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OPENSEQ.org
Full
Genes: A B A+B
Length: 720 147 802
Sequences: 2459 5421 415
Seq/Len: 3.42 36.88 0.52
MirrorTree (Pazo et al. 2001) 0.76
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.02 0.42
2 0.00 0.02 0.44
5 0.01 0.02 0.45
10 0.01 0.02 0.47
20 0.01 0.03 0.48
100 0.04 0.04 0.57
∞ 0.13 0.13 1.04
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
561_I 117_Y 1.51 0.58 0.00
700_R 19_A 1.46 0.55 0.00
603_K 101_V 1.39 0.49 0.00
349_Q 19_A 1.29 0.41 0.00
201_T 7_V 1.29 0.41 0.00
233_T 8_V 1.27 0.39 0.00
443_V 113_I 1.26 0.39 0.00
247_N 77_D 1.25 0.38 0.00
62_V 77_D 1.22 0.36 0.00
350_A 45_A 1.21 0.35 0.00
659_V 77_D 1.19 0.34 0.00
294_R 45_A 1.16 0.32 0.00
640_L 114_P 1.15 0.31 0.00
331_S 76_Y 1.15 0.31 0.00
567_K 124_F 1.14 0.30 0.00
326_K 101_V 1.13 0.30 0.00
18_I 64_C 1.11 0.29 0.00
521_M 79_I 1.11 0.29 0.00
641_I 125_A 1.11 0.28 0.00
563_C 132_E 1.10 0.28 0.00
683_F 13_I 1.10 0.28 0.00
85_P 127_V 1.09 0.28 0.00
248_S 104_F 1.09 0.28 0.00
64_I 131_L 1.09 0.27 0.00
207_T 131_L 1.08 0.27 0.00
98_L 114_P 1.08 0.27 0.00
89_A 86_H 1.08 0.27 0.00
295_Q 45_A 1.08 0.27 0.00
596_A 126_A 1.08 0.27 0.00
347_K 102_M 1.07 0.26 0.00
427_I 85_R 1.06 0.26 0.00
141_F 74_R 1.06 0.25 0.00
543_V 122_E 1.05 0.25 0.00
214_L 114_P 1.04 0.24 0.00
557_R 65_A 1.03 0.24 0.00
607_I 101_V 1.02 0.23 0.00
652_A 22_L 1.02 0.23 0.00
646_I 133_R 1.02 0.23 0.00
417_P 114_P 1.01 0.23 0.00
523_Q 130_L 1.01 0.23 0.00
528_V 134_S 1.01 0.23 0.00
703_S 128_Y 1.01 0.23 0.00
643_T 124_F 0.99 0.22 0.00
238_D 71_R 0.99 0.22 0.00
584_E 100_K 0.99 0.21 0.00
453_I 101_V 0.98 0.21 0.00
559_L 105_G 0.98 0.21 0.00
258_I 8_V 0.97 0.21 0.00
62_V 8_V 0.97 0.20 0.00
250_A 79_I 0.97 0.20 0.00
665_V 77_D 0.97 0.20 0.00
629_V 76_Y 0.96 0.20 0.00
319_Q 101_V 0.96 0.20 0.00
275_Q 42_G 0.96 0.20 0.00
655_V 117_Y 0.96 0.20 0.00
306_A 79_I 0.96 0.20 0.00
679_S 90_L 0.96 0.20 0.00
63_Q 99_G 0.95 0.20 0.00
261_K 141_A 0.95 0.20 0.00
17_E 104_F 0.95 0.20 0.00
554_T 65_A 0.95 0.19 0.00
262_S 68_I 0.95 0.19 0.00
532_T 38_G 0.94 0.19 0.00
644_P 101_V 0.93 0.19 0.00
458_V 42_G 0.93 0.19 0.00
327_E 102_M 0.93 0.18 0.00
300_V 137_Q 0.93 0.18 0.00
297_K 73_C 0.93 0.18 0.00
227_A 141_A 0.93 0.18 0.00
586_L 7_V 0.92 0.18 0.00
324_T 19_A 0.92 0.18 0.00
701_R 32_V 0.92 0.18 0.00
234_Y 111_C 0.92 0.18 0.00
637_D 27_H 0.91 0.18 0.00
510_I 113_I 0.91 0.18 0.00
697_S 10_V 0.91 0.18 0.00
458_V 106_H 0.91 0.18 0.00
104_V 67_Q 0.91 0.18 0.00
507_I 24_Q 0.91 0.17 0.00
490_R 32_V 0.91 0.17 0.00
549_A 22_L 0.91 0.17 0.00
357_K 102_M 0.90 0.17 0.00
554_T 27_H 0.90 0.17 0.00
261_K 113_I 0.90 0.17 0.00
464_I 46_D 0.90 0.17 0.00
630_N 46_D 0.90 0.17 0.00
545_A 42_G 0.90 0.17 0.00
372_I 104_F 0.90 0.17 0.00
659_V 112_E 0.89 0.17 0.00
