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OPENSEQ.org
YidC_YibN
Genes: A B A+B
Length: 548 143 684
Sequences: 1547 1023 409
Seq/Len: 2.82 7.15 0.6
MirrorTree (Pazo et al. 2001) 0.79
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 0.08 0.00 0.00
2 0.08 0.00 0.00
5 0.08 0.00 0.00
10 0.08 0.00 0.00
20 0.08 0.00 0.01
100 0.08 0.01 0.10
∞ 0.08 0.02 0.59
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
26_D 11_H 1.75 0.78 0.03
27_K 10_R 1.67 0.74 0.02
27_K 11_H 1.45 0.58 0.01
7_L 97_V 1.43 0.57 0.01
26_D 10_R 1.36 0.51 0.01
282_G 107_C 1.31 0.47 0.01
19_I 11_H 1.27 0.44 0.01
362_T 60_R 1.21 0.39 0.01
397_L 70_I 1.20 0.38 0.01
347_I 76_L 1.20 0.38 0.01
12_L 21_L 1.19 0.37 0.01
360_I 99_V 1.19 0.37 0.01
529_Q 95_K 1.17 0.36 0.01
451_F 74_I 1.17 0.35 0.01
15_V 21_L 1.15 0.34 0.01
524_T 61_Q 1.14 0.33 0.01
58_G 129_V 1.14 0.33 0.01
27_K 3_E 1.12 0.32 0.01
95_Q 119_F 1.11 0.31 0.01
363_F 116_K 1.11 0.31 0.01
12_L 111_A 1.07 0.29 0.00
371_P 12_P 1.07 0.29 0.00
408_M 96_P 1.06 0.28 0.00
172_Y 74_I 1.06 0.28 0.00
118_D 40_I 1.06 0.28 0.00
12_L 22_L 1.04 0.27 0.00
404_I 96_P 1.03 0.26 0.00
452_A 72_G 1.03 0.26 0.00
144_Q 40_I 1.02 0.26 0.00
347_I 57_V 1.01 0.25 0.00
511_S 103_S 1.00 0.24 0.00
233_Y 93_K 1.00 0.24 0.00
394_R 116_K 0.99 0.24 0.00
366_R 3_E 0.99 0.24 0.00
343_L 96_P 0.99 0.23 0.00
245_N 12_P 0.99 0.23 0.00
313_I 49_I 0.98 0.23 0.00
142_E 73_S 0.98 0.23 0.00
174_V 74_I 0.97 0.23 0.00
151_M 81_I 0.97 0.22 0.00
368_I 112_N 0.96 0.22 0.00
110_A 119_F 0.96 0.22 0.00
231_E 139_L 0.95 0.22 0.00
474_T 53_D 0.95 0.21 0.00
268_N 97_V 0.95 0.21 0.00
225_T 53_D 0.94 0.21 0.00
37_T 97_V 0.94 0.21 0.00
166_V 139_L 0.94 0.21 0.00
237_T 54_A 0.94 0.21 0.00
367_G 20_A 0.94 0.21 0.00
351_V 97_V 0.94 0.21 0.00
295_V 72_G 0.93 0.20 0.00
404_I 133_A 0.93 0.20 0.00
291_Q 133_A 0.92 0.20 0.00
306_T 64_D 0.92 0.20 0.00
275_Y 103_S 0.92 0.20 0.00
225_T 117_A 0.91 0.20 0.00
65_T 99_V 0.91 0.19 0.00
401_K 63_D 0.90 0.19 0.00
299_Q 57_V 0.90 0.19 0.00
532_Y 93_K 0.89 0.18 0.00
518_I 46_T 0.89 0.18 0.00
7_L 91_K 0.89 0.18 0.00
27_K 6_Q 0.89 0.18 0.00
77_G 93_K 0.88 0.18 0.00
180_V 1_M 0.88 0.18 0.00
363_F 127_E 0.88 0.18 0.00
98_Q 102_G 0.88 0.18 0.00
131_Y 90_E 0.88 0.18 0.00
242_E 109_E 0.88 0.18 0.00
294_L 40_I 0.88 0.18 0.00
19_I 12_P 0.88 0.18 0.00
141_A 99_V 0.88 0.18 0.00
20_W 46_T 0.88 0.18 0.00
166_V 52_E 0.87 0.17 0.00
537_K 129_V 0.87 0.17 0.00
503_T 99_V 0.87 0.17 0.00
352_G 14_L 0.87 0.17 0.00
261_A 92_H 0.86 0.17 0.00
349_S 57_V 0.86 0.17 0.00
413_K 30_F 0.86 0.17 0.00
70_L 57_V 0.86 0.17 0.00
