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OPENSEQ.org
cI_D_F
Genes: A B A+B
Length: 485 184 654
Sequences: 1691 2037 1487
Seq/Len: 3.49 11.07 2.27
MirrorTree (Pazo et al. 2001) 0.80
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 1.93
10 0.00 0.00 2.06
20 0.01 0.00 2.07
100 0.01 0.01 2.12
∞ 0.02 0.02 2.22
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
118_L 143_L 3.27 1.00 1.00
141_G 154_V 1.99 0.99 0.97
130_L 143_L 1.62 0.96 0.91
161_I 73_M 1.50 0.93 0.86
175_A 60_A 1.43 0.90 0.82
126_A 140_A 1.40 0.89 0.81
138_P 150_A 1.35 0.87 0.77
118_L 139_L 1.29 0.83 0.72
337_S 139_L 1.27 0.81 0.70
127_S 143_L 1.21 0.77 0.64
66_L 140_A 1.18 0.75 0.62
309_L 20_I 1.17 0.74 0.61
422_L 139_L 1.16 0.73 0.60
219_S 53_A 1.13 0.70 0.57
113_A 149_L 1.09 0.66 0.52
11_L 13_I 1.07 0.64 0.50
398_V 67_F 1.07 0.64 0.49
283_F 14_L 1.06 0.63 0.48
148_R 160_R 1.05 0.62 0.47
134_L 150_A 1.04 0.60 0.45
114_L 146_M 1.03 0.59 0.44
131_G 67_F 1.01 0.57 0.42
134_L 147_L 1.01 0.57 0.42
457_V 9_G 0.99 0.55 0.40
161_I 43_F 0.99 0.55 0.40
184_L 52_G 0.97 0.53 0.38
144_G 145_S 0.97 0.53 0.38
304_S 10_L 0.97 0.52 0.37
421_G 71_V 0.95 0.50 0.35
242_L 124_I 0.94 0.49 0.34
140_F 135_G 0.94 0.49 0.34
169_F 16_T 0.94 0.49 0.34
416_V 15_A 0.93 0.48 0.33
111_I 146_M 0.91 0.45 0.30
246_S 152_L 0.91 0.45 0.30
147_F 162_E 0.90 0.45 0.29
162_L 74_L 0.90 0.44 0.29
215_G 149_L 0.89 0.44 0.29
210_M 63_I 0.89 0.44 0.29
312_A 44_F 0.88 0.42 0.27
308_Y 68_V 0.87 0.42 0.27
297_L 94_I 0.87 0.41 0.27
424_Y 130_G 0.87 0.41 0.27
210_M 4_A 0.87 0.41 0.26
433_Y 133_L 0.86 0.40 0.26
145_Y 157_H 0.86 0.40 0.26
170_L 62_A 0.86 0.40 0.26
405_A 103_M 0.86 0.40 0.25
389_T 152_L 0.86 0.40 0.25
306_L 73_M 0.85 0.39 0.25
119_L 58_V 0.85 0.39 0.24
162_L 70_V 0.85 0.39 0.24
246_S 156_F 0.84 0.38 0.24
465_L 66_L 0.84 0.38 0.24
243_A 102_I 0.84 0.38 0.24
165_A 75_N 0.84 0.38 0.24
220_L 40_S 0.83 0.37 0.23
122_A 105_V 0.83 0.37 0.23
237_P 40_S 0.83 0.37 0.23
424_Y 152_L 0.83 0.37 0.23
162_L 73_M 0.83 0.36 0.22
175_A 70_V 0.83 0.36 0.22
186_F 122_T 0.82 0.36 0.22
43_I 101_A 0.82 0.35 0.21
339_G 48_A 0.81 0.35 0.21
311_V 68_V 0.81 0.35 0.21
313_L 45_S 0.81 0.35 0.21
266_S 56_I 0.81 0.34 0.21
204_L 146_M 0.81 0.34 0.20
130_L 144_A 0.80 0.34 0.20
252_G 71_V 0.80 0.34 0.20
178_Y 45_S 0.80 0.34 0.20
436_A 93_W 0.80 0.34 0.20
294_I 133_L 0.79 0.33 0.19
418_S 58_V 0.79 0.33 0.19
421_G 129_V 0.79 0.33 0.19
165_A 58_V 0.79 0.33 0.19
287_M 96_P 0.79 0.32 0.19