665_V 118_R 0.89 0.17 0.00
347_K 60_L 0.89 0.17 0.00
615_N 67_Q 0.89 0.17 0.00
247_N 27_H 0.89 0.17 0.00
263_A 131_L 0.89 0.17 0.00
424_K 30_L 0.89 0.17 0.00
459_L 76_Y 0.89 0.17 0.00
294_R 28_P 0.89 0.17 0.00
538_I 24_Q 0.88 0.17 0.00
404_V 32_V 0.88 0.16 0.00
128_L 104_F 0.88 0.16 0.00
538_I 73_C 0.88 0.16 0.00
521_M 125_A 0.88 0.16 0.00
522_M 67_Q 0.88 0.16 0.00
557_R 33_E 0.88 0.16 0.00
584_E 32_V 0.88 0.16 0.00
227_A 30_L 0.88 0.16 0.00
533_G 104_F 0.87 0.16 0.00
467_Y 130_L 0.87 0.16 0.00
458_V 127_V 0.87 0.16 0.00
532_T 72_L 0.87 0.16 0.00
538_I 68_I 0.87 0.16 0.00
236_G 28_P 0.87 0.16 0.00
585_I 90_L 0.86 0.16 0.00
575_G 8_V 0.86 0.16 0.00
383_Q 102_M 0.86 0.16 0.00
464_I 67_Q 0.86 0.16 0.00
343_T 69_S 0.86 0.16 0.00
512_S 10_V 0.86 0.15 0.00
445_L 79_I 0.86 0.15 0.00
639_V 112_E 0.86 0.15 0.00
320_L 45_A 0.86 0.15 0.00
388_Q 102_M 0.85 0.15 0.00
242_I 45_A 0.85 0.15 0.00
574_L 125_A 0.85 0.15 0.00
694_I 124_F 0.85 0.15 0.00
262_S 141_A 0.85 0.15 0.00
681_S 87_I 0.85 0.15 0.00
92_Q 24_Q 0.85 0.15 0.00
441_V 24_Q 0.85 0.15 0.00
402_S 84_K 0.85 0.15 0.00
279_V 68_I 0.84 0.15 0.00
16_D 104_F 0.84 0.15 0.00
51_F 44_G 0.84 0.15 0.00
100_L 26_Y 0.84 0.15 0.00
43_L 90_L 0.84 0.15 0.00
354_E 102_M 0.84 0.15 0.00
574_L 90_L 0.84 0.15 0.00
512_S 22_L 0.84 0.15 0.00
343_T 90_L 0.84 0.15 0.00
532_T 75_N 0.84 0.15 0.00
48_Y 90_L 0.83 0.14 0.00
47_V 44_G 0.83 0.14 0.00
551_I 94_A 0.83 0.14 0.00
459_L 106_H 0.83 0.14 0.00
663_L 118_R 0.83 0.14 0.00
541_T 93_M 0.83 0.14 0.00
61_L 38_G 0.82 0.14 0.00
318_A 18_T 0.82 0.14 0.00
572_E 131_L 0.82 0.14 0.00
95_R 86_H 0.82 0.14 0.00
453_I 25_R 0.82 0.14 0.00
127_R 118_R 0.82 0.14 0.00
476_Q 73_C 0.82 0.14 0.00
430_G 68_I 0.82 0.14 0.00
328_A 104_F 0.82 0.14 0.00
509_A 118_R 0.82 0.14 0.00
528_V 84_K 0.82 0.14 0.00
362_V 69_S 0.82 0.14 0.00
470_I 143_N 0.82 0.14 0.00
287_E 101_V 0.82 0.14 0.00
62_V 60_L 0.82 0.14 0.00
276_L 128_Y 0.82 0.14 0.00
580_N 131_L 0.82 0.14 0.00
188_M 125_A 0.82 0.14 0.00
207_T 81_T 0.81 0.14 0.00
409_I 122_E 0.81 0.14 0.00
694_I 77_D 0.81 0.14 0.00
252_N 86_H 0.81 0.14 0.00
410_V 135_A 0.81 0.14 0.00
123_A 84_K 0.81 0.14 0.00
641_I 7_V 0.81 0.14 0.00
445_L 33_E 0.81 0.13 0.00
120_I 131_L 0.81 0.13 0.00
62_V 81_T 0.80 0.13 0.00
307_K 60_L 0.80 0.13 0.00
45_A 85_R 0.80 0.13 0.00
333_L 83_E 0.80 0.13 0.00
58_A 142_L 0.80 0.13 0.00
158_D 71_R 0.80 0.13 0.00
548_A 101_V 0.80 0.13 0.00
640_L 126_A 0.80 0.13 0.00
147_M 130_L 0.80 0.13 0.00
282_R 90_L 0.80 0.13 0.00
328_A 30_L 0.80 0.13 0.00
234_Y 8_V 0.79 0.13 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
13816 0.52 Full Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13106 1.08 WzC_WzB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
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