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OPENSEQ.org
DNAN_DPO3B_SALTY-UMUD_SALTY
Genes: A B A+B
Length: 366 139 494
Sequences: 7006 7987 50
Seq/Len: 19.14 57.46 0.1
MirrorTree (Pazo et al. 2001) 0.48
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 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.03
20 0.00 0.01 0.10
100 0.00 0.02 0.45
∞ 0.01 0.05 3.88
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
173_D 70_D 1.74 0.29 0.00
206_M 105_V 1.50 0.20 0.00
99_V 96_V 1.40 0.17 0.00
193_V 52_Y 1.38 0.17 0.00
328_L 52_Y 1.34 0.15 0.00
160_F 90_I 1.33 0.15 0.00
108_L 52_Y 1.25 0.13 0.00
146_M 131_V 1.20 0.12 0.00
7_R 37_R 1.19 0.12 0.00
349_I 62_I 1.17 0.12 0.00
238_D 21_L 1.17 0.12 0.00
263_L 22_V 1.16 0.12 0.00
48_D 15_L 1.16 0.11 0.00
42_L 135_I 1.14 0.11 0.00
222_N 117_I 1.14 0.11 0.00
147_A 119_V 1.14 0.11 0.00
35_L 32_D 1.14 0.11 0.00
360_V 113_A 1.13 0.11 0.00
145_S 52_Y 1.12 0.11 0.00
331_L 15_L 1.12 0.11 0.00
219_G 34_I 1.11 0.10 0.00
363_P 70_D 1.11 0.10 0.00
363_P 107_L 1.11 0.10 0.00
229_D 114_Y 1.11 0.10 0.00
63_H 99_L 1.10 0.10 0.00
102_G 47_H 1.09 0.10 0.00
322_S 99_L 1.09 0.10 0.00
157_G 95_T 1.08 0.10 0.00
139_I 71_L 1.07 0.10 0.00
18_S 71_L 1.07 0.10 0.00
14_L 52_Y 1.06 0.10 0.00
116_F 63_E 1.06 0.10 0.00
21_L 64_A 1.05 0.09 0.00
82_L 28_S 1.05 0.09 0.00
139_I 90_I 1.05 0.09 0.00
203_L 38_I 1.04 0.09 0.00
10_L 70_D 1.04 0.09 0.00
152_R 93_E 1.04 0.09 0.00
348_Q 77_S 1.03 0.09 0.00
48_D 114_Y 1.03 0.09 0.00
323_Y 16_P 1.02 0.09 0.00
256_L 127_I 1.01 0.09 0.00
334_E 136_K 1.01 0.09 0.00
331_L 68_D 1.01 0.09 0.00
35_L 136_K 1.00 0.09 0.00
328_L 131_V 1.00 0.09 0.00
88_I 127_I 1.00 0.09 0.00
57_V 17_F 1.00 0.09 0.00
301_E 39_D 1.00 0.09 0.00
173_D 66_I 0.99 0.08 0.00
300_E 54_V 0.99 0.08 0.00
232_F 113_A 0.98 0.08 0.00
173_D 107_L 0.98 0.08 0.00
99_V 119_V 0.98 0.08 0.00
244_Y 70_D 0.97 0.08 0.00
22_G 130_V 0.97 0.08 0.00
336_V 21_L 0.97 0.08 0.00
118_N 56_A 0.96 0.08 0.00
349_I 123_D 0.96 0.08 0.00
139_I 17_F 0.96 0.08 0.00
338_I 62_I 0.96 0.08 0.00
85_G 63_E 0.96 0.08 0.00
221_N 98_R 0.95 0.08 0.00
82_L 116_P 0.94 0.08 0.00
75_F 92_G 0.94 0.08 0.00
14_L 96_V 0.94 0.08 0.00
327_V 89_A 0.94 0.08 0.00
120_D 52_Y 0.94 0.08 0.00
223_I 38_I 0.94 0.08 0.00
260_C 32_D 0.94 0.08 0.00
58_T 114_Y 0.93 0.07 0.00
99_V 73_V 0.93 0.07 0.00
256_L 30_A 0.93 0.07 0.00
336_V 72_L 0.93 0.07 0.00
218_I 127_I 0.93 0.07 0.00
249_P 107_L 0.93 0.07 0.00
37_V 15_L 0.93 0.07 0.00
328_L 74_V 0.93 0.07 0.00
241_F 135_I 0.93 0.07 0.00