33_N 126_A 0.79 0.32 0.19
162_L 67_F 0.79 0.32 0.19
246_S 25_P 0.79 0.32 0.19
245_A 34_I 0.78 0.32 0.18
45_L 153_V 0.78 0.32 0.18
103_D 129_V 0.78 0.32 0.18
287_M 52_G 0.78 0.32 0.18
92_Y 11_I 0.78 0.31 0.18
336_S 145_S 0.78 0.31 0.18
239_S 164_A 0.77 0.31 0.18
139_L 54_L 0.77 0.31 0.17
297_L 53_A 0.77 0.31 0.17
196_G 40_S 0.77 0.30 0.17
216_F 61_G 0.77 0.30 0.17
140_F 151_G 0.76 0.30 0.17
285_N 57_I 0.76 0.30 0.17
227_T 63_I 0.76 0.30 0.17
460_S 15_A 0.76 0.30 0.17
177_V 97_A 0.76 0.30 0.17
142_L 56_I 0.76 0.30 0.17
431_S 51_A 0.76 0.30 0.17
168_S 55_E 0.76 0.30 0.17
51_S 104_L 0.76 0.29 0.16
157_I 158_V 0.76 0.29 0.16
85_L 52_G 0.76 0.29 0.16
82_L 113_G 0.76 0.29 0.16
347_M 102_I 0.75 0.29 0.16
79_L 27_H 0.75 0.29 0.16
398_V 125_S 0.75 0.29 0.16
252_G 39_I 0.75 0.29 0.16
306_L 55_E 0.75 0.29 0.16
180_Q 156_F 0.75 0.29 0.16
243_A 62_A 0.75 0.28 0.16
313_L 114_V 0.75 0.28 0.16
141_G 42_V 0.75 0.28 0.15
108_L 150_A 0.74 0.28 0.15
353_G 163_R 0.74 0.28 0.15
306_L 43_F 0.74 0.28 0.15
124_H 159_G 0.74 0.28 0.15
175_A 49_Y 0.74 0.28 0.15
149_Q 80_E 0.74 0.28 0.15
419_A 44_F 0.74 0.28 0.15
465_L 121_G 0.74 0.28 0.15
426_L 28_A 0.74 0.28 0.15
251_F 124_I 0.74 0.27 0.15
49_L 56_I 0.73 0.27 0.15
285_N 177_K 0.73 0.27 0.15
386_I 130_G 0.73 0.27 0.15
118_L 140_A 0.73 0.27 0.15
474_L 63_I 0.73 0.27 0.15
293_N 82_E 0.73 0.27 0.15
163_S 68_V 0.73 0.27 0.15
255_M 20_I 0.73 0.27 0.14
127_S 140_A 0.73 0.27 0.14
252_G 104_L 0.73 0.27 0.14
389_T 129_V 0.73 0.27 0.14
127_S 139_L 0.73 0.27 0.14
77_T 134_F 0.73 0.27 0.14
141_G 57_I 0.73 0.27 0.14
332_G 163_R 0.73 0.27 0.14
83_A 7_I 0.73 0.27 0.14
239_S 98_I 0.73 0.27 0.14
167_S 82_E 0.72 0.26 0.14
420_I 102_I 0.72 0.26 0.14
271_V 41_G 0.72 0.26 0.14
251_F 19_V 0.72 0.26 0.14
85_L 91_Q 0.72 0.26 0.14
104_E 27_H 0.72 0.26 0.14
160_T 68_V 0.72 0.26 0.14
244_T 33_I 0.72 0.26 0.14
185_S 9_G 0.72 0.26 0.14
283_F 108_V 0.72 0.26 0.14
277_A 15_A 0.72 0.26 0.14
175_A 159_G 0.72 0.26 0.14
126_A 37_L 0.72 0.26 0.14
160_T 49_Y 0.72 0.26 0.14
274_A 144_A 0.72 0.26 0.14
71_G 52_G 0.72 0.26 0.14
272_V 15_A 0.72 0.26 0.13
118_L 109_Y 0.72 0.26 0.13
426_L 30_L 0.71 0.26 0.13
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
7432 3.01 3rko_2_D_F Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done - Shared
2404 2.27 cI_D_F Δgene:(1, ∞) A:(1E-40, 1) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
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