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OPENSEQ.org
subunit_I_PDB_vs_subunit_D
Genes: A B A+B
Length: 357 223 558
Sequences: 1169 815 739
Seq/Len: 3.27 3.65 1.32
MirrorTree (Pazo et al. 2001) 0.76
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 0.23
2 0.01 0.00 0.25
5 0.01 0.00 0.32
10 0.01 0.00 1.15
20 0.01 0.00 1.16
100 0.02 0.01 1.19
∞ 0.03 0.03 1.27
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
348_L 140_V 1.72 0.92 0.51
291_G 7_T 1.64 0.90 0.45
272_A 96_V 1.47 0.82 0.32
121_E 117_V 1.26 0.66 0.18
273_R 155_K 1.26 0.66 0.18
349_N 146_R 1.24 0.64 0.16
265_T 8_R 1.23 0.63 0.16
334_N 114_L 1.21 0.61 0.15
349_N 8_R 1.21 0.61 0.15
34_Q 158_T 1.17 0.58 0.13
273_R 8_R 1.14 0.55 0.12
312_I 66_L 1.14 0.55 0.12
14_M 157_T 1.14 0.54 0.12
294_P 35_L 1.13 0.53 0.11
345_H 32_R 1.12 0.53 0.11
334_N 97_W 1.12 0.53 0.11
340_P 164_L 1.10 0.51 0.10
293_V 103_R 1.10 0.51 0.10
117_A 150_I 1.09 0.49 0.10
37_G 167_V 1.08 0.49 0.10
41_I 146_R 1.05 0.46 0.09
18_I 91_A 1.04 0.45 0.08
336_A 89_V 1.04 0.45 0.08
34_Q 147_L 1.04 0.44 0.08
242_L 96_V 1.03 0.43 0.08
292_W 101_V 1.03 0.43 0.08
14_M 7_T 1.00 0.41 0.07
166_K 174_A 1.00 0.41 0.07
103_P 55_Q 1.00 0.41 0.07
348_L 27_L 0.99 0.40 0.07
351_P 198_K 0.99 0.40 0.07
260_L 202_E 0.98 0.39 0.07
135_L 130_F 0.98 0.39 0.07
345_H 188_R 0.98 0.39 0.07
147_R 43_V 0.98 0.39 0.07
265_T 39_F 0.97 0.38 0.06
135_L 158_T 0.97 0.38 0.06
348_L 188_R 0.96 0.37 0.06
336_A 42_L 0.96 0.37 0.06
337_W 3_Q 0.96 0.37 0.06
309_R 150_I 0.96 0.37 0.06
286_G 8_R 0.95 0.36 0.06
353_Y 98_G 0.95 0.36 0.06
69_V 172_I 0.95 0.36 0.06
273_R 158_T 0.95 0.36 0.06
328_V 201_I 0.94 0.35 0.06
142_L 61_Y 0.94 0.35 0.06
341_F 192_F 0.94 0.35 0.06
191_V 153_E 0.94 0.35 0.06
335_P 36_V 0.94 0.35 0.06
305_L 24_G 0.93 0.34 0.05
234_R 55_Q 0.93 0.34 0.05
143_D 3_Q 0.92 0.34 0.05
334_N 198_K 0.92 0.33 0.05
124_T 135_E 0.92 0.33 0.05
153_F 185_Q 0.91 0.32 0.05
338_A 184_E 0.91 0.32 0.05
331_T 168_V 0.91 0.32 0.05
251_R 59_E 0.91 0.32 0.05
355_S 101_V 0.90 0.32 0.05
346_G 193_R 0.90 0.32 0.05
34_Q 18_L 0.90 0.32 0.05
40_H 164_L 0.90 0.32 0.05
138_L 182_V 0.90 0.32 0.05
334_N 29_K 0.90 0.31 0.05
40_H 197_I 0.89 0.31 0.05
241_E 56_A 0.89 0.31 0.04
210_L 15_R 0.89 0.30 0.04
293_V 4_V 0.89 0.30 0.04
292_W 187_E 0.88 0.30 0.04
292_W 40_F 0.87 0.29 0.04
341_F 184_E 0.87 0.29 0.04
118_L 22_Q 0.87 0.29 0.04
273_R 39_F 0.87 0.29 0.04
334_N 154_I 0.87 0.29 0.04
190_L 74_E 0.86 0.28 0.04
33_L 57_A 0.86 0.28 0.04
205_L 137_L 0.85 0.28 0.04
311_Q 132_R 0.85 0.28 0.04
213_L 41_G 0.85 0.28 0.04
329_P 162_N 0.85 0.28 0.04
273_R 159_R 0.85 0.28 0.04
117_A 123_T 0.85 0.27 0.04
