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OPENSEQ.org
3TYG
Genes: A B A+B
Length: 253 87 319
Sequences: 1095 1083 758
Seq/Len: 4.33 12.45 2.38
MirrorTree (Pazo et al. 2001) 0.54
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 1.55
2 0.00 0.00 1.64
5 0.00 0.00 1.83
10 0.00 0.00 1.86
20 0.00 0.00 1.87
100 0.00 0.00 1.92
∞ 0.00 0.00 2.23
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
81_R 56_E 2.62 1.00 1.00
90_G 83_F 1.97 0.99 0.97
92_C 83_F 1.42 0.91 0.82
88_A 54_I 1.10 0.69 0.54
59_L 81_V 1.07 0.66 0.50
85_L 61_I 1.06 0.65 0.49
22_S 72_L 1.01 0.58 0.42
82_I 54_I 0.99 0.56 0.40
90_G 56_E 0.97 0.54 0.39
78_E 84_V 0.95 0.52 0.36
43_R 79_E 0.95 0.52 0.36
80_V 55_V 0.94 0.51 0.35
92_C 85_G 0.93 0.50 0.34
88_A 63_G 0.93 0.49 0.34
89_S 67_Y 0.92 0.49 0.33
89_S 52_I 0.92 0.48 0.32
36_D 39_I 0.91 0.48 0.32
84_R 56_E 0.87 0.42 0.27
45_M 67_Y 0.86 0.42 0.27
92_C 56_E 0.86 0.41 0.26
220_A 72_L 0.85 0.41 0.26
100_I 84_V 0.85 0.40 0.25
81_R 61_I 0.85 0.40 0.25
232_Y 44_A 0.84 0.39 0.24
80_V 32_W 0.84 0.39 0.24
180_I 63_G 0.83 0.38 0.24
43_R 81_V 0.83 0.38 0.23
92_C 52_I 0.82 0.37 0.23
80_V 39_I 0.80 0.35 0.21
81_R 85_G 0.80 0.35 0.21
85_L 56_E 0.80 0.35 0.20
17_T 56_E 0.79 0.34 0.20
222_K 62_I 0.79 0.33 0.19
153_A 25_L 0.76 0.31 0.17
34_E 54_I 0.76 0.30 0.17
122_E 23_L 0.76 0.30 0.17
166_L 83_F 0.76 0.30 0.17
138_A 79_E 0.74 0.29 0.16
144_L 21_H 0.74 0.29 0.16
218_A 27_G 0.74 0.29 0.15
215_V 35_D 0.73 0.28 0.15
224_A 49_E 0.73 0.28 0.15
131_T 84_V 0.73 0.27 0.15
93_D 53_V 0.72 0.27 0.14
48_F 28_K 0.72 0.27 0.14
77_E 59_K 0.72 0.26 0.14
63_K 64_K 0.71 0.26 0.13
112_E 52_I 0.71 0.26 0.13
73_A 85_G 0.70 0.25 0.13
107_L 36_T 0.69 0.24 0.12
162_I 73_C 0.69 0.24 0.12
154_S 47_Q 0.69 0.24 0.12
155_P 64_K 0.68 0.24 0.12
99_V 52_I 0.68 0.23 0.11
235_G 84_V 0.68 0.23 0.11
84_R 53_V 0.68 0.23 0.11
100_I 78_I 0.67 0.22 0.11
122_E 40_Q 0.67 0.22 0.11
139_R 53_V 0.67 0.22 0.11
77_E 56_E 0.67 0.22 0.11
19_K 85_G 0.67 0.22 0.11
226_E 22_M 0.66 0.22 0.10
158_S 36_T 0.66 0.21 0.10
67_L 63_G 0.66 0.21 0.10
139_R 62_I 0.66 0.21 0.10
138_A 81_V 0.66 0.21 0.10
84_R 73_C 0.65 0.21 0.10
173_E 59_K 0.65 0.21 0.10
78_E 21_H 0.65 0.21 0.10
8_S 28_K 0.65 0.21 0.10
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
8320 0 1tyg Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
1267 2.38 3TYG Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
1266 0 3TYG Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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