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OPENSEQ.org
3OAA G y H
Genes: A B A+B
Length: 286 138 420
Sequences: 2360 1818 1435
Seq/Len: 8.25 13.17 3.42
MirrorTree (Pazo et al. 2001) 0.75
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 0.04
2 0.00 0.00 3.05
5 0.00 0.00 3.15
10 0.00 0.00 3.15
20 0.00 0.00 3.19
100 0.00 0.00 3.24
∞ 0.01 0.00 3.38
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
55_L 42_L 1.37 0.94 0.54
206_L 39_A 1.36 0.93 0.52
220_R 68_I 1.10 0.79 0.29
214_L 29_E 0.96 0.65 0.19
176_N 16_F 0.96 0.64 0.19
208_E 29_E 0.94 0.62 0.18
221_R 81_D 0.94 0.62 0.18
284_A 123_K 0.94 0.61 0.17
208_E 27_G 0.93 0.61 0.17
9_K 87_Q 0.92 0.59 0.16
47_T 70_E 0.92 0.59 0.16
4_K 48_G 0.90 0.56 0.15
222_Y 33_G 0.90 0.56 0.15
214_L 8_V 0.89 0.55 0.14
47_T 7_D 0.89 0.55 0.14
145_L 11_A 0.88 0.54 0.14
214_L 44_A 0.88 0.54 0.14
54_H 37_G 0.87 0.53 0.14
276_L 35_Y 0.87 0.53 0.14
143_P 83_A 0.86 0.51 0.13
54_H 72_Q 0.86 0.51 0.13
64_H 40_P 0.86 0.51 0.13
205_Y 70_E 0.85 0.50 0.12
167_L 81_D 0.84 0.49 0.12
267_A 63_Y 0.84 0.48 0.12
243_M 70_E 0.82 0.47 0.11
102_M 21_E 0.81 0.46 0.11
145_L 77_T 0.81 0.46 0.11
171_S 130_V 0.81 0.45 0.11
188_L 94_A 0.81 0.45 0.10
231_V 103_E 0.80 0.43 0.10
281_S 25_V 0.80 0.43 0.10
153_K 8_V 0.80 0.43 0.10
51_V 83_A 0.80 0.43 0.10
5_E 11_A 0.79 0.43 0.10
227_V 78_V 0.79 0.42 0.10
52_I 128_L 0.78 0.41 0.09
259_E 95_M 0.78 0.41 0.09
164_L 80_A 0.77 0.39 0.09
241_A 24_Q 0.76 0.39 0.09
89_G 51_R 0.76 0.39 0.09
223_V 31_E 0.76 0.39 0.09
134_A 99_R 0.76 0.39 0.09
82_T 101_A 0.75 0.37 0.08
205_Y 9_V 0.74 0.36 0.08
62_Y 32_L 0.74 0.36 0.08
210_D 41_L 0.74 0.36 0.08
203_W 40_P 0.73 0.36 0.08
263_V 78_V 0.73 0.36 0.08
45_A 4_Y 0.73 0.35 0.08
15_N 22_K 0.73 0.35 0.07
11_A 52_I 0.73 0.35 0.07
52_I 45_I 0.73 0.35 0.07
239_Q 27_G 0.72 0.35 0.07
25_M 85_R 0.72 0.34 0.07
91_N 48_G 0.72 0.34 0.07
77_Y 57_G 0.72 0.34 0.07
4_K 33_G 0.72 0.34 0.07
164_L 20_V 0.72 0.34 0.07
68_E 71_V 0.72 0.34 0.07
159_Y 78_V 0.71 0.33 0.07
203_W 73_P 0.71 0.33 0.07
51_V 42_L 0.71 0.33 0.07
30_K 48_G 0.71 0.33 0.07
176_N 131_I 0.70 0.32 0.07
222_Y 83_A 0.70 0.32 0.07
250_T 29_E 0.69 0.31 0.06
135_Q 100_K 0.69 0.31 0.06
34_S 76_V 0.69 0.31 0.06
25_M 46_K 0.69 0.30 0.06
29_S 11_A 0.68 0.29 0.06
13_V 133_L 0.68 0.29 0.06
241_A 22_K 0.67 0.29 0.06
29_S 47_P 0.67 0.29 0.06
214_L 135_K 0.67 0.29 0.06
79_V 102_E 0.67 0.29 0.06
81_S 27_G 0.67 0.29 0.06
114_L 135_K 0.66 0.28 0.06
99_L 128_L 0.66 0.27 0.05
257_I 10_S 0.66 0.27 0.05
271_S 65_S 0.66 0.27 0.05
75_V 70_E 0.66 0.27 0.05
248_A 69_L 0.65 0.27 0.05
132_V 97_A 0.65 0.27 0.05
89_G 107_S 0.65 0.27 0.05
234_N 63_Y 0.65 0.27 0.05
13_V 103_E 0.65 0.26 0.05
66_Y 50_I 0.65 0.26 0.05
57_H 64_L 0.65 0.26 0.05
100_A 31_E 0.65 0.26 0.05
222_Y 18_G 0.65 0.26 0.05
255_S 60_E 0.65 0.26 0.05
231_V 76_V 0.65 0.26 0.05
51_V 72_Q 0.65 0.26 0.05
66_Y 3_T 0.64 0.26 0.05
190_L 10_S 0.64 0.26 0.05
106_T 90_D 0.64 0.26 0.05
236_A 50_I 0.64 0.26 0.05
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
1264 3.42 3OAA G y H Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.54 Done - Shared
1263 2.57 3OAA G y H Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.89 Done - Shared
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