308_V 15_L 0.93 0.07 0.00
323_Y 64_A 0.92 0.07 0.00
83_P 68_D 0.92 0.07 0.00
88_I 115_R 0.92 0.07 0.00
301_E 44_L 0.92 0.07 0.00
117_P 25_G 0.92 0.07 0.00
92_L 43_L 0.91 0.07 0.00
211_E 126_D 0.91 0.07 0.00
258_A 38_I 0.91 0.07 0.00
42_L 96_V 0.91 0.07 0.00
247_V 99_L 0.91 0.07 0.00
35_L 15_L 0.91 0.07 0.00
361_V 114_Y 0.91 0.07 0.00
300_E 20_Y 0.90 0.07 0.00
107_S 38_I 0.90 0.07 0.00
325_L 17_F 0.90 0.07 0.00
336_V 120_G 0.90 0.07 0.00
142_T 87_I 0.89 0.07 0.00
24_R 79_N 0.89 0.07 0.00
111_L 133_F 0.89 0.07 0.00
365_R 65_G 0.89 0.07 0.00
174_G 86_V 0.89 0.07 0.00
241_F 103_P 0.89 0.07 0.00
103_R 40_L 0.89 0.07 0.00
29_I 109_P 0.89 0.07 0.00
241_F 70_D 0.89 0.07 0.00
195_V 105_V 0.88 0.07 0.00
328_L 96_V 0.88 0.07 0.00
227_V 82_H 0.88 0.07 0.00
224_R 56_A 0.88 0.07 0.00
319_F 91_E 0.88 0.07 0.00
26_T 27_P 0.88 0.07 0.00
30_L 83_G 0.88 0.07 0.00
309_S 63_E 0.88 0.07 0.00
132_Q 32_D 0.87 0.07 0.00
146_M 128_F 0.87 0.07 0.00
266_A 73_V 0.87 0.07 0.00
75_F 74_V 0.87 0.07 0.00
363_P 25_G 0.86 0.07 0.00
206_M 98_R 0.86 0.07 0.00
244_Y 99_L 0.86 0.07 0.00
343_S 123_D 0.86 0.07 0.00
294_A 63_E 0.86 0.07 0.00
242_P 25_G 0.86 0.07 0.00
267_F 134_I 0.86 0.07 0.00
256_L 88_A 0.86 0.07 0.00
102_G 28_S 0.86 0.07 0.00
241_F 64_A 0.85 0.07 0.00
194_I 127_I 0.85 0.07 0.00
24_R 80_A 0.85 0.07 0.00
70_V 48_P 0.85 0.07 0.00
157_G 109_P 0.85 0.07 0.00
173_D 30_A 0.85 0.07 0.00
10_L 65_G 0.85 0.07 0.00
42_L 92_G 0.85 0.07 0.00
279_R 68_D 0.85 0.06 0.00
77_D 76_S 0.85 0.06 0.00
73_R 55_K 0.84 0.06 0.00
361_V 113_A 0.84 0.06 0.00
173_D 80_A 0.84 0.06 0.00
160_F 135_I 0.84 0.06 0.00
39_D 105_V 0.84 0.06 0.00
161_E 96_V 0.84 0.06 0.00
204_M 130_V 0.84 0.06 0.00
334_E 134_I 0.84 0.06 0.00
318_G 70_D 0.83 0.06 0.00
20_P 96_V 0.83 0.06 0.00
84_E 99_L 0.83 0.06 0.00
340_L 15_L 0.83 0.06 0.00
143_Q 119_V 0.83 0.06 0.00
290_L 99_L 0.83 0.06 0.00
354_S 102_R 0.83 0.06 0.00
237_V 37_R 0.83 0.06 0.00
211_E 108_I 0.83 0.06 0.00
362_M 110_M 0.83 0.06 0.00
290_L 74_V 0.83 0.06 0.00
281_V 20_Y 0.82 0.06 0.00
351_D 52_Y 0.82 0.06 0.00
95_D 76_S 0.82 0.06 0.00
232_F 114_Y 0.82 0.06 0.00
272_I 110_M 0.82 0.06 0.00
157_G 107_L 0.82 0.06 0.00
119_L 59_D 0.82 0.06 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
7083 3.96 DNAN_DPO3B_SALTY-UMUD_SALTY Jackhammer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done - Shared
6892 0.1 DNAN_DPO3B_SALTY-UMUD_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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