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OPENSEQ.org
PvQ
Genes: A B A+B
Length: 244 89 294
Sequences: 1392 1545 1254
Seq/Len: 5.7 17.36 4.27
MirrorTree (Pazo et al. 2001) 0.76
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 0.01 3.29
2 0.00 0.01 3.33
5 0.00 0.01 3.47
10 0.00 0.01 3.57
20 0.01 0.01 3.77
100 0.01 0.01 3.94
∞ 0.08 0.07 4.11
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 2.65 1.00 1.00
228_V 77_T 2.00 1.00 0.99
190_L 13_T 1.79 1.00 0.97
202_V 24_M 1.66 0.99 0.96
187_L 80_I 1.57 0.99 0.94
53_A 55_I 1.33 0.95 0.85
197_M 17_T 1.27 0.93 0.81
90_T 66_M 1.17 0.88 0.74
80_Q 47_M 1.16 0.88 0.73
204_M 66_M 1.09 0.83 0.67
234_L 81_L 1.08 0.82 0.65
209_M 35_I 1.06 0.81 0.63
187_L 9_L 1.05 0.80 0.62
212_P 55_I 1.05 0.80 0.62
148_L 67_P 1.04 0.79 0.61
217_S 22_L 1.03 0.78 0.60
223_L 66_M 1.03 0.78 0.59
188_I 81_L 1.03 0.78 0.59
228_V 81_L 1.01 0.76 0.57
215_M 36_S 0.99 0.74 0.55
205_A 64_F 0.98 0.73 0.54
198_V 56_I 0.96 0.71 0.52
140_N 30_I 0.96 0.70 0.51
194_V 76_F 0.96 0.70 0.51
227_L 6_L 0.95 0.69 0.50
156_P 30_I 0.94 0.69 0.49
68_V 63_I 0.94 0.68 0.48
181_A 33_L 0.92 0.66 0.46
78_G 41_T 0.90 0.64 0.44
107_S 58_V 0.90 0.64 0.44
160_T 79_N 0.89 0.62 0.43
212_P 25_L 0.89 0.62 0.42
198_V 20_L 0.87 0.60 0.40
84_P 23_P 0.86 0.58 0.39
229_D 46_E 0.86 0.58 0.39
133_F 62_L 0.85 0.57 0.38
218_L 43_Q 0.85 0.56 0.37
193_L 43_Q 0.84 0.56 0.37
194_V 17_T 0.83 0.55 0.35
228_V 74_I 0.83 0.54 0.35
200_S 48_T 0.83 0.54 0.35
71_S 43_Q 0.83 0.54 0.35
71_S 84_I 0.83 0.54 0.35
174_M 85_P 0.83 0.54 0.35
69_V 33_L 0.82 0.53 0.34
222_L 83_Q 0.82 0.53 0.34
139_K 56_I 0.81 0.51 0.32
131_K 60_V 0.81 0.51 0.32
146_L 43_Q 0.80 0.50 0.32
70_F 54_K 0.80 0.50 0.32
242_F 72_T 0.80 0.50 0.31
84_P 37_I 0.80 0.50 0.31
128_K 60_V 0.80 0.49 0.31
71_S 40_A 0.79 0.49 0.31
197_M 59_V 0.79 0.48 0.30
73_L 47_M 0.78 0.48 0.29
197_M 71_T 0.78 0.48 0.29
215_M 37_I 0.78 0.47 0.29
194_V 13_T 0.78 0.47 0.28
222_L 72_T 0.77 0.46 0.28
197_M 37_I 0.77 0.46 0.28
199_V 84_I 0.77 0.46 0.28
194_V 77_T 0.77 0.45 0.28
206_M 32_G 0.77 0.45 0.27
75_Q 63_I 0.76 0.45 0.27
112_I 16_I 0.76 0.45 0.27
198_V 28_G 0.75 0.44 0.26
209_M 38_F 0.75 0.44 0.26
140_N 76_F 0.74 0.42 0.25
209_M 51_F 0.74 0.42 0.24
165_P 69_M 0.74 0.41 0.24
198_V 17_T 0.74 0.41 0.24
57_V 6_L 0.73 0.41 0.24
39_T 41_T 0.73 0.41 0.24
237_R 80_I 0.73 0.41 0.24
112_I 37_I 0.73 0.41 0.24
90_T 47_M 0.73 0.40 0.24
187_L 54_K 0.73 0.40 0.24
217_S 56_I 0.72 0.40 0.23
39_T 43_Q 0.72 0.40 0.23
152_I 50_S 0.72 0.40 0.23
80_Q 38_F 0.71 0.39 0.22
197_M 14_F 0.71 0.38 0.22
216_I 24_M 0.71 0.38 0.22
82_M 76_F 0.71 0.38 0.22
44_V 59_V 0.71 0.38 0.21
79_T 23_P 0.70 0.37 0.21
205_A 57_L 0.70 0.37 0.21
114_P 53_P 0.70 0.37 0.21
175_I 41_T 0.70 0.37 0.21
206_M 35_I 0.70 0.37 0.21
170_V 9_L 0.70 0.36 0.20
198_V 73_M 0.69 0.36 0.20
234_L 76_F 0.69 0.36 0.20
105_T 27_A 0.69 0.35 0.20
112_I 26_L 0.69 0.35 0.20
97_F 18_L 0.69 0.35 0.20
179_K 41_T 0.69 0.35 0.20
124_E 2_D 0.69 0.35 0.20
49_I 78_E 0.69 0.35 0.20
202_V 67_P 0.69 0.35 0.19
165_P 2_D 0.69 0.35 0.19
150_Y 26_L 0.69 0.35 0.19
94_I 84_I 0.69 0.35 0.19
209_M 29_L 0.68 0.35 0.19
81_S 18_L 0.68 0.35 0.19
92_A 30_I 0.68 0.35 0.19
188_I 30_I 0.68 0.35 0.19
78_G 43_Q 0.68 0.34 0.19
241_S 81_L 0.68 0.34 0.19
76_A 45_N 0.68 0.34 0.19
151_R 20_L 0.68 0.34 0.19
210_M 51_F 0.68 0.34 0.18
218_L 46_E 0.67 0.33 0.18
201_S 18_L 0.67 0.33 0.18
118_E 73_M 0.67 0.33 0.18
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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