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OPENSEQ.org
yidc-yibn
Genes: A B A+B
Length: 548 143 682
Sequences: 887 396 242
Seq/Len: 1.62 2.77 0.35
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.00 0.06
∞ 0.00 0.00 0.35
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
15_V 21_L 1.63 0.55 0.00
451_F 74_I 1.54 0.49 0.00
393_M 111_A 1.48 0.45 0.00
71_T 57_V 1.42 0.40 0.00
362_T 60_R 1.37 0.37 0.00
12_L 111_A 1.36 0.36 0.00
534_G 99_V 1.28 0.31 0.00
265_I 139_L 1.26 0.30 0.00
344_L 64_D 1.23 0.28 0.00
465_Y 74_I 1.23 0.28 0.00
368_I 135_E 1.19 0.26 0.00
411_L 123_F 1.18 0.26 0.00
254_A 75_N 1.18 0.26 0.00
171_D 65_F 1.17 0.25 0.00
453_L 11_H 1.16 0.25 0.00
475_M 60_R 1.14 0.24 0.00
40_T 55_V 1.14 0.23 0.00
8_L 95_K 1.13 0.23 0.00
170_G 99_V 1.12 0.22 0.00
337_S 1_M 1.10 0.21 0.00
146_E 40_I 1.09 0.21 0.00
159_N 108_Q 1.09 0.21 0.00
313_I 75_N 1.09 0.21 0.00
86_A 40_I 1.07 0.20 0.00
225_T 73_S 1.07 0.20 0.00
253_V 5_M 1.07 0.20 0.00
181_Q 131_G 1.07 0.20 0.00
65_T 99_V 1.06 0.20 0.00
12_L 22_L 1.06 0.20 0.00
366_R 3_E 1.06 0.20 0.00
63_V 39_V 1.06 0.20 0.00
61_I 140_V 1.06 0.20 0.00
347_I 57_V 1.06 0.20 0.00
79_V 107_C 1.05 0.19 0.00
481_M 127_E 1.04 0.19 0.00
494_I 134_G 1.03 0.19 0.00
108_Y 141_R 1.03 0.19 0.00
111_Q 111_A 1.03 0.19 0.00
146_E 122_V 1.03 0.19 0.00
84_L 7_F 1.03 0.18 0.00
460_A 129_V 1.03 0.18 0.00
234_K 21_L 1.03 0.18 0.00
307_L 16_I 1.02 0.18 0.00
318_A 41_T 1.02 0.18 0.00
474_T 142_G 1.01 0.18 0.00
441_M 135_E 1.01 0.18 0.00
472_G 60_R 1.01 0.18 0.00
390_I 46_T 1.01 0.18 0.00
46_S 107_C 1.01 0.17 0.00
85_P 137_L 1.00 0.17 0.00
469_I 44_E 1.00 0.17 0.00
466_I 5_M 0.99 0.17 0.00
338_Q 91_K 0.99 0.17 0.00
374_K 18_W 0.99 0.17 0.00
149_V 68_G 0.98 0.17 0.00
167_L 41_T 0.98 0.16 0.00
511_S 123_F 0.98 0.16 0.00
337_S 107_C 0.98 0.16 0.00
176_V 40_I 0.98 0.16 0.00
367_G 57_V 0.98 0.16 0.00
236_D 56_V 0.97 0.16 0.00
511_S 103_S 0.97 0.16 0.00
518_I 46_T 0.97 0.16 0.00
533_R 31_K 0.97 0.16 0.00
225_T 57_V 0.96 0.16 0.00
295_V 37_V 0.96 0.16 0.00
266_P 125_L 0.96 0.16 0.00
323_H 25_V 0.96 0.16 0.00
274_F 111_A 0.96 0.15 0.00
318_A 139_L 0.96 0.15 0.00
308_W 76_L 0.95 0.15 0.00
26_D 10_R 0.95 0.15 0.00
141_A 99_V 0.95 0.15 0.00
265_I 129_V 0.95 0.15 0.00
325_D 102_G 0.95 0.15 0.00
188_L 29_T 0.94 0.15 0.00
53_P 17_A 0.94 0.15 0.00
323_H 131_G 0.94 0.15 0.00
180_V 24_A 0.94 0.15 0.00
363_F 16_I 0.94 0.15 0.00
470_L 42_R 0.94 0.15 0.00
168_K 49_I 0.93 0.15 0.00
276_T 135_E 0.93 0.15 0.00
479_Q 22_L 0.93 0.14 0.00
29_P 107_C 0.93 0.14 0.00
26_D 11_H 0.93 0.14 0.00
2_D 136_N 0.92 0.14 0.00
116_G 93_K 0.92 0.14 0.00
281_N 97_V 0.92 0.14 0.00
302_A 65_F 0.92 0.14 0.00
336_I 13_I 0.92 0.14 0.00
521_N 60_R 0.92 0.14 0.00
73_N 100_V 0.92 0.14 0.00
511_S 108_Q 0.91 0.14 0.00
352_G 14_L 0.90 0.14 0.00
414_A 73_S 0.90 0.14 0.00
508_W 15_S 0.90 0.14 0.00
