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OPENSEQ.org
BamA-BamD (A, 210-810)
Genes: A B A+B
Length: 601 245 794
Sequences: 4403 1309 935
Seq/Len: 7.33 5.34 1.18
MirrorTree (Pazo et al. 2001) 0.27
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 0.01 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.01 0.01
10 0.01 0.01 0.02
20 0.02 0.01 0.04
100 0.04 0.01 0.21
∞ 0.19 0.01 1.11
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
17_L 221_A 1.27 0.63 0.00
65_S 227_M 1.16 0.53 0.00
57_Y 55_L 1.14 0.52 0.00
327_L 13_L 1.05 0.43 0.00
458_T 221_A 1.04 0.42 0.00
220_G 26_E 1.02 0.40 0.00
593_F 17_L 1.02 0.39 0.00
132_V 154_Y 1.01 0.39 0.00
152_K 225_M 0.98 0.36 0.00
574_L 16_F 0.97 0.35 0.00
109_A 64_F 0.96 0.34 0.00
132_V 189_G 0.96 0.34 0.00
56_Q 156_N 0.95 0.34 0.00
94_K 56_E 0.95 0.33 0.00
77_Q 163_A 0.95 0.33 0.00
302_T 205_Y 0.95 0.33 0.00
458_T 39_A 0.95 0.33 0.00
358_T 19_G 0.94 0.33 0.00
596_N 184_Y 0.93 0.32 0.00
59_L 177_Y 0.93 0.32 0.00
51_I 80_Y 0.93 0.32 0.00
247_V 88_A 0.93 0.31 0.00
412_I 195_V 0.92 0.30 0.00
374_R 46_G 0.92 0.30 0.00
558_R 151_V 0.90 0.29 0.00
317_R 242_S 0.90 0.29 0.00
55_D 154_Y 0.90 0.29 0.00
236_Q 163_A 0.90 0.29 0.00
582_F 43_L 0.89 0.28 0.00
446_G 206_P 0.88 0.28 0.00
459_I 58_L 0.88 0.28 0.00
436_E 19_G 0.88 0.28 0.00
297_N 11_A 0.88 0.27 0.00
51_I 49_R 0.87 0.27 0.00
536_W 205_Y 0.87 0.27 0.00
405_D 205_Y 0.86 0.27 0.00
140_V 95_F 0.86 0.26 0.00
26_Y 25_E 0.86 0.26 0.00
508_E 143_A 0.86 0.26 0.00
145_F 43_L 0.86 0.26 0.00
412_I 16_F 0.86 0.26 0.00
513_T 52_I 0.86 0.26 0.00
126_V 192_V 0.85 0.26 0.00
184_G 62_Y 0.85 0.25 0.00
318_A 191_W 0.83 0.24 0.00
205_V 52_I 0.83 0.24 0.00
236_Q 102_H 0.83 0.24 0.00
365_Y 48_W 0.83 0.24 0.00
236_Q 213_D 0.82 0.23 0.00
111_P 202_L 0.82 0.23 0.00
229_V 21_S 0.82 0.23 0.00
249_I 15_L 0.82 0.23 0.00
295_Y 39_A 0.82 0.23 0.00
299_S 99_N 0.81 0.23 0.00
433_G 216_P 0.81 0.23 0.00
30_N 58_L 0.81 0.23 0.00
515_F 35_I 0.81 0.22 0.00
168_L 87_L 0.81 0.22 0.00
321_G 174_L 0.81 0.22 0.00
413_D 39_A 0.80 0.22 0.00
413_D 154_Y 0.80 0.22 0.00
246_A 49_R 0.80 0.22 0.00
29_F 114_L 0.79 0.21 0.00
62_V 123_A 0.79 0.21 0.00
26_Y 234_V 0.79 0.21 0.00
207_Y 82_N 0.79 0.21 0.00
579_A 241_N 0.79 0.21 0.00
128_L 11_A 0.79 0.21 0.00
131_N 221_A 0.79 0.21 0.00
249_I 71_V 0.79 0.21 0.00
510_I 76_I 0.79 0.21 0.00
399_Y 210_A 0.78 0.21 0.00
456_S 181_V 0.78 0.21 0.00
437_M 216_P 0.78 0.21 0.00
536_W 174_L 0.78 0.20 0.00
452_R 95_F 0.78 0.20 0.00
180_L 60_N 0.77 0.20 0.00
190_D 160_T 0.77 0.20 0.00
571_L 18_A 0.77 0.20 0.00
391_T 143_A 0.77 0.20 0.00
132_V 96_I 0.77 0.20 0.00
305_T 99_N 0.77 0.20 0.00
180_L 73_L 0.77 0.20 0.00
440_Y 184_Y 0.77 0.20 0.00
419_V 103_P 0.77 0.20 0.00
254_N 151_V 0.76 0.20 0.00
99_I 146_D 0.76 0.20 0.00
17_L 238_I 0.76 0.20 0.00
528_F 55_L 0.76 0.20 0.00
532_M 189_G 0.76 0.19 0.00
281_F 15_L 0.76 0.19 0.00
217_F 59_D 0.76 0.19 0.00
527_S 80_Y 0.76 0.19 0.00
509_F 148_S 0.76 0.19 0.00
145_F 76_I 0.76 0.19 0.00
392_I 124_L 0.76 0.19 0.00
64_V 104_N 0.75 0.19 0.00
261_E 127_F 0.75 0.19 0.00
6_Q 99_N 0.75 0.19 0.00
128_L 204_D 0.75 0.19 0.00
62_V 44_Q 0.75 0.19 0.00
128_L 12_T 0.75 0.19 0.00
65_S 245_T 0.75 0.19 0.00
286_Q 239_A 0.75 0.19 0.00
81_I 113_G 0.75 0.19 0.00
406_T 117_M 0.75 0.19 0.00
574_L 39_A 0.75 0.19 0.00
281_F 79_Y 0.74 0.18 0.00
168_L 98_L 0.74 0.18 0.00
143_I 231_A 0.74 0.18 0.00
593_F 147_F 0.74 0.18 0.00
563_I 10_A 0.74 0.18 0.00
43_K 99_N 0.74 0.18 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)
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