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OPENSEQ.org
PxQ
Genes: A B A+B
Length: 244 89 319
Sequences: 1471 1330 1187
Seq/Len: 6.03 14.94 3.72
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 2.94
2 0.00 0.00 2.97
5 0.01 0.00 3.11
10 0.01 0.01 3.19
20 0.02 0.01 3.42
100 0.03 0.02 3.56
∞ 0.07 0.05 3.71
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
184_I 84_I 2.66 1.00 1.00
228_V 77_T 2.08 1.00 0.99
202_V 24_M 1.68 0.99 0.95
187_L 80_I 1.64 0.99 0.95
53_A 55_I 1.54 0.98 0.93
190_L 13_T 1.52 0.97 0.92
197_M 17_T 1.42 0.96 0.89
187_L 9_L 1.39 0.95 0.87
148_L 67_P 1.37 0.94 0.86
215_M 36_S 1.31 0.93 0.82
90_T 66_M 1.24 0.90 0.78
212_P 25_L 1.20 0.88 0.75
212_P 55_I 1.15 0.84 0.70
223_L 66_M 1.08 0.79 0.63
80_Q 47_M 1.08 0.79 0.63
218_L 43_Q 1.06 0.77 0.61
228_V 81_L 1.05 0.76 0.60
140_N 30_I 1.03 0.74 0.57
217_S 22_L 1.01 0.72 0.55
68_V 63_I 0.99 0.70 0.53
209_M 35_I 0.99 0.70 0.53
190_L 6_L 0.98 0.69 0.52
90_T 47_M 0.95 0.66 0.48
217_S 56_I 0.95 0.65 0.48
188_I 66_M 0.93 0.63 0.46
73_L 47_M 0.93 0.63 0.46
188_I 81_L 0.93 0.62 0.45
242_F 72_T 0.92 0.62 0.44
194_V 17_T 0.91 0.60 0.42
107_S 58_V 0.90 0.59 0.41
205_A 64_F 0.89 0.58 0.41
16_A 11_V 0.89 0.57 0.40
175_I 41_T 0.87 0.55 0.38
88_L 57_L 0.86 0.54 0.37
38_V 50_S 0.86 0.54 0.37
48_T 69_M 0.86 0.54 0.36
198_V 28_G 0.86 0.54 0.36
160_T 79_N 0.85 0.53 0.35
205_A 36_S 0.85 0.53 0.35
103_V 62_L 0.84 0.52 0.34
198_V 56_I 0.84 0.51 0.34
84_P 37_I 0.83 0.50 0.33
108_Y 77_T 0.82 0.48 0.31
59_V 47_M 0.82 0.48 0.31
45_I 60_V 0.81 0.48 0.31
179_K 40_A 0.81 0.48 0.31
92_A 82_N 0.81 0.47 0.31
114_P 53_P 0.81 0.47 0.30
91_L 36_S 0.81 0.47 0.30
78_G 41_T 0.80 0.46 0.30
95_L 69_M 0.80 0.46 0.29
128_K 60_V 0.80 0.46 0.29
179_K 41_T 0.79 0.45 0.29
153_R 75_D 0.79 0.45 0.28
204_M 66_M 0.79 0.44 0.28
71_S 84_I 0.78 0.43 0.27
41_L 3_E 0.77 0.41 0.26
104_A 12_Q 0.76 0.41 0.25
162_D 59_V 0.76 0.41 0.25
241_S 81_L 0.76 0.41 0.25
198_V 17_T 0.76 0.40 0.25
199_V 35_I 0.75 0.40 0.24
63_F 84_I 0.75 0.40 0.24
194_V 76_F 0.75 0.40 0.24
198_V 20_L 0.75 0.39 0.24
181_A 33_L 0.74 0.38 0.23
152_I 50_S 0.73 0.38 0.23
149_F 40_A 0.73 0.38 0.22
227_L 84_I 0.73 0.37 0.22
99_I 48_T 0.73 0.37 0.22
79_T 25_L 0.72 0.36 0.21
228_V 74_I 0.72 0.36 0.21
212_P 17_T 0.72 0.36 0.21
137_M 66_M 0.72 0.36 0.21
56_I 58_V 0.72 0.36 0.21
175_I 45_N 0.71 0.35 0.20
199_V 84_I 0.71 0.35 0.20
72_F 43_Q 0.70 0.34 0.20
107_S 65_L 0.70 0.34 0.20
76_A 50_S 0.70 0.34 0.20
190_L 64_F 0.70 0.34 0.19
222_L 83_Q 0.70 0.33 0.19
99_I 22_L 0.70 0.33 0.19
49_I 78_E 0.69 0.33 0.18
169_L 28_G 0.69 0.32 0.18
174_M 85_P 0.69 0.32 0.18
46_V 64_F 0.69 0.32 0.18
60_M 70_T 0.69 0.32 0.18
71_S 80_I 0.68 0.32 0.18
188_I 30_I 0.68 0.32 0.18
149_F 11_V 0.68 0.32 0.18
153_R 24_M 0.68 0.31 0.18
52_L 52_V 0.68 0.31 0.18
242_F 33_L 0.68 0.31 0.18
227_L 70_T 0.68 0.31 0.17
237_R 80_I 0.68 0.31 0.17
75_Q 58_V 0.68 0.31 0.17
151_R 16_I 0.68 0.31 0.17
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
10517 4.27 PvQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7211 8.63 FliP FliQ camju jh 2 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
7208 8.87 FliP FliQ camju jh Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
7152 4.62 FliP FliQ camju Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
3578 3.72 PxQ Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared
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