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OPENSEQ.org
subunit_I_PDB_vs_subunit_D
Genes: A B A+B
Length: 357 223 557
Sequences: 1153 812 731
Seq/Len: 3.23 3.64 1.31
MirrorTree (Pazo et al. 2001) 0.77
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 0.01 0.00 0.22
2 0.01 0.00 0.24
5 0.01 0.00 0.31
10 0.01 0.00 1.14
20 0.01 0.00 1.15
100 0.02 0.01 1.18
∞ 0.03 0.03 1.26
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
291_G 7_T 1.71 0.92 0.48
348_L 140_V 1.68 0.91 0.46
272_A 96_V 1.49 0.83 0.31
92_G 105_K 1.32 0.71 0.20
349_N 8_R 1.27 0.67 0.17
121_E 117_V 1.26 0.66 0.17
273_R 155_K 1.23 0.63 0.15
349_N 146_R 1.21 0.61 0.14
34_Q 158_T 1.19 0.59 0.13
265_T 8_R 1.18 0.58 0.13
273_R 8_R 1.17 0.58 0.12
293_V 103_R 1.16 0.56 0.12
345_H 32_R 1.16 0.56 0.12
37_G 167_V 1.15 0.55 0.11
294_P 35_L 1.14 0.54 0.11
334_N 114_L 1.14 0.54 0.11
340_P 164_L 1.10 0.50 0.10
210_L 15_R 1.10 0.50 0.10
292_W 101_V 1.09 0.49 0.09
242_L 96_V 1.07 0.48 0.09
334_N 97_W 1.07 0.48 0.09
312_I 66_L 1.07 0.48 0.09
351_P 198_K 1.05 0.46 0.08
153_F 185_Q 1.03 0.44 0.08
164_V 138_I 1.03 0.44 0.07
34_Q 147_L 1.02 0.43 0.07
251_R 59_E 1.02 0.43 0.07
103_P 55_Q 1.02 0.42 0.07
41_I 146_R 1.02 0.42 0.07
164_V 173_R 1.02 0.42 0.07
18_I 91_A 1.01 0.42 0.07
336_A 89_V 1.01 0.41 0.07
265_T 39_F 1.01 0.41 0.07
348_L 27_L 1.01 0.41 0.07
234_R 55_Q 1.00 0.41 0.07
328_V 201_I 1.00 0.40 0.07
14_M 157_T 0.99 0.40 0.07
353_Y 98_G 0.99 0.39 0.06
164_V 92_E 0.98 0.39 0.06
135_L 130_F 0.98 0.39 0.06
49_L 173_R 0.98 0.38 0.06
135_L 158_T 0.97 0.38 0.06
292_W 187_E 0.97 0.38 0.06
355_S 101_V 0.97 0.38 0.06
205_L 137_L 0.97 0.37 0.06
331_T 168_V 0.96 0.36 0.06
242_L 138_I 0.96 0.36 0.06
336_A 42_L 0.95 0.36 0.06
117_A 150_I 0.95 0.36 0.06
241_E 56_A 0.95 0.36 0.05
142_L 61_Y 0.95 0.36 0.05
303_E 59_E 0.95 0.36 0.05
345_H 188_R 0.95 0.36 0.05
135_L 149_K 0.94 0.35 0.05
162_E 173_R 0.94 0.35 0.05
273_R 158_T 0.94 0.34 0.05
338_A 184_E 0.91 0.33 0.05
341_F 184_E 0.91 0.33 0.05
153_F 24_G 0.91 0.32 0.05
305_L 24_G 0.91 0.32 0.04
52_Y 150_I 0.90 0.32 0.04
273_R 159_R 0.90 0.31 0.04
14_M 7_T 0.90 0.31 0.04
335_P 36_V 0.90 0.31 0.04
153_F 6_P 0.90 0.31 0.04
341_F 192_F 0.90 0.31 0.04
286_G 8_R 0.89 0.31 0.04
334_N 198_K 0.89 0.31 0.04
139_A 94_E 0.89 0.30 0.04
17_L 72_G 0.89 0.30 0.04
309_R 150_I 0.88 0.30 0.04
19_V 75_V 0.88 0.30 0.04
33_L 57_A 0.88 0.30 0.04
344_L 153_E 0.88 0.29 0.04
34_Q 18_L 0.88 0.29 0.04
240_E 55_Q 0.88 0.29 0.04
337_W 3_Q 0.88 0.29 0.04
155_V 101_V 0.87 0.29 0.04
273_R 50_R 0.87 0.28 0.04
129_G 148_K 0.86 0.28 0.04
292_W 78_G 0.86 0.28 0.04
83_T 90_E 0.86 0.28 0.04
300_K 132_R 0.85 0.28 0.04
355_S 157_T 0.85 0.27 0.04
329_P 162_N 0.85 0.27 0.04
135_L 34_A 0.85 0.27 0.04
333_E 133_Y 0.85 0.27 0.04
334_N 29_K 0.85 0.27 0.04
153_F 169_I 0.84 0.27 0.04
206_S 71_D 0.84 0.27 0.04