292_W 180_Q 0.84 0.27 0.04
300_K 132_R 0.84 0.27 0.04
292_W 78_G 0.84 0.27 0.04
49_L 173_R 0.84 0.27 0.04
135_L 34_A 0.84 0.26 0.04
283_G 159_R 0.84 0.26 0.04
155_V 101_V 0.84 0.26 0.04
233_E 105_K 0.83 0.26 0.04
112_G 177_R 0.83 0.26 0.04
201_A 93_V 0.83 0.26 0.04
177_V 4_V 0.83 0.26 0.04
346_G 21_A 0.83 0.26 0.04
21_G 32_R 0.83 0.26 0.04
341_F 6_P 0.83 0.26 0.04
164_V 92_E 0.83 0.26 0.04
330_V 30_K 0.82 0.25 0.03
291_G 35_L 0.82 0.25 0.03
333_E 133_Y 0.82 0.25 0.03
283_G 155_K 0.82 0.25 0.03
136_A 163_A 0.82 0.25 0.03
330_V 164_L 0.82 0.25 0.03
40_H 39_F 0.82 0.25 0.03
135_L 149_K 0.81 0.25 0.03
34_Q 39_F 0.81 0.25 0.03
303_E 59_E 0.81 0.25 0.03
107_R 51_K 0.81 0.25 0.03
29_L 39_F 0.81 0.24 0.03
344_L 161_V 0.81 0.24 0.03
72_A 101_V 0.81 0.24 0.03
239_P 55_Q 0.81 0.24 0.03
26_A 95_N 0.81 0.24 0.03
177_V 139_R 0.81 0.24 0.03
113_K 52_A 0.81 0.24 0.03
139_A 94_E 0.80 0.24 0.03
205_L 75_V 0.80 0.24 0.03
265_T 155_K 0.80 0.24 0.03
225_G 89_V 0.80 0.23 0.03
265_T 10_N 0.80 0.23 0.03
16_K 5_S 0.80 0.23 0.03
315_T 79_A 0.80 0.23 0.03
94_L 128_R 0.79 0.23 0.03
194_K 8_R 0.79 0.23 0.03
344_L 130_F 0.79 0.23 0.03
300_K 117_V 0.79 0.23 0.03
259_A 177_R 0.79 0.23 0.03
256_S 145_T 0.78 0.22 0.03
266_R 195_K 0.78 0.22 0.03
348_L 137_L 0.78 0.22 0.03
48_E 189_E 0.78 0.22 0.03
344_L 153_E 0.78 0.22 0.03
260_L 134_A 0.78 0.22 0.03
229_A 203_A 0.78 0.22 0.03
234_R 58_K 0.78 0.22 0.03
248_E 48_E 0.78 0.22 0.03
263_L 60_A 0.78 0.22 0.03
118_L 76_V 0.78 0.22 0.03
207_R 146_R 0.78 0.22 0.03
242_L 138_I 0.78 0.22 0.03
265_T 195_K 0.78 0.22 0.03
35_K 47_M 0.78 0.22 0.03
34_Q 42_L 0.78 0.22 0.03
347_F 143_T 0.78 0.22 0.03
26_A 34_A 0.78 0.22 0.03
349_N 29_K 0.78 0.22 0.03
338_A 155_K 0.78 0.22 0.03
247_E 128_R 0.77 0.22 0.03
121_E 19_R 0.77 0.22 0.03
354_G 119_T 0.77 0.22 0.03
106_S 62_A 0.77 0.22 0.03
276_A 101_V 0.77 0.22 0.03
289_L 19_R 0.77 0.22 0.03
234_R 19_R 0.77 0.21 0.03
355_S 157_T 0.77 0.21 0.03
46_P 133_Y 0.77 0.21 0.03
149_G 22_Q 0.77 0.21 0.03
34_Q 34_A 0.77 0.21 0.03
355_S 43_V 0.77 0.21 0.03
232_K 134_A 0.77 0.21 0.03
220_G 165_E 0.77 0.21 0.03
107_R 108_F 0.76 0.21 0.03
328_V 50_R 0.76 0.21 0.03
301_V 16_G 0.76 0.21 0.03
272_A 27_L 0.76 0.21 0.03
26_A 28_L 0.76 0.21 0.03
229_A 55_Q 0.76 0.21 0.03
14_M 98_G 0.76 0.21 0.03
349_N 40_F 0.76 0.21 0.03
138_L 25_V 0.76 0.21 0.03
179_E 36_V 0.76 0.21 0.03
301_V 128_R 0.76 0.20 0.03
91_T 143_T 0.76 0.20 0.03
117_A 59_E 0.76 0.20 0.03
341_F 172_I 0.76 0.20 0.03
234_R 146_R 0.75 0.20 0.03
332_L 35_L 0.75 0.20 0.02
229_A 92_E 0.75 0.20 0.02
135_L 189_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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