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I_sub_Membound_L_sub (B, 20-99)
Genes: A B A+B
Length: 330 80 388
Sequences: 1118 2754 677
Seq/Len: 3.39 34.42 1.74
MirrorTree (Pazo et al. 2001) 0.84
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 0.01 0.00 1.58
2 0.01 0.01 1.59
5 0.01 0.01 1.60
10 0.01 0.01 1.65
20 0.01 0.01 1.66
100 0.02 0.02 1.71
∞ 0.03 0.05 1.90
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
259_V 74_F 1.33 0.79 0.05
294_H 61_L 1.21 0.70 0.04
297_Q 30_T 1.20 0.69 0.04
278_V 43_G 1.15 0.64 0.03
292_L 29_G 1.13 0.62 0.03
302_I 73_A 1.11 0.60 0.03
209_G 40_A 1.11 0.60 0.03
282_L 43_G 1.10 0.59 0.03
11_L 18_G 1.09 0.58 0.03
46_Y 62_P 1.09 0.58 0.03
252_L 52_F 1.09 0.57 0.03
246_G 60_L 1.08 0.56 0.03
278_V 40_A 1.05 0.53 0.02
297_Q 65_L 1.03 0.52 0.02
239_H 62_P 1.03 0.52 0.02
227_P 63_E 1.02 0.51 0.02
304_V 62_P 1.02 0.50 0.02
153_V 26_A 0.99 0.47 0.02
257_T 62_P 0.97 0.45 0.02
234_G 67_I 0.97 0.45 0.02
293_G 65_L 0.97 0.45 0.02
97_V 40_A 0.97 0.45 0.02
142_I 67_I 0.96 0.45 0.02
7_P 23_V 0.94 0.42 0.02
285_L 52_F 0.94 0.42 0.02
50_F 76_L 0.94 0.42 0.02
277_V 14_L 0.94 0.41 0.02
142_I 26_A 0.93 0.41 0.01
244_A 53_G 0.93 0.41 0.01
251_I 74_F 0.93 0.40 0.01
221_S 67_I 0.91 0.39 0.01
104_E 68_F 0.90 0.38 0.01
260_G 32_V 0.90 0.38 0.01
262_A 43_G 0.90 0.38 0.01
7_P 76_L 0.88 0.36 0.01
280_G 75_I 0.87 0.35 0.01
53_V 71_L 0.87 0.35 0.01
280_G 57_I 0.87 0.35 0.01
252_L 37_I 0.87 0.34 0.01
46_Y 64_T 0.86 0.34 0.01
36_W 62_P 0.86 0.34 0.01
283_H 62_P 0.86 0.34 0.01
308_T 34_Q 0.86 0.34 0.01
225_M 60_L 0.85 0.33 0.01
297_Q 63_E 0.85 0.33 0.01
297_Q 31_G 0.85 0.33 0.01
235_H 65_L 0.85 0.33 0.01
35_F 28_L 0.85 0.33 0.01
287_L 71_L 0.85 0.33 0.01
37_F 34_Q 0.84 0.32 0.01
42_G 44_A 0.84 0.32 0.01
46_Y 30_T 0.84 0.32 0.01
262_A 74_F 0.83 0.31 0.01
170_M 50_S 0.83 0.31 0.01
306_F 42_V 0.83 0.31 0.01
251_I 71_L 0.82 0.30 0.01
169_H 38_G 0.82 0.30 0.01
303_W 18_G 0.82 0.30 0.01
296_L 31_G 0.81 0.30 0.01
59_G 11_D 0.81 0.29 0.01
251_I 70_L 0.81 0.29 0.01
293_G 30_T 0.81 0.29 0.01
284_L 72_I 0.81 0.29 0.01
264_A 17_V 0.81 0.29 0.01
212_V 17_V 0.81 0.29 0.01
323_F 43_G 0.80 0.29 0.01
255_L 40_A 0.80 0.28 0.01
286_I 38_G 0.80 0.28 0.01
206_M 17_V 0.80 0.28 0.01
249_G 65_L 0.79 0.28 0.01
233_A 18_G 0.79 0.28 0.01
257_T 33_A 0.79 0.28 0.01
302_I 46_A 0.79 0.27 0.01
249_G 64_T 0.79 0.27 0.01
55_R 18_G 0.79 0.27 0.01
248_A 52_F 0.79 0.27 0.01
53_V 79_R 0.79 0.27 0.01
97_V 21_L 0.79 0.27 0.01
233_A 60_L 0.78 0.27 0.01
228_E 68_F 0.78 0.27 0.01
28_V 47_E 0.78 0.26 0.01
2_P 20_G 0.78 0.26 0.01
156_G 42_V 0.77 0.26 0.01
235_H 30_T 0.77 0.26 0.01
294_H 60_L 0.77 0.26 0.01
46_Y 65_L 0.76 0.25 0.01
304_V 64_T 0.76 0.25 0.01
297_Q 33_A 0.76 0.25 0.01
283_H 64_T 0.76 0.25 0.01
225_M 56_L 0.76 0.25 0.01
236_I 64_T 0.76 0.25 0.01
227_P 66_V 0.76 0.24 0.01
140_L 24_G 0.76 0.24 0.01
106_F 28_L 0.75 0.24 0.01
244_A 62_P 0.75 0.24 0.01
246_G 62_P 0.75 0.24 0.01
15_L 27_A 0.75 0.24 0.01
29_V 21_L 0.75 0.24 0.01
25_P 47_E 0.74 0.24 0.01
197_L 20_G 0.74 0.24 0.01
258_D 70_L 0.74 0.24 0.01
248_A 13_G 0.74 0.23 0.01
231_T 33_A 0.74 0.23 0.01
257_T 27_A 0.74 0.23 0.01
146_V 44_A 0.74 0.23 0.01
178_G 54_T 0.74 0.23 0.01
249_G 62_P 0.73 0.23 0.01
105_F 52_F 0.73 0.23 0.01
1_N 15_I 0.73 0.23 0.01
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
1394 1.74 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 10) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.05 Done
1387 1.12 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 10) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1385 1.13 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 100) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
1384 1.05 I_sub_Membound_L_sub (B, 20-99) Δgene:(1, 5) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2013_03) 0.01 Done - Shared
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