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OPENSEQ.org
BamA-BamE
Genes: A B A+B
Length: 810 113 835
Sequences: 1557 575 293
Seq/Len: 1.92 5.09 0.35
MirrorTree (Pazo et al. 2001) 0.80
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 0.02 0.01 0.00
2 0.02 0.01 0.00
5 0.02 0.01 0.00
10 0.02 0.01 0.00
20 0.02 0.01 0.01
100 0.02 0.01 0.06
∞ 0.04 0.01 0.32
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
652_F 45_K 1.69 0.59 0.00
240_I 16_L 1.68 0.58 0.00
382_V 59_L 1.51 0.46 0.00
185_N 50_M 1.50 0.46 0.00
342_D 66_D 1.35 0.36 0.00
109_M 93_L 1.34 0.35 0.00
256_V 64_M 1.30 0.33 0.00
378_G 27_V 1.28 0.31 0.00
406_P 19_G 1.27 0.31 0.00
430_I 96_N 1.24 0.29 0.00
709_N 40_A 1.23 0.28 0.00
95_A 101_L 1.22 0.28 0.00
417_K 51_T 1.19 0.26 0.00
317_Y 102_T 1.18 0.26 0.00
165_L 76_V 1.17 0.25 0.00
414_V 43_V 1.15 0.24 0.00
467_T 31_D 1.15 0.24 0.00
260_I 67_P 1.15 0.24 0.00
468_Y 107_K 1.15 0.24 0.00
256_V 101_L 1.14 0.23 0.00
212_R 59_L 1.14 0.23 0.00
611_V 71_N 1.14 0.23 0.00
344_G 36_N 1.13 0.23 0.00
221_G 19_G 1.13 0.23 0.00
642_G 76_V 1.11 0.22 0.00
440_F 64_M 1.10 0.22 0.00
174_S 91_L 1.10 0.21 0.00
783_L 45_K 1.09 0.21 0.00
77_V 21_S 1.09 0.21 0.00
419_K 59_L 1.09 0.21 0.00
633_T 57_Y 1.09 0.21 0.00
192_E 52_Q 1.09 0.21 0.00
452_T 97_S 1.08 0.21 0.00
633_T 59_L 1.08 0.21 0.00
457_G 61_T 1.08 0.21 0.00
746_D 32_I 1.08 0.20 0.00
273_V 32_I 1.07 0.20 0.00
492_N 72_T 1.06 0.20 0.00
85_L 82_G 1.06 0.20 0.00
739_W 59_L 1.06 0.20 0.00
428_F 12_V 1.05 0.20 0.00
178_Q 19_G 1.05 0.20 0.00
300_K 107_K 1.03 0.18 0.00
525_L 27_V 1.03 0.18 0.00
409_P 44_S 1.02 0.18 0.00
151_V 94_T 1.02 0.18 0.00
266_Y 20_C 1.01 0.18 0.00
352_I 17_T 1.01 0.18 0.00
802_F 57_Y 1.01 0.17 0.00
617_T 111_S 1.01 0.17 0.00
521_E 31_D 1.00 0.17 0.00
115_E 45_K 1.00 0.17 0.00
207_N 100_V 0.99 0.17 0.00
440_F 29_R 0.99 0.17 0.00
182_I 59_L 0.98 0.17 0.00
321_R 77_F 0.98 0.17 0.00
314_R 71_N 0.98 0.16 0.00
419_K 91_L 0.98 0.16 0.00
93_T 66_D 0.97 0.16 0.00
80_D 58_A 0.97 0.16 0.00
392_L 22_T 0.97 0.16 0.00
452_T 41_N 0.96 0.16 0.00
437_G 37_Y 0.96 0.16 0.00
323_Q 77_F 0.96 0.16 0.00
777_M 12_V 0.96 0.16 0.00
507_K 38_L 0.96 0.16 0.00
177_I 36_N 0.96 0.16 0.00
480_V 38_L 0.96 0.16 0.00
544_A 105_D 0.95 0.15 0.00
475_N 13_L 0.95 0.15 0.00
354_F 57_Y 0.95 0.15 0.00
433_G 28_Y 0.95 0.15 0.00
217_Q 47_R 0.95 0.15 0.00
266_Y 51_T 0.95 0.15 0.00
785_F 31_D 0.94 0.15 0.00
709_N 21_S 0.94 0.15 0.00
85_L 14_L 0.94 0.15 0.00
741_M 21_S 0.94 0.15 0.00
777_M 97_S 0.94 0.15 0.00
61_N 41_N 0.94 0.15 0.00
621_I 91_L 0.94 0.15 0.00
704_D 64_M 0.94 0.15 0.00
189_T 85_G 0.94 0.15 0.00
654_A 91_L 0.94 0.15 0.00
174_S 59_L 0.94 0.15 0.00
598_K 56_A 0.94 0.15 0.00
232_D 92_T 0.94 0.15 0.00
149_A 103_N 0.93 0.15 0.00
641_L 38_L 0.93 0.15 0.00
570_F 11_A 0.93 0.15 0.00