188_L 35_S 0.90 0.14 0.00
92_N 99_V 0.90 0.14 0.00
63_V 57_V 0.90 0.13 0.00
230_Y 11_H 0.89 0.13 0.00
11_A 21_L 0.89 0.13 0.00
299_Q 57_V 0.89 0.13 0.00
474_T 47_R 0.89 0.13 0.00
231_E 40_I 0.89 0.13 0.00
342_K 17_A 0.89 0.13 0.00
97_F 86_V 0.89 0.13 0.00
165_F 49_I 0.89 0.13 0.00
160_T 86_V 0.88 0.13 0.00
312_E 5_M 0.88 0.13 0.00
469_I 59_L 0.88 0.13 0.00
408_M 116_K 0.88 0.13 0.00
74_T 56_V 0.88 0.13 0.00
64_K 112_N 0.88 0.13 0.00
476_F 87_G 0.88 0.13 0.00
428_I 14_L 0.87 0.13 0.00
351_V 107_C 0.87 0.13 0.00
452_A 72_G 0.87 0.13 0.00
354_W 50_N 0.87 0.13 0.00
392_A 78_P 0.87 0.13 0.00
511_S 141_R 0.87 0.13 0.00
171_D 75_N 0.87 0.13 0.00
173_A 117_A 0.87 0.13 0.00
129_P 18_W 0.87 0.12 0.00
365_V 40_I 0.86 0.12 0.00
417_V 64_D 0.86 0.12 0.00
298_G 89_L 0.86 0.12 0.00
100_L 43_G 0.85 0.12 0.00
402_Q 126_K 0.85 0.12 0.00
167_L 6_Q 0.85 0.12 0.00
27_K 11_H 0.85 0.12 0.00
501_I 79_S 0.85 0.12 0.00
77_G 56_V 0.85 0.12 0.00
265_I 19_I 0.85 0.12 0.00
375_A 80_E 0.85 0.12 0.00
179_N 123_F 0.85 0.12 0.00
305_S 117_A 0.85 0.12 0.00
493_K 101_D 0.85 0.12 0.00
147_L 70_I 0.85 0.12 0.00
170_G 49_I 0.84 0.12 0.00
327_T 92_H 0.84 0.12 0.00
219_R 131_G 0.84 0.12 0.00
430_M 48_L 0.84 0.12 0.00
360_I 99_V 0.84 0.12 0.00
434_L 45_A 0.83 0.12 0.00
464_Y 119_F 0.83 0.12 0.00
207_D 97_V 0.83 0.12 0.00
348_H 23_V 0.83 0.12 0.00
216_H 112_N 0.83 0.12 0.00
417_V 51_K 0.83 0.12 0.00
406_Q 52_E 0.83 0.11 0.00
503_T 49_I 0.83 0.11 0.00
218_F 87_G 0.83 0.11 0.00
265_I 8_V 0.83 0.11 0.00
168_K 8_V 0.83 0.11 0.00
469_I 16_I 0.83 0.11 0.00
320_V 133_A 0.83 0.11 0.00
131_Y 107_C 0.83 0.11 0.00
363_F 127_E 0.83 0.11 0.00
61_I 129_V 0.82 0.11 0.00
398_G 20_A 0.82 0.11 0.00
359_I 56_V 0.82 0.11 0.00
203_P 97_V 0.82 0.11 0.00
434_L 75_N 0.82 0.11 0.00
323_H 127_E 0.82 0.11 0.00
128_R 57_V 0.82 0.11 0.00
245_N 12_P 0.82 0.11 0.00
12_L 21_L 0.82 0.11 0.00
13_L 8_V 0.81 0.11 0.00
428_I 6_Q 0.81 0.11 0.00
85_P 41_T 0.81 0.11 0.00
340_L 111_A 0.81 0.11 0.00
196_L 99_V 0.81 0.11 0.00
460_A 79_S 0.81 0.11 0.00
262_T 43_G 0.81 0.11 0.00
161_F 6_Q 0.81 0.11 0.00
19_I 11_H 0.81 0.11 0.00
335_F 141_R 0.81 0.11 0.00
248_S 98_I 0.81 0.11 0.00
356_F 40_I 0.81 0.11 0.00
351_V 24_A 0.81 0.11 0.00
492_Q 3_E 0.81 0.11 0.00
236_D 107_C 0.81 0.11 0.00
474_T 97_V 0.81 0.11 0.00
456_H 70_I 0.81 0.11 0.00
180_V 99_V 0.81 0.11 0.00
414_A 133_A 0.81 0.11 0.00
174_V 139_L 0.81 0.11 0.00
501_I 28_T 0.81 0.11 0.00
230_Y 70_I 0.81 0.11 0.00
522_L 48_L 0.80 0.11 0.00
237_T 55_V 0.80 0.11 0.00
4_Q 40_I 0.80 0.11 0.00
105_Q 116_K 0.80 0.11 0.00
390_I 3_E 0.80 0.11 0.00
285_A 24_A 0.80 0.11 0.00
465_Y 31_K 0.80 0.11 0.00
469_I 45_A 0.80 0.11 0.00
107_I 99_V 0.80 0.11 0.00
501_I 63_D 0.80 0.10 0.00
221_A 95_K 0.80 0.10 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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