494_I 99_V 0.86 0.17 0.00
466_I 79_S 0.86 0.17 0.00
54_A 64_D 0.86 0.17 0.00
294_L 57_V 0.86 0.17 0.00
390_I 56_V 0.86 0.17 0.00
218_F 112_N 0.85 0.17 0.00
295_V 65_F 0.85 0.17 0.00
180_V 36_K 0.85 0.17 0.00
230_Y 139_L 0.85 0.16 0.00
79_V 107_C 0.85 0.16 0.00
189_E 98_I 0.85 0.16 0.00
91_L 42_R 0.85 0.16 0.00
337_S 26_L 0.84 0.16 0.00
63_V 59_L 0.84 0.16 0.00
143_G 64_D 0.84 0.16 0.00
184_G 83_A 0.84 0.16 0.00
413_K 122_V 0.84 0.16 0.00
203_P 10_R 0.84 0.16 0.00
262_T 121_Q 0.84 0.16 0.00
269_D 65_F 0.84 0.16 0.00
309_V 67_K 0.84 0.16 0.00
51_G 73_S 0.83 0.16 0.00
390_I 96_P 0.83 0.16 0.00
108_Y 141_R 0.83 0.15 0.00
14_F 90_E 0.82 0.15 0.00
480_K 94_D 0.82 0.15 0.00
30_Q 140_V 0.82 0.15 0.00
493_K 12_P 0.82 0.15 0.00
275_Y 45_A 0.82 0.15 0.00
453_L 17_A 0.82 0.15 0.00
464_Y 131_G 0.82 0.15 0.00
344_L 72_G 0.82 0.15 0.00
386_L 57_V 0.82 0.15 0.00
166_V 77_L 0.82 0.15 0.00
362_T 95_K 0.81 0.15 0.00
295_V 38_K 0.81 0.15 0.00
80_E 74_I 0.81 0.15 0.00
222_A 133_A 0.81 0.15 0.00
54_A 65_F 0.81 0.15 0.00
231_E 129_V 0.81 0.15 0.00
336_I 13_I 0.81 0.15 0.00
109_Q 5_M 0.81 0.15 0.00
4_Q 117_A 0.81 0.15 0.00
469_I 63_D 0.81 0.15 0.00
73_N 40_I 0.81 0.15 0.00
55_S 94_D 0.81 0.15 0.00
169_R 114_L 0.81 0.15 0.00
131_Y 112_N 0.80 0.14 0.00
319_A 115_T 0.80 0.14 0.00
228_E 110_P 0.80 0.14 0.00
161_F 140_V 0.80 0.14 0.00
448_Q 103_S 0.80 0.14 0.00
420_L 57_V 0.80 0.14 0.00
318_A 141_R 0.80 0.14 0.00
438_Y 110_P 0.80 0.14 0.00
9_V 20_A 0.80 0.14 0.00
493_K 19_I 0.80 0.14 0.00
473_V 99_V 0.80 0.14 0.00
313_I 23_V 0.80 0.14 0.00
254_A 120_A 0.80 0.14 0.00
159_N 131_G 0.80 0.14 0.00
268_N 19_I 0.79 0.14 0.00
265_I 18_W 0.79 0.14 0.00
78_D 90_E 0.79 0.14 0.00
452_A 94_D 0.79 0.14 0.00
83_L 16_I 0.79 0.14 0.00
285_A 126_K 0.79 0.14 0.00
184_G 44_E 0.79 0.14 0.00
226_P 64_D 0.79 0.14 0.00
399_D 8_V 0.78 0.14 0.00
408_M 116_K 0.78 0.14 0.00
241_N 72_G 0.78 0.14 0.00
390_I 70_I 0.78 0.14 0.00
366_R 84_N 0.78 0.14 0.00
319_A 30_F 0.78 0.14 0.00
129_P 18_W 0.78 0.14 0.00
184_G 49_I 0.78 0.14 0.00
170_G 59_L 0.78 0.14 0.00
301_G 65_F 0.78 0.14 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
11984 0.6 YidC_YibN Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done
1330 0.35 yidc-yibn Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: HHblits (2013_03) 0.00 Done
1132 0.59 Yidb Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0163 0.01 yibn-yidc Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed
0161 0.58 yidcp1-yibn Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed
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