508_S 82_G 0.93 0.14 0.00
800_E 89_Q 0.93 0.14 0.00
25_V 51_T 0.93 0.14 0.00
245_V 36_N 0.93 0.14 0.00
800_E 17_T 0.92 0.14 0.00
155_V 111_S 0.92 0.14 0.00
305_E 43_V 0.92 0.14 0.00
341_V 14_L 0.92 0.14 0.00
461_T 41_N 0.92 0.14 0.00
220_A 19_G 0.92 0.14 0.00
86_V 56_A 0.92 0.14 0.00
478_F 77_F 0.91 0.14 0.00
536_L 80_Q 0.91 0.14 0.00
247_L 74_F 0.91 0.14 0.00
93_T 45_K 0.91 0.14 0.00
174_S 45_K 0.91 0.14 0.00
94_I 32_I 0.91 0.14 0.00
384_Q 93_L 0.90 0.14 0.00
382_V 38_L 0.90 0.14 0.00
459_N 19_G 0.90 0.14 0.00
334_T 45_K 0.90 0.14 0.00
299_T 44_S 0.90 0.13 0.00
446_Q 31_D 0.90 0.13 0.00
83_T 53_Q 0.89 0.13 0.00
768_M 71_N 0.89 0.13 0.00
75_V 105_D 0.89 0.13 0.00
489_L 91_L 0.89 0.13 0.00
806_I 108_P 0.88 0.13 0.00
642_G 32_I 0.88 0.13 0.00
721_P 50_M 0.88 0.13 0.00
486_G 36_N 0.88 0.13 0.00
669_G 49_G 0.88 0.13 0.00
802_F 65_S 0.88 0.13 0.00
532_V 92_T 0.88 0.13 0.00
317_Y 66_D 0.88 0.13 0.00
773_A 58_A 0.87 0.13 0.00
761_S 64_M 0.87 0.13 0.00
81_G 61_T 0.87 0.13 0.00
195_S 32_I 0.87 0.13 0.00
337_L 53_Q 0.87 0.13 0.00
305_E 38_L 0.87 0.13 0.00
446_Q 68_F 0.87 0.13 0.00
449_W 27_V 0.87 0.12 0.00
656_G 34_Q 0.87 0.12 0.00
54_V 27_V 0.86 0.12 0.00
393_G 55_V 0.86 0.12 0.00
469_A 77_F 0.86 0.12 0.00
460_G 93_L 0.86 0.12 0.00
601_I 103_N 0.86 0.12 0.00
414_V 57_Y 0.86 0.12 0.00
200_R 78_R 0.85 0.12 0.00
174_S 88_Q 0.85 0.12 0.00
717_E 42_D 0.85 0.12 0.00
258_V 19_G 0.85 0.12 0.00
791_F 98_S 0.85 0.12 0.00
372_M 19_G 0.85 0.12 0.00
268_L 10_A 0.85 0.12 0.00
74_D 101_L 0.85 0.12 0.00
148_S 110_L 0.85 0.12 0.00
418_V 55_V 0.85 0.12 0.00
85_L 45_K 0.85 0.12 0.00
352_I 81_P 0.84 0.12 0.00
468_Y 19_G 0.84 0.12 0.00
593_V 40_A 0.84 0.12 0.00
48_V 87_T 0.84 0.12 0.00
229_Y 94_T 0.84 0.12 0.00
450_L 101_L 0.84 0.12 0.00
432_Y 18_A 0.84 0.12 0.00
654_A 82_G 0.84 0.12 0.00
362_D 66_D 0.84 0.12 0.00
467_T 93_L 0.84 0.12 0.00
258_V 13_L 0.83 0.12 0.00
267_K 93_L 0.83 0.12 0.00
23_G 76_V 0.83 0.12 0.00
765_N 48_V 0.83 0.12 0.00
336_K 45_K 0.83 0.12 0.00
109_M 101_L 0.83 0.11 0.00
630_L 103_N 0.83 0.11 0.00
444_V 38_L 0.83 0.11 0.00
119_V 103_N 0.83 0.11 0.00
236_A 27_V 0.83 0.11 0.00
197_F 12_V 0.83 0.11 0.00
446_Q 39_T 0.83 0.11 0.00
119_V 43_V 0.83 0.11 0.00
519_I 93_L 0.83 0.11 0.00
790_P 11_A 0.82 0.11 0.00
774_L 39_T 0.82 0.11 0.00
735_T 33_N 0.82 0.11 0.00
493_D 12_V 0.82 0.11 0.00
571_T 39_T 0.82 0.11 0.00
766_I 74_F 0.82 0.11 0.00
706_V 47_R 0.82 0.11 0.00
274_S 32_I 0.82 0.11 0.00
608_Y 96_N 0.82 0.11 0.00
247_L 106_N 0.82 0.11 0.00
438_V 102_T 0.82 0.11 0.00
165_L 105_D 0.82 0.11 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
11526 0.35 BamA-BamE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
1441 0.02 BamAE Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2014_03) Killed
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