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OPENSEQ.org
Yidb
Genes: A B A+B
Length: 548 143 681
Sequences: 886 1508 400
Seq/Len: 1.62 10.55 0.59
MirrorTree (Pazo et al. 2001) 0.47
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 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.00 0.02 0.08
∞ 0.00 0.09 0.58
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
435_A 57_V 1.47 0.59 0.00
12_L 111_A 1.18 0.36 0.00
15_V 21_L 1.14 0.33 0.00
414_A 73_S 1.13 0.32 0.00
359_I 74_I 1.09 0.30 0.00
492_Q 73_S 1.09 0.29 0.00
265_I 139_L 1.08 0.29 0.00
398_G 70_I 1.06 0.28 0.00
494_I 119_F 1.06 0.28 0.00
407_E 70_I 1.02 0.26 0.00
2_D 136_N 1.01 0.25 0.00
300_T 86_V 1.01 0.25 0.00
149_V 91_K 0.99 0.24 0.00
480_K 70_I 0.99 0.23 0.00
343_L 75_N 0.98 0.23 0.00
61_I 129_V 0.96 0.22 0.00
511_S 73_S 0.96 0.22 0.00
357_S 44_E 0.95 0.21 0.00
221_A 95_K 0.95 0.21 0.00
347_I 129_V 0.94 0.21 0.00
454_W 69_H 0.93 0.20 0.00
476_F 86_V 0.93 0.20 0.00
390_I 139_L 0.92 0.20 0.00
338_Q 91_K 0.92 0.20 0.00
371_P 12_P 0.92 0.19 0.00
362_T 60_R 0.91 0.19 0.00
357_S 107_C 0.91 0.19 0.00
451_F 74_I 0.91 0.19 0.00
108_Y 70_I 0.90 0.19 0.00
12_L 22_L 0.90 0.18 0.00
394_R 107_C 0.90 0.18 0.00
73_N 98_I 0.87 0.17 0.00
77_G 136_N 0.87 0.17 0.00
180_V 34_T 0.87 0.17 0.00
79_V 36_K 0.86 0.17 0.00
298_G 89_L 0.86 0.17 0.00
337_S 1_M 0.86 0.17 0.00
254_A 99_V 0.86 0.17 0.00
511_S 71_A 0.86 0.17 0.00
16_S 18_W 0.86 0.17 0.00
325_D 102_G 0.85 0.16 0.00
61_I 73_S 0.85 0.16 0.00
511_S 41_T 0.85 0.16 0.00
530_L 119_F 0.85 0.16 0.00
406_Q 52_E 0.85 0.16 0.00
11_A 21_L 0.84 0.16 0.00
411_L 114_L 0.84 0.16 0.00
420_L 97_V 0.83 0.16 0.00
526_I 139_L 0.83 0.15 0.00
357_S 26_L 0.83 0.15 0.00
181_Q 96_P 0.82 0.15 0.00
234_K 21_L 0.82 0.15 0.00
146_E 122_V 0.82 0.15 0.00
159_N 4_I 0.81 0.15 0.00
470_L 42_R 0.81 0.15 0.00
26_D 10_R 0.81 0.15 0.00
136_D 139_L 0.81 0.15 0.00
236_D 56_V 0.81 0.15 0.00
72_I 38_K 0.81 0.14 0.00
12_L 21_L 0.80 0.14 0.00
370_Y 116_K 0.80 0.14 0.00
13_L 8_V 0.80 0.14 0.00
79_V 40_I 0.79 0.14 0.00
87_Y 136_N 0.79 0.14 0.00
363_F 89_L 0.79 0.14 0.00
103_S 73_S 0.79 0.14 0.00
397_L 94_D 0.79 0.14 0.00
248_S 114_L 0.79 0.14 0.00
393_M 129_V 0.79 0.14 0.00
357_S 11_H 0.79 0.14 0.00
322_P 74_I 0.79 0.14 0.00
510_P 110_P 0.78 0.14 0.00
65_T 99_V 0.78 0.14 0.00
244_L 125_L 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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