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OPENSEQ.org
SecYSecE (B, 60-127)
Genes: A B A+B
Length: 443 68 498
Sequences: 1696 1523 923
Seq/Len: 3.83 22.4 1.85
MirrorTree (Pazo et al. 2001) 0.68
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 0.02
100 0.00 0.00 1.01
∞ 0.02 0.00 1.81
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. Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on HHsearch results which uses the overall probability and per-site alignment confidence. Inter-chain contacts in the pdb are in shades of red. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
35_I 56_L 3.33 1.00 1.00
31_I 52_L 2.33 1.00 0.99
376_V 20_V 2.23 1.00 0.98
192_F 45_M 1.88 0.98 0.95
368_K 15_E 1.60 0.93 0.87
30_L 49_L 1.57 0.93 0.86
414_M 34_T 1.49 0.89 0.81
376_V 23_V 1.42 0.86 0.77
232_F 35_T 1.38 0.84 0.74
242_R 19_E 1.38 0.84 0.74
193_A 49_L 1.35 0.82 0.72
228_F 39_A 1.27 0.77 0.64
320_L 29_Q 1.27 0.76 0.64
23_L 48_I 1.26 0.76 0.63
126_V 44_V 1.26 0.76 0.63
413_I 41_V 1.23 0.73 0.60
239_R 30_E 1.23 0.73 0.59
77_I 63_I 1.22 0.72 0.59
240_G 25_W 1.22 0.72 0.58
251_R 28_R 1.13 0.64 0.49
65_N 50_W 1.11 0.62 0.47
35_I 55_I 1.09 0.59 0.44
243_R 24_I 1.07 0.58 0.42
240_G 26_P 1.06 0.57 0.41
347_K 31_T 1.04 0.55 0.39
375_L 16_A 1.04 0.55 0.39
366_I 21_R 1.03 0.54 0.38
232_F 31_T 1.03 0.54 0.38
39_I 36_L 1.01 0.51 0.35
371_T 12_F 1.00 0.50 0.34
45_D 47_L 0.98 0.48 0.32
269_V 45_M 0.98 0.48 0.32
379_L 18_T 0.97 0.47 0.31
95_L 37_I 0.97 0.47 0.31
33_F 12_F 0.96 0.45 0.29
380_Y 31_T 0.95 0.45 0.29
31_I 56_L 0.93 0.43 0.27
269_V 20_V 0.93 0.42 0.26
353_V 44_V 0.91 0.40 0.25
162_V 43_A 0.91 0.40 0.24
389_E 24_I 0.91 0.40 0.24
235_V 28_R 0.91 0.40 0.24
18_E 40_A 0.90 0.40 0.24
223_V 41_V 0.90 0.40 0.24
282_S 21_R 0.90 0.39 0.24
23_L 46_S 0.90 0.39 0.23
343_A 35_T 0.89 0.38 0.23
222_L 57_V 0.88 0.38 0.22
39_I 21_R 0.88 0.37 0.22
172_M 42_T 0.88 0.37 0.22
190_I 23_V 0.88 0.37 0.21
240_G 16_A 0.85 0.34 0.20
376_V 16_A 0.85 0.34 0.20
141_N 60_V 0.85 0.34 0.19
165_V 22_K 0.85 0.34 0.19
264_H 15_E 0.85 0.34 0.19
116_I 49_L 0.85 0.34 0.19
373_L 18_T 0.85 0.34 0.19
132_S 11_A 0.84 0.33 0.18
199_L 43_A 0.83 0.33 0.18
384_I 24_I 0.83 0.33 0.18
343_A 45_M 0.83 0.32 0.18
239_R 31_T 0.83 0.32 0.17
413_I 48_I 0.83 0.32 0.17
422_T 12_F 0.82 0.31 0.17
245_V 20_V 0.81 0.31 0.17
414_M 31_T 0.81 0.31 0.17
358_P 25_W 0.81 0.31 0.16
50_A 63_I 0.81 0.31 0.16
81_G 49_L 0.81 0.30 0.16
243_R 55_I 0.81 0.30 0.16
233_F 24_I 0.80 0.29 0.16
243_R 31_T 0.80 0.29 0.15
432_A 35_T 0.80 0.29 0.15
345_N 12_F 0.79 0.29 0.15
260_A 29_Q 0.79 0.29 0.15
418_A 34_T 0.79 0.28 0.15
357_R 28_R 0.79 0.28 0.14
285_L 21_R 0.79 0.28 0.14
81_G 26_P 0.78 0.28 0.14
157_Y 59_L 0.78 0.28 0.14
306_I 43_A 0.78 0.28 0.14
239_R 34_T 0.77 0.27 0.14
32_V 63_I 0.77 0.27 0.13
333_T 50_W 0.77 0.27 0.13
193_A 57_V 0.77 0.27 0.13
196_V 49_L 0.77 0.27 0.13
302_W 51_G 0.77 0.26 0.13
382_T 56_L 0.76 0.26 0.13
222_L 12_F 0.76 0.26 0.13
135_I 48_I 0.76 0.26 0.13
390_F 58_R 0.75 0.25 0.12
178_I 48_I 0.75 0.25 0.12
249_A 18_T 0.75 0.25 0.12
227_V 39_A 0.75 0.25 0.12
126_V 51_G 0.75 0.25 0.12
129_I 10_V 0.75 0.25 0.12
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)
HHsearch results
3j00A:BContact Map
2zjsY:EContact Map
3dinCF:DGContact Map
3dl8GH:CDContact Map
1rh5A:BContact Map
3mp7A:BContact Map
2ww9A:BContact Map
2wwbA:BContact Map
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