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OPENSEQ.org
3OAA G y H
Genes: A B A+B
Length: 286 138 421
Sequences: 1912 1467 1082
Seq/Len: 6.69 10.63 2.57
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 0.00 0.03
2 0.00 0.00 2.25
5 0.00 0.00 2.30
10 0.00 0.00 2.31
20 0.00 0.00 2.34
100 0.00 0.00 2.40
∞ 0.02 0.01 2.55
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 1.71 0.98 0.89
206_L 39_A 1.18 0.78 0.51
214_L 8_V 1.17 0.77 0.50
220_R 68_I 1.10 0.71 0.42
15_N 22_K 1.09 0.70 0.41
243_M 70_E 1.08 0.69 0.40
188_L 94_A 1.06 0.67 0.38
159_Y 58_H 1.00 0.60 0.32
208_E 27_G 1.00 0.60 0.32
241_A 88_D 1.00 0.60 0.32
223_V 31_E 0.99 0.59 0.31
5_E 11_A 0.98 0.57 0.29
4_K 48_G 0.96 0.55 0.28
221_R 66_G 0.96 0.55 0.28
25_M 70_E 0.94 0.53 0.26
96_K 4_Y 0.94 0.53 0.26
208_E 29_E 0.92 0.50 0.24
222_Y 33_G 0.92 0.50 0.24
196_D 74_G 0.91 0.49 0.23
236_A 50_I 0.90 0.48 0.22
205_Y 40_P 0.90 0.48 0.22
214_L 29_E 0.89 0.47 0.22
47_T 70_E 0.89 0.46 0.21
171_S 130_V 0.88 0.46 0.21
241_A 71_V 0.88 0.46 0.21
143_P 83_A 0.88 0.45 0.20
159_Y 78_V 0.87 0.45 0.20
214_L 44_A 0.87 0.45 0.20
47_T 7_D 0.87 0.44 0.20
52_I 45_I 0.86 0.43 0.19
176_N 16_F 0.84 0.42 0.18
90_L 11_A 0.84 0.41 0.18
221_R 81_D 0.84 0.41 0.18
276_L 35_Y 0.84 0.41 0.18
18_K 126_A 0.83 0.40 0.17
234_N 63_Y 0.81 0.38 0.16
169_I 49_M 0.80 0.36 0.15
267_A 63_Y 0.80 0.36 0.15
91_N 48_G 0.80 0.36 0.15
214_L 114_Y 0.79 0.35 0.14
9_K 87_Q 0.78 0.35 0.14
51_V 42_L 0.78 0.35 0.14
232_V 9_V 0.78 0.34 0.14
276_L 20_V 0.78 0.34 0.14
59_N 16_F 0.78 0.34 0.14
230_G 9_V 0.77 0.34 0.13
117_I 58_H 0.77 0.33 0.13
29_S 47_P 0.77 0.33 0.13
89_G 51_R 0.77 0.33 0.13
71_D 44_A 0.77 0.33 0.13
33_K 12_E 0.77 0.33 0.13
211_P 25_V 0.76 0.33 0.13
153_K 8_V 0.76 0.33 0.13
64_H 23_I 0.76 0.32 0.13
178_M 75_N 0.76 0.32 0.12
177_T 81_D 0.76 0.32 0.12
81_S 27_G 0.76 0.32 0.12
51_V 63_Y 0.76 0.32 0.12
48_M 65_S 0.75 0.32 0.12
223_V 87_Q 0.75 0.31 0.12
54_H 72_Q 0.74 0.31 0.12
11_A 52_I 0.74 0.30 0.12
146_S 25_V 0.74 0.30 0.12
98_L 21_E 0.74 0.30 0.12
159_Y 65_S 0.74 0.30 0.11
34_S 76_V 0.74 0.30 0.11
227_V 44_A 0.73 0.29 0.11
144_S 99_R 0.73 0.29 0.11
281_S 24_Q 0.73 0.29 0.11
228_Y 92_A 0.73 0.29 0.11
127_S 26_T 0.73 0.29 0.11
135_Q 100_K 0.73 0.29 0.11
95_F 47_P 0.73 0.29 0.11
104_T 21_E 0.72 0.29 0.11
4_K 33_G 0.72 0.28 0.10
177_T 113_D 0.72 0.28 0.10
51_V 83_A 0.72 0.28 0.10
259_E 131_I 0.72 0.28 0.10
256_L 7_D 0.72 0.28 0.10
56_A 44_A 0.72 0.28 0.10
237_S 68_I 0.72 0.28 0.10
139_M 68_I 0.72 0.28 0.10
266_K 33_G 0.71 0.28 0.10
125_F 8_V 0.71 0.28 0.10
176_N 131_I 0.71 0.28 0.10
1_A 23_I 0.71 0.27 0.10
119_S 105_I 0.71 0.27 0.10
13_V 63_Y 0.71 0.27 0.10
187_L 61_F 0.71 0.27 0.10
54_H 37_G 0.71 0.27 0.10
250_T 29_E 0.71 0.27 0.10
25_M 15_M 0.71 0.27 0.10
214_L 135_K 0.70 0.27 0.10
96_K 94_A 0.70 0.27 0.10
34_S 79_L 0.70 0.27 0.10
114_L 45_I 0.70 0.27 0.10
257_I 10_S 0.70 0.27 0.10
81_S 15_M 0.70 0.27 0.10
175_I 3_T 0.70 0.27 0.10
205_Y 70_E 0.70 0.26 0.10
263_V 132_E 0.70 0.26 0.09
27_A 66_G 0.70 0.26 0.09
236_A 38_H 0.69 0.26 0.09
222_Y 18_G 0.69 0.26 0.09
13_V 26_T 0.69 0.26 0.09
281_S 9_V 0.69 0.26 0.09
252_N 40_P 0.69 0.25 0.09
44_Y 66_G 0.69 0.25 0.09
230_G 58_H 0.69 0.25 0.09
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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