrorTree (Pazo et al. 2001) 0.75
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 0.06 0.00 0.39
2 0.06 0.00 0.40
5 0.06 0.00 0.40
10 0.06 0.00 0.40
20 0.06 0.00 0.40
100 0.06 0.00 0.40
∞ 0.06 0.01 0.40
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
187_A 200_V 1.55 0.55 0.00
21_A 188_D 1.47 0.49 0.00
65_G 137_I 1.45 0.47 0.00
102_A 164_M 1.45 0.47 0.00
94_A 60_R 1.39 0.43 0.00
44_V 167_A 1.31 0.37 0.00
125_T 93_V 1.30 0.37 0.00
103_A 167_A 1.20 0.30 0.00
81_I 84_I 1.20 0.30 0.00
139_S 128_I 1.18 0.29 0.00
54_K 187_D 1.15 0.27 0.00
137_N 84_I 1.14 0.27 0.00
139_S 174_I 1.09 0.24 0.00
147_A 166_R 1.09 0.24 0.00
138_S 155_I 1.08 0.23 0.00
83_A 107_D 1.07 0.23 0.00
70_L 153_V 1.07 0.23 0.00
205_L 64_F 1.06 0.22 0.00
50_S 86_R 1.05 0.22 0.00
181_N 31_L 1.04 0.21 0.00
158_L 80_A 1.03 0.21 0.00
96_T 54_K 1.03 0.20 0.00
22_A 140_D 1.02 0.20 0.00
167_N 67_L 1.02 0.20 0.00
148_A 36_S 1.02 0.20 0.00
99_A 136_K 1.02 0.20 0.00
132_N 113_T 1.01 0.20 0.00
70_L 125_L 1.01 0.20 0.00
167_N 164_M 1.01 0.20 0.00
210_N 212_L 1.01 0.20 0.00
51_K 137_I 1.00 0.19 0.00
59_K 181_N 1.00 0.19 0.00
136_N 236_M 1.00 0.19 0.00
124_G 63_R 0.99 0.19 0.00
181_N 57_E 0.98 0.18 0.00
98_S 233_A 0.98 0.18 0.00
130_L 137_I 0.98 0.18 0.00
96_T 44_S 0.98 0.18 0.00
23_Q 174_I 0.98 0.18 0.00
151_G 181_N 0.97 0.18 0.00
189_S 55_K 0.97 0.18 0.00
146_V 164_M 0.96 0.18 0.00
70_L 200_V 0.95 0.17 0.00
62_N 238_F 0.95 0.17 0.00
177_V 140_D 0.95 0.17 0.00
88_Q 243_S 0.95 0.17 0.00
28_E 63_R 0.94 0.17 0.00
62_N 124_Y 0.94 0.17 0.00
18_M 123_R 0.94 0.17 0.00
125_T 155_I 0.94 0.17 0.00
139_S 175_G 0.94 0.17 0.00
74_K 130_M 0.93 0.16 0.00
160_I 41_M 0.93 0.16 0.00
65_G 238_F 0.93 0.16 0.00
44_V 169_K 0.93 0.16 0.00
139_S 54_K 0.93 0.16 0.00
117_D 67_L 0.93 0.16 0.00
44_V 88_A 0.92 0.16 0.00
107_A 28_L 0.92 0.16 0.00
74_K 82_A 0.92 0.16 0.00
62_N 135_Y 0.91 0.15 0.00
12_F 178_V 0.91 0.15 0.00
48_Q 163_V 0.90 0.15 0.00
157_N 207_K 0.90 0.15 0.00
99_A 111_V 0.90 0.15 0.00
63_N 24_A 0.90 0.15 0.00
95_I 27_C 0.90 0.15 0.00
158_L 96_E 0.90 0.15 0.00
104_T 133_R 0.90 0.15 0.00
68_G 30_L 0.90 0.15 0.00
148_A 51_V 0.90 0.15 0.00
29_K 106_A 0.89 0.15 0.00
178_S 63_R 0.89 0.15 0.00
166_K 188_D 0.89 0.15 0.00
88_Q 188_D 0.89 0.15 0.00
25_G 98_V 0.89 0.15 0.00