191_V 56_A 0.84 0.27 0.04
265_T 155_K 0.84 0.27 0.04
292_W 40_F 0.84 0.26 0.03
265_T 10_N 0.84 0.26 0.03
234_R 146_R 0.84 0.26 0.03
233_E 105_K 0.84 0.26 0.03
346_G 193_R 0.84 0.26 0.03
115_R 23_K 0.84 0.26 0.03
107_R 108_F 0.84 0.26 0.03
341_F 6_P 0.83 0.26 0.03
34_Q 42_L 0.83 0.26 0.03
330_V 30_K 0.83 0.26 0.03
26_A 95_N 0.83 0.26 0.03
273_R 39_F 0.83 0.26 0.03
112_G 171_G 0.83 0.26 0.03
16_K 5_S 0.83 0.25 0.03
344_L 161_V 0.82 0.25 0.03
21_G 32_R 0.82 0.25 0.03
46_P 133_Y 0.82 0.25 0.03
14_M 98_G 0.82 0.25 0.03
263_L 60_A 0.82 0.25 0.03
229_A 55_Q 0.82 0.25 0.03
29_L 39_F 0.82 0.25 0.03
330_V 164_L 0.82 0.25 0.03
136_A 163_A 0.82 0.25 0.03
297_A 19_R 0.81 0.24 0.03
291_G 35_L 0.81 0.24 0.03
260_L 202_E 0.81 0.24 0.03
354_G 119_T 0.81 0.24 0.03
292_W 180_Q 0.81 0.24 0.03
40_H 27_L 0.81 0.24 0.03
138_L 182_V 0.81 0.24 0.03
232_K 134_A 0.81 0.24 0.03
319_V 68_Q 0.81 0.24 0.03
282_A 133_Y 0.81 0.24 0.03
292_W 77_A 0.81 0.24 0.03
287_A 60_A 0.80 0.24 0.03
153_F 140_V 0.80 0.24 0.03
346_G 21_A 0.80 0.24 0.03
338_A 155_K 0.80 0.24 0.03
143_D 55_Q 0.80 0.23 0.03
348_L 188_R 0.80 0.23 0.03
239_P 55_Q 0.80 0.23 0.03
344_L 130_F 0.80 0.23 0.03
34_Q 39_F 0.80 0.23 0.03
71_Q 184_E 0.80 0.23 0.03
40_H 164_L 0.80 0.23 0.03
153_F 25_V 0.80 0.23 0.03
296_K 58_K 0.79 0.23 0.03
332_L 35_L 0.79 0.23 0.03
118_L 76_V 0.79 0.23 0.03
191_V 153_E 0.79 0.23 0.03
34_Q 34_A 0.79 0.23 0.03
283_G 155_K 0.79 0.23 0.03
69_V 172_I 0.79 0.23 0.03
260_L 62_A 0.79 0.22 0.03
266_R 195_K 0.79 0.22 0.03
23_K 127_S 0.78 0.22 0.03
335_P 199_G 0.78 0.22 0.03
104_V 110_D 0.78 0.22 0.03
113_K 52_A 0.78 0.22 0.03
347_F 143_T 0.78 0.22 0.03
175_R 178_F 0.78 0.22 0.03
138_L 43_V 0.78 0.22 0.03
201_A 93_V 0.78 0.22 0.03
283_G 159_R 0.78 0.22 0.03
265_T 195_K 0.78 0.22 0.03
349_N 29_K 0.77 0.22 0.03
124_T 135_E 0.77 0.21 0.03
117_A 123_T 0.77 0.21 0.03
276_A 101_V 0.77 0.21 0.03
300_K 52_A 0.77 0.21 0.03
118_L 22_Q 0.77 0.21 0.03
68_V 204_R 0.77 0.21 0.03
114_E 26_D 0.77 0.21 0.03
334_N 154_I 0.77 0.21 0.03
349_N 158_T 0.77 0.21 0.03
82_A 52_A 0.76 0.21 0.02
281_A 97_W 0.76 0.21 0.02
238_A 63_A 0.76 0.21 0.02
273_R 165_E 0.76 0.21 0.02
140_H 55_Q 0.76 0.21 0.02
40_H 39_F 0.76 0.21 0.02
229_A 92_E 0.76 0.21 0.02
341_F 172_I 0.76 0.21 0.02
355_S 43_V 0.76 0.21 0.02
233_E 55_Q 0.76 0.21 0.02
307_R 22_Q 0.76 0.21 0.02
40_H 197_I 0.76 0.20 0.02
272_A 27_L 0.76 0.20 0.02
116_A 43_V 0.75 0.20 0.02
291_G 157_T 0.75 0.20 0.02
332_L 114_L 0.75 0.20 0.02
283_G 153_E 0.75 0.20 0.02
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
0555 1.32 subunit_I_PDB_vs_subunit_D Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.51 Done
0554 1.31 subunit_I_PDB_vs_subunit_D Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.48 Done - Shared
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