100_G 212_L 0.89 0.15 0.00
138_S 147_I 0.89 0.15 0.00
57_D 136_K 0.88 0.14 0.00
105_V 65_A 0.88 0.14 0.00
38_G 43_I 0.88 0.14 0.00
148_A 35_P 0.88 0.14 0.00
14_L 87_Q 0.88 0.14 0.00
130_L 42_A 0.88 0.14 0.00
65_G 56_V 0.88 0.14 0.00
177_V 31_L 0.87 0.14 0.00
74_K 110_L 0.87 0.14 0.00
92_A 149_V 0.87 0.14 0.00
74_K 59_I 0.86 0.14 0.00
71_S 174_I 0.86 0.14 0.00
230_T 240_F 0.86 0.14 0.00
174_T 81_L 0.86 0.14 0.00
44_V 45_A 0.86 0.14 0.00
86_G 97_H 0.86 0.14 0.00
90_D 90_W 0.86 0.14 0.00
70_L 167_A 0.86 0.14 0.00
38_G 146_K 0.85 0.14 0.00
135_A 178_V 0.85 0.13 0.00
20_V 64_F 0.85 0.13 0.00
221_A 27_C 0.85 0.13 0.00
15_A 88_A 0.85 0.13 0.00
202_A 71_K 0.85 0.13 0.00
114_E 31_L 0.85 0.13 0.00
95_I 201_L 0.84 0.13 0.00
96_T 174_I 0.84 0.13 0.00
8_K 86_R 0.84 0.13 0.00
203_G 50_A 0.84 0.13 0.00
162_T 154_E 0.84 0.13 0.00
79_A 194_N 0.84 0.13 0.00
81_I 136_K 0.84 0.13 0.00
168_V 228_R 0.84 0.13 0.00
100_G 164_M 0.83 0.13 0.00
20_V 188_D 0.83 0.13 0.00
52_D 50_A 0.83 0.13 0.00
18_M 217_P 0.83 0.13 0.00
8_K 221_K 0.83 0.13 0.00
94_A 62_R 0.83 0.13 0.00
137_N 34_G 0.83 0.13 0.00
117_D 175_G 0.83 0.13 0.00
183_F 91_L 0.83 0.13 0.00
65_G 174_I 0.83 0.12 0.00
227_Q 130_M 0.82 0.12 0.00
105_V 109_D 0.82 0.12 0.00
67_N 167_A 0.82 0.12 0.00
111_I 46_M 0.82 0.12 0.00
127_N 78_A 0.82 0.12 0.00
160_I 178_V 0.82 0.12 0.00
165_G 92_D 0.82 0.12 0.00
51_K 108_Q 0.82 0.12 0.00
9_P 173_Y 0.82 0.12 0.00
68_G 27_C 0.82 0.12 0.00
201_N 153_V 0.82 0.12 0.00
92_A 234_E 0.82 0.12 0.00
5_M 94_D 0.82 0.12 0.00
52_D 140_D 0.82 0.12 0.00
58_T 67_L 0.81 0.12 0.00
217_V 130_M 0.81 0.12 0.00
39_T 203_E 0.81 0.12 0.00
109_A 141_T 0.81 0.12 0.00
27_A 109_D 0.81 0.12 0.00
68_G 84_I 0.81 0.12 0.00
209_N 80_A 0.81 0.12 0.00
81_I 67_L 0.80 0.12 0.00
193_Y 27_C 0.80 0.12 0.00
57_D 103_L 0.80 0.12 0.00
191_H 144_T 0.80 0.12 0.00
219_V 112_R 0.80 0.12 0.00
81_I 51_V 0.80 0.12 0.00
159_A 110_L 0.80 0.12 0.00
193_Y 36_S 0.80 0.12 0.00
9_P 206_D 0.80 0.12 0.00
72_N 106_A 0.80 0.12 0.00
231_L 63_R 0.80 0.12 0.00
95_I 132_A 0.80 0.12 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
7916 0.42 C D jackhammer Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7908 0.13 C